Article ID 0114 Published: 4 December 2019 REVIEW ARTICLE
Amphibians show a very high level of diversity and endemism and are facing global declines from the past few decades. Studies have shown that the molecular tools can be helpful in their conservation efforts. In India, more than 80% of amphibians are endemic and most show a narrow range of distribution. Most of the Indian amphibians lack information on their genetic diversity. In this study, were view the overall trend on amphibian studies in India with the specific focus on conservation genetics. Overall, of the 173 studies, only 14 dealt with the conservation of amphibians through genetic tools and five studies estimated the genetic diversity or gene structure. Here, we discuss the gaps and provide future directions on how genetic studies can be helpful in Indian amphibian conservation.
Article ID 0113 Published: 4 December 2019 RESEARCH ARTICLE
The brown planthopper (BPH) Nilaparvata lugens (Stål) (Homoptera: Delphacidae) is considered a threat to rice (Oryza sativa ssp.) crop in many parts of the world including India. Among the BPH-resistance (R) genes so far reported in rice, most of them are ineffective against BPH biotype 4 predominant in the Indian sub-continent. In this study, we show the introgression line RPBio4918-230S was identified as BPH resistant after five years of rigorous screening at seedling stage and two years at tillering and reproductive stages. The inheritance of resistance indicated that two recessive genes are involved at seedling and reproductive stages. The allelic relation with known genes using linked reported markers suggested that the genes present in RPBio4918-230S are different. We report here the genetics of the two newly introgressed BPH resistance genes from O. nivara in the background of Swarna which are effective at all the important growth stages. The genes have been tentatively named as bph39(t) and bph40(t). The honeydew area (feeding rate) and days to wilt parameters observed at 30 days after sowing in BC1F3 indicated that newly introgressed genes have both antibiosis and tolerance mechanisms for resistance. The BPH resistance genes identified in this study would facilitate the breeding of broad spectrum and durable resistance in rice against BPH biotype 4.
Article ID 0108 Published: 22 November 2019 RESEARCH NOTE
Mutations in genes involved in chromatin remodelling have been implicated in broad phenotypes of congenital abnormalities and neurodevelopment. However, limited genotype–phenotype correlations are available for some of the rarestgenetic disorders that affect chromatin regulation. We hereby describe a 12-year-old girl presented at birth with severe hypotonia, developmental delay, a mid-line capillary malformation and distinctive craniofacial features. During the natural history of her disease, the girl developed severe spasticity and drug-resistant seizures, leading to a diagnosis of Bohring–Opitz syndrome (BOS). We performed whole-exome sequencing (WES) and identified a de novo mutation in ASXL1 (c.2033dupG) which results in the introduction of a premature stop codon (p.R678fs*6). ASXL1 encodes a polycomb repressive complex protein implicated in chromatin regulation and de novo mutations are a known cause of BOS. Phenotypes with segmental craniofacial overgrowth associated to midline capillary malformations enlarge the clinical spectrum of BOS at onset and further expand the differential diagnosis in ASXL1 mutation carriers.
Article ID 0109 Published: 22 November 2019 RESEARCH NOTE
The present paper reports for the first time the characteristics of the complete plastid genome of Surianaceae (Suriana maritima L.) in the order Fabales. The circular complete plastid genome is 163,747 bp in length with a typical quadripartite organization containing 115 unique genes, of which 80 are protein-coding genes, 31 tRNA genes and four rRNA genes. The plastid genome of S. maritima is characterized by absence of intron in the atpF gene, which has never been reported for any other species of the Fabales. The gene content and their orders in the plastid genome of Surianaceae are similar to the basal lineages of the legume family (Cercidoideae, Detarioideae) and Quillajaceae, supporting a likely common ancestor for the three families. Phylogenetic analysis supported the sister relationship between Surianaceae and Leguminosae, with strongly supported by Bayesian method and moderately supported by likelihood method. The complete plastid genome of Surianaceae could provide potential benefit in resolving the long-standing unresolved interfamily relationships of Fabaleswhen a more comprehensive sampling from Polygalaceae and Leguminosae is available for future studies.
Article ID 0112 Published: 22 November 2019 RESEARCH ARTICLE
A wide range of diploid number of chromosomes and the body size of Channa congeners are useful combination of characters for studying the factors controlling the body size. In this study, the karyological information was superimposed on the evolutionary tree generated by 16S rRNA mitochondrial gene sequences. Here, the metaphase chromosome complements stained with Giemsa, AgNO3 and CMA3 were prepared from six snakehead murrel fish species collected from northeast India. The diploid chromosome numbers and the fundamental arms of C. aurantimaculata (2n = 52, NF = 98), C. gachua (2n = 56, NF = 84), C. marulius (2n = 44, NF = 58), C. orientalis (2n = 52, NF = 74), C. punctata (2n = 32, NF = 60) and C. striata (2n = 40, NF = 48) were calculated by the analysis of metaphase chromosome complements. Both methods of nucleolar organizer region (NOR) localization, silver nitrate and chromomycin A3, revealed NOR pairs of 1, 2, 3, 1, 4 and 3 in C. aurantimaculata, C. gachua, C. marulius, C. orientalis, C. punctata and C. striata, respectively. The subject species showed primitive type of asymmetrical chromosomes, except the C. punctata. The variation in 2n for C. orientalis (2n = 52, 78) and C. gachua (2n = 52, 78, 104) of a complete haploid set indicates the possibility of either ploidy change in . orientalisC and C. gachua, if we consider 2n = 52 or the Robertsonian rearrangements in different populations of these two species. The chromosome evolution tree was constructed on 16S rRNA ML-phylogenetic tree using ChromEvol 1.3. The analysis of chromosome evolution explained the loss or gain of chromosome, duplications or semiduplications mechanism. For time scaling the chromosomeevolution, the node age of available 16S rRNA gene of Channa species were estimated, which was also used for estimating the time when chromosomal changes occurred in context of geological time-scale.
Article ID 0110 Published: 22 November 2019 RESEARCH ARTICLE
Congenital heart defects can decrease the quality of life and life expectancy in affected individuals, and constitute a major burden for the health care systems. Endocardial cushion defects are among the most prevalent heart malformations in the general population, and are extremely frequent (approximately a 100-fold higher prevalence) in children with Down syndrome. Several genes have been proposed to be involved in the pathogenesis of these malformations, but no common pathogenic DNA variants have been identified so far. Here, we focussed on constitutive, epigenetic alterations of function of selected genes, potentially important for endocardial cushion development. We used two types of microarrays, dedicated for assessment of gene promoter methylation and whole genome expression. First, we compared the gene promoter methylation profiles between two groups of Down syndrome patients, with and without heart defects of endocardial cushion-type. Then, to determine the functional role of the detected methylation alterations, we assessed the expression of the genes of interest. We detected significant hypermethylation of the NRG1 gene promoter region in children with heart defects. NRG1 is a key factor in maturation of endocardial cushions. Supplementary gene expression assessment revealed significantly decreased activity of the ERBB3, SHC3 and SHC4 genes in children with heart defects. The above three genes are closely related to the NRG1 gene and are crucial elements of the NRG/ErbB pathway. The results of this pilot study show that hypermethylation of the NRG1 gene promoter can reflect the functional genome alteration contributing to development of congenital heart defects of endocardial cushion-type.
Article ID 0111 Published: 22 November 2019 RESEARCH ARTICLE
A study was conducted to examine the genetic divergence and to determine the genetic loci and genes associated with natural variation of grain zinc (Zn) concentration among 28 landraces, improved varieties and advanced breeding lines of rice using candidate gene specific primers. Field evaluation of the experimental material was conducted in randomized block design with three replications and Zn content in unpolished grains of the entries was determined by addition of nitric acid and perchloric acid (1:3) following the procedure ofdiacid digestion method. Statistical analysis revealed the exploitable extent of variability with respect to grain Zn concentration among the entries. Eighteen entries were selected from the two extremes of grain Zn distribution range and subjected to molecular profiling using a panel of 14 candidate genes specific 12 reported and 14 designed primer pairs. Only eight (OsZIP1-1, OsZIP3a, OsZIP4a, OsZIP5-3, OsZIP7-2, OsZIP8b, OsNRAMP7 and OsNAAT1) reported and eight (OsZIP3K, OsZIP4K, OsZIP5K, OsZIP7K, OsNRAMP7K, OsNAAT1K, OsNACK and OsYSL14K) designed primers generated polymorphic amplified products showing sequence length variation due to targeted amplification of candidate genes specific genomic regions. Ample genetic differentiation and divergence were revealed among the entries, which were accommodated into similarity coefficient-based six clusters, remarkably consistent with grain Zn concentrationof the entries. Hierarchical classification pattern of entries was almost completely corroborated by principal co-ordinate analysisbased spatial distribution pattern of their genetic profiles. Molecular analysis based on candidate genes specific primers appeared to be an efficient approach for the elucidation of genetic differentiation and divergence in relation to variation of grain Zn concentration among entries. Hence, these markers can be effectively and efficiently utilized for grain Zn concentration related discrimination of rice genotypes and selection of parental genotypes for grain Zn biofortification. Microsatellites were detected within the candidate genes and amplicons, thereby providing a basis to deduce that the repeat sequence length variation in candidate genes may be a role player in the differential grain Zn accumulation in rice varieties. Single marker analysis established the association of OsNACK, OsZIP1-1, OsNRAMP7 and OsNRAMP7K with grain Zn concentration. Thus, these four markers can be effectively used in marker-assisted selection programme for grainZn biofortification in rice.
Article ID 0107 Published: 19 November 2019 RESEARCH ARTICLE
Haematopoiesis is a complex process in which the regulatory mechanisms of several implicated transcription factors remain uncertain. Drosophila melanogaster is an excellent model to resolve the unanswered questions about the blood cell development. This study describes the role of Beadex, a Drosophila homologue of LIM domain only 2 (LMO2), in haematopoiesis. Mutants of Beadex were analysed for blood cell abnormalities. Crystal cells, a subset of haemocytes, were significantly more in Beadex hypermorphic flies. Similarly, Beadex misexpression in prohemocytes altered the crystal cell numbers. Stage-specific misexpression analyses demonstrated that Beadex functions after the prohemocytes enter the crystal cell lineage. We also discovered that Pannier–U-shaped complex is a negative regulator of the crystal cell differentiation and is possibly negatively regulated by Beadex through its interaction with Pannier. We, therefore, suggest the mechanism of two novel regulators of crystal cell specification—Beadex and Pannier—during Drosophila haematopoiesis.
Article ID 0105 Published: 15 November 2019 RESEARCH ARTICLE
The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish, Carinotetraodon travancoricus (dwarf pufferfish or Malabar pufferfish) endemic to southwest India. The genome is 16487 bp in length and consist of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region like all the other vertebrate mitogenomes. The protein-coding genes ranged from 165 bp (ATP synthase subunit 8) to 1812 bp (NADH dehydrogenase subunit 5) and comprised of 11310 bp in total, constituting 68.5% of the complete mitogenome. Some overlaps have been observed in protein-coding genes by a total of 7 bp. The AT skew (0.032166) and GC skew (-0.29746) of the mitogenome indicated that heavy strand consists equal amount of A and T, but the overall base composition was mainly C skewed. The noncoding D-loop region comprised 869 bp. The conserved motifs ATGTA and its complement TACAT associated with thermostable hairpin structure formation were identified in the control region. The phylogenetic analysis depicted a sister group relationship of C. travancoricus with euryhaline species Dichotomyctere nigroviridis and D. ocellatus with 100% bootstrap value rather than with the other freshwater members of Carinotetraodon species from Southeast Asia. The data from this study will be useful for proper identification, genetic differentiation, management and conservation of the dwarf Indian pufferfish.
Article ID 0106 Published: 15 November 2019 Cataloguing of blast resistance genes in landraces and breeding lines of rice from India
The rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice and can lead to complete failure of the crop under severe cases. The first step in breeding for blast resistance in rice is therefore to identify the novel sources of resistance and cataloguing different blast resistant genes in these genotypes. In the present study, a set of 37 rice genotypes comprising of landraces, advanced breeding lines and released varieties were first characterized for blast resistance under epiphytotic conditions and subsequently different blast resistant genes were catalogued with the help of markers tightly linked to these genes. A total of 22 different blast resistant genes were catalogued in these genotypes. Lot of diversity was found to be present for different genes in the rice genotypes studied. In addition, a set of 2–3 markers were identified which could distinguish genotypes of a particular geographic area from each other.The results are useful for identifying the right combination of genotypes in the resistance breeding programme.
Article ID 0103 Published: 14 November 2019 CORRECTION
Article ID 0104 Published: 14 November 2019 RESEARCH ARTICLE
Cancer is one of the deadliest complex diseases having multigene nature where the role of single-nucleotide polymorphism (SNP) has been well explored in multiple genes. TOX high mobility group box family member 3 (TOX3) is one such gene, in which SNPs have been found to be associated with breast cancer. In this study, we have examined the potentially damaging nonsynonymous SNPs(nsSNPs) in TOX3 gene using in silico tools, namely PolyPhen2, SNP&GO, PhD-SNP and PROVEAN, which were further confirmed by I-Mutant, MutPred1.2 and ConSurf for their stability, functional and structural effects. nsSNPs rs368713418 (A266D), rs751141352 (P273S, P273T), rs200878352 (A275T) have been found to be the most deleterious that may have a vital role in breast cancer. Premature stop codon producing SNPs (Q527STOP), rs1259790811 (G495STOP), rs1294465822 (S395STOP) and rs1335372738 (G8STOP) were also found having prime importance in truncated and malfunctional protein formation. We also characterized regulatory SNPs for its potential effect on TOX3 gene regulation and found nine SNPs that may affect the gene regulation. Further, we have also designed 3D models using I-TASSER for the wild type and four mutant TOX3 proteins. Our study concludes that these SNPs can be of prime importance while studying breast cancer and other associated diseases as well. They are required to be studied in model organisms and cell cultures, and may have potential importance in personalized medicines and gene therapy.
Article ID 0102 Published: 6 November 2019 RESEARCH ARTICLE
Access to dense panels of molecular markers has facilitated genomic selection in animal breeding. The purpose of this study was to compare the nonparametric (random forest and support vector machine), semiparametric reproducing kernel Hilbert spaces (RKHS), and parametric methods (ridge regression and Bayes A) in prediction of genomic breeding values for traits with different genetic architecture. The predictive performance of different methods was compared in different combinations of distribution of QTL effects (normal and uniform), two levels of QTL numbers (50 and 200), three levels of heritability (0.1, 0.3 and 0.5), and two levels of training set individuals (1000 and 2000). To do this, a genome containing four chromosomes each 100-cM long was simulated on which 500, 1000 and 2000 evenly spaced single-nucleotide markers were distributed. With an increase in heritability and the number of markers, all the methods showed an increase in prediction accuracy (P<0.05). By increasing the number of QTLs from 50 to 200, we found a significant decrease in the prediction accuracy of breeding value in all methods (P<0.05). Also, with the increase in the number of training set individuals, the prediction accuracy increased significantly in all statistical methods (P<0.05). In all the various simulation scenarios, parametric methods showed higher prediction accuracy than semiparametric and nonparametric methods. This superior mean value of prediction accuracy for parametric methods was not statistically significant compared to the semiparametric method, but it was statistically significant compared to the nonparametric method. Bayes A had the highest accuracy of prediction among all the tested methods and, is therefore, recommended for genomic evaluation.
Article ID 0101 Published: 5 November 2019 RESEARCH ARTICLE
Most of the grasses of the genus Cenchrus (20–25 species) and Pennisetum (80–140 species) are distributed throughout the tropical and subtropical regions of the world and reproduce both by sexual and apomictic modes. However, the relationships among the Cenchrus–Pennisetum species are not very clear yet. Molecular markers like expressed sequence tag-simple sequence repeats (EST-SSRs) have been reported to be a better choice for resolving the phylogenetic relationships and to estimate the genetic diversity. The present study describes the identification of EST-SSR markers based on the transcriptome data of Cenchrus ciliaris inflorescence and illustrates the genetic diversity and phylogenetic relationships among these species. Of the 378 primer pairs used across 33 accessions of 21 Cenchrus, Pennisetum, and related grass (Bothriochloa, Dichanthium and Panicum) species, 116 EST-SSR markers were found to be polymorphic with an average polymorphism information content (PIC) of 0.49. Fifty-one EST-SSR loci and 520 alleles showed that where the PIC value is >0.5 there the GAG repeat motif was highly polymorphic. Two EST-SSR markers, CcSSR_80 and CcSSR_102, are polymorphic among the Cenchrus species, while they are absent in Pennisetum and the allied species. Five SSR markers (CcSSR_75, CcSSR_85, CcSSR_87, CcSSR_88 and CcSSR_114) showed 100% cross-transferability among the 21 Cenchrus–Pennisetum species. Species-specific alleles could also be detected for seven species of Cenchrus, Pennisetum and Panicum across 10 SSR markers. Assay of polymorphism across these agamic complexes showed that the three SSR markers (CcSSR_26, CcSSR_97 and CcSSR_109) were associated with Cenchrus–Pennisetum complex, and one (CcSSR_47) with Bothriochloa–Dichanthium complex. Markers with high discriminating power, namely CcSSR_4, CcSSR_38, CcSSR_48, CcSSR_66, CcSSR_67 and CcSSR_70, can be used to estimate the allelic sequence divergence across the sexual and apomictic lineages. Genetic diversity analysis using neighbour-joining (NJ) and principal co-ordinate analysis (PCoA) based approaches showed six and five clusters for the 33 accessions, respectively, having congruence in the pattern of clustering. These accessions were grouped according to their mode of reproduction. Cenchrus and Pennisetum species were grouped separately within the same clade, implying monophyletic group within a ‘bristle clade’. Thus, this study showed high discrimination power of microsatellite (EST-SSR) markers to resolve the phylogenetic relationships.
Article ID 0100 Published: 4 November 2019 RESEARCH ARTICLE
Rattans, the spiny climbing palms of Arecaceae (Palmae) family exhibit high endemism to the biodiversity hot spots in India. Of the five rattan genera, Calamus is the only genus found in peninsular India with 15 of 21 species, endemic to the Western Ghats. The extensive utilization of rattans owing to their strength, durability and huge demand has resulted in depletion of their natural resources. Ofthe 15 endemic species, C. nagbettai is the most affected species on account of endemism, low population size and restricted distribution with fragmented populations. The present study revealed high amount of genetic diversity in the surviving scattered populations of the species using microsatellite markers. High gene flow (Nm = 1.498) observed across the populations resulted in low genetic differentiation (14%). A clear genetic admixture could be seen in Kerala as well as one of the Karnataka’s populations while the remaining two populations were genetically distinct. UPGMA, PCoA and STRUCTURE analyses showed significantly different genetic composition in Kerala population compared to other populations. Kerala and Karnataka populations of C. nagbettai were also unique in their genetic structure and allelic composition. Therefore, effective management and conservation strategies have to be implemented to preserve the rarealleles with adaptive potential to protect this economically valuable Calamus species from endangerment. Overexploitation, low seed set and poor regeneration, as well as habitat fragmentation can further threaten the survival of this endemic, narrowly distributed dioecious rattan species in the Western Ghats region.
Article ID 0099 Published: 4 November 2019 RESEARCH ARTICLE
Studies have shown that many complex diseases are sex-determined. When conducting genetic association studies on Xchromosome, there are two important epigenetic factors which should be considered simultaneously: X-chromosome inactivation and genomic imprinting. Currently, there have been several association tests accounting for the information on X-chromosome inactivation. However, these tests do not take the imprinting effects into account. In this paper, we propose a novel association test simultaneously incorporating X-chromosome inactivation and imprinting effects based on case–parent trios and control–parent trios for female offspring and case–control data for male offspring, denoted by MLRXCII. Extensive simulation studies are carried out to investigate the type I error rate and the test power of the proposed MLRXCII . Simulation results demonstrate that the proposed test controls the type I error rate well andis more powerful than the existing method when imprinting effects exist. The proposed MLRXCII test is valid and powerful in genetic association studies on X-chromosome for qualitative traits and thus is recommended in practice.
Article ID 0098 Published: 25 October 2019 RESEARCH ARTICLE
Seedling and adult plant (field) resistance to yellow rust in the durum wheat (Triticum turgidum ssp. durum) cross Kunduru-1149 x Cham-1 was characterized using a functionally-targeted DNA marker system, NBS-profiling. Chi-squared analysis indicated a four gene model conferring seedling yellow rust resistance against Puccinia striiformis f. sp. tritici isolate WYR85/22 (virulent on Yr2, Yr6, Yr7 and Yr9). Interval mapping located two QTL for yellow rust resistance on the long arm of chromosome 1B, while Kruskal–Wallis single marker regression identified a number of additional marker loci associated with seedling and/or adult plant, field resistance to yellow rust. These results suggested that much of the yellow rust resistance seen in the field may be due to seedling expressed resistance (R) genes. Characterization of the DNA sequence of three NBS marker loci indicated that all showed significant homology to functionally-characterized R-genes and resistance gene analogues (RGAs), with the greatest homology being NBS-LRR-type R-genes and RGAs from cereal species.
Article ID 0097 Published: 24 October 2019 RESEARCH ARTICLE
Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one A + T rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Start codons for all the 13 PCGs were ATN codon and abbreviated/truncated stop codons were observed in ND1, ND2, COX3, ND3 and ND4. The phylogenetic analysis revealed that the Andaman buffalo is closely related to buffalo from India and China. The results from this study will help in sketching the conservation plan of the threatened breed.
Article ID 0096 Published: 22 October 2019 RESEARCH ARTICLE
Various honey bees, especially subspecies Apis mellifera, occur in Africa and are distribute across the continent. The genetic relationships and identical genetic characteristics between honey bee subspecies in Africa (African bee subspecies) have not been widely investigated using sequence analysis. On the other hand, bioinformatics are developed rapidly and have diverse applications. It is anticipated that bioinformatics can show the genetic relationships and similarities among subspecies. These points have high importance, especially subspecies with identical genetic characteristics can be infected with the same group of pathogens, which have implications on honey bee health. In this study, the mitochondrial DNA sequences of four African subspecies and Africanized bees were subjected to the analyses of base composition, phylogeny, shared gene clusters, enzymatic digestion, and open reading frames. High identical base composition was detected in the studied subspecies, and high identical results from all tests were found between A. m. scutellata and A. m. capensis followed by A. m. intermissa and A. m. monticola. The least genetic relationships were found between A. m. lamarckii and the other subspecies. This study presents insights into the genetic aspects of African bee subspecies and highlights similarity and dissimilarity aspects. Also, Africanized honey bees derived from A. m. scutellata showed high genetic similarities to other African bees, especially A. m.capensis. Additionally, specific primers to identify these subspecies were designed and tested.
Article ID 0095 Published: 18 October 2019 REVIEW ARTICLE
Primary progressive aphasia (PPA) is a progressive neurodegenerative disease that disrupts the language capacity of an individual by selectively affecting the language network of brain. Although aphasic literature is replete with reports of brain damage responsible for various types of PPA, it does not provide a comprehensive understanding of whether PPA is an independent pathological condition or an atypical syndrome of neurodegenerative diseases (NDD). To address this ambiguity, we provide a detailed description of PPA, its variants and their brain anatomy. Subsequently, we unravel the relationship between PPA and NDDs like Alzheimer’s, Parkinson’s and Dyslexia. To substantiate the relationship further, we also provide a brief account of their genetic aetiology. In the final section, we offer an exhaustive approach towards the treatment of PPA by combining the existing language the rapies with clinical and pharmacological interventions.
Article ID 0094 Published: 15 October 2019 RESEARCH ARTICLE
The diversity on fruit colouration in plants directly depends on the flavonoids that explain the development of different pigmentation patterns. Anthocyanins are the major class of flavonoid pigments that are synthesized through flavonoid biosynthetic pathway. In the present study, two genes: PgUFGT gene and R2R3-PgMYB gene, involved in anthocyanin biosynthesis were analysed in four tissues of wild pomegranate. The structural genes, UDP-glucose: flavonoid-3-O-glucosyl transferase (PgUFGT; GenBank accession number: MK058491) and its myeloblastosis transcription factor (R2R3-PgMYB; GenBank accession number: MK092063) were isolated and their expression pattern were studied. Molecular modelling indicated that the main secondary structures of PgUFGT and R2R3-PgMYB genes are α-helix and random coil. In addition, expression profiling of PgUFGTand R2R3-PgMYB by quantitative-real time PCR indicated a positive correlation between anthocyanin content and their expression in leaves, flowers, green and red fruits of wild pomegranate. Among all the tissues, the red fruit exhibited high transcripts levels of PgUFGT as well as R2R3-PgMYB transcription factor. An extensive homology with UFGTs from other plants was revealed on comparative and bioinformatic analyses. Present study reveals that PgUFGT plays a predominant role in anthocyanin content in wild pomegranate fruits. Further, it is strongly suggested that R2R3-PgMYB transcription factor regulates the anthocyanin biosynthesis in wild pomegranate via expression of PgUFGT gene. This is the first study which provides an insight on expression profile of PgUFGT and R2R3-PgMYB that are involved in colour development and fruit ripening in wild pomegranate.
Article ID 0093 Published: 26 September 2019 RESEARCH ARTICLE
The development of human–computer interfaces in different individuals occurwith different efficiencies, this is due to the individual characteristics of the genotype determined by the single-nucleotide polymorphism (SNP) of a person. Here, we checked the connection between the success of the acquisition of the brain-computer, eye-tracking, electromyographic, and respiratory interfaces and SNP of the TOMM40, BDNF, HTR2A and TPH2 genes. Here, we show that the T-allele in rs6313 of the HTR2A gene is associated with an increase in the number of correctly submitted commands of the electromyographic and eye-tracking interfaces. This is probably due to the fact that, the T-allele carriers decrease expression of this serotonin receptor. The decreased expression of HTR2A may be a reason for an increase in the number of accurately submitted commands. It was shown that the TT genotype of rs4290270 polymorphism was associated with an increase in the accuracy of work with the myographic interface. In addition, the association of subjective interfaces work time with polymorphisms rs429358 and rs2030324 was noted. Thus, the genotypic characteristics of individuals can be a predictive sign for the degree of success of mastering human–computer interfaces, which can allow to expand the understanding of training the neural mechanisms when working with this class of devices.
Article ID 0092 Published: 6 September 2019 RESEARCH ARTICLE
Rice germplasms collected from different regions could be used as valuable resources for the future breeding programme. For the utilization of such collections, knowledge about the level and distribution of genetic diversity among these collections will facilitate the breeder. In this study, we report the phenotypic correlation, biochemical quality parameters and population genetic analysis of 35 rice accessions including 34 aromatic rice from different countries and a nonaromatic, Nagina 22, a well-known drought resistance variety. Further biochemical quality analysis, gel consistency test, molecular diversity analysis with 55 simple sequence repeat markers, population structure analysis and pair wise FST analysis were also conducted to assess the genetic diversity. The collected rice genotypes showed significant variability in different agronomic traits, i.e. spikelet per panicle, branches per panicle etc. Results obtained from the above tests demonstrated the importance of regional genetic studies for understanding the diversification of aromatic rice in Asian and African rice.
Article ID 0091 Published: 5 September 2019 RESEARCH ARTICLE
The chloroplast genome sequence of Nitraria tangutorum, a desert shrub, was sequenced using high-throughput sequencing technology and analysed phylogenetically in the present study. The chloroplast genome is 159,414 bp in length, including a large single copy region of 87,924 bp and small single copy region of 18,318 bp, and a pair of inverted repeat regions of 26,586 bp. The chloroplast genome contains 110 unique genes, including 77 protein-coding genes, four ribosomal RNA genes, and 29 tRNA genes. Most of these genes are present as a single copy and in two or more copies 19 genes occurred. Seventeen genes have one intron, and clpP and ycf3 genes contain two introns. A total of 81 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition to SSRs, 66 repeats were identified, including 41 tandem repeats, 10 palindromic repeats, and 15 forward repeats. The phylogenetic analysis based on 54 protein-coding genes demonstrated a close relationship between N. tangutorum and other plant species in Sapindales. The complete chloroplast genome sequence of N. tangutorum will provide important data for further study of taxonomy and systematics of the genus Nitraria.
Article ID 0090 Published: 5 September 2019 RESEARCH NOTE
The species of Oryza rufipogon. dw was first discovered at Dongxiang, Jiangxi in 1978. It is recognized as abundant in genetic resources with the characteristics of cold and insect resistance. A total of 100.15 Gb raw data was obtained from seven pair-end libraries by Illumina Hiseq4000 platform. Subsequently, a draft assembly genome of O. rufipogon. dw was generated with a final size of 422.7 Mb with a contig N50 of 15 kb and a scaffold N50 of 296.2 bb. The assembly genome size was higher than the estimated genome size (413 Mb) based on k-mer analysis. The identified repeat sequences accounted for 40.09% of the entire genome, and 32,521 protein-coding genes with an average of 4.59 exons per gene was annotated in five databases. Phylogenetic analysis using 1460 single-copy gene, O. rufipogon. dw was close with O. rufipogon by Bayes method. The wild rice species of O. rufipogon. dw divergence was estimated at ∼0.3 million years ago (Mya) from O. rufipogon, and ∼0.6 Mya from the O. sativa. The draft genome of O. rufipogon. dw provided an essential resource for its origin and evolution study.
Article ID 0089 Published: 31 August 2019 RESEARCH ARTICLE
Quantitative trait loci (QTL) mapping analysis was performed for the mandible morphology in DDD.Cg-Ay/Sgn and C57BL/6J inbred mice. The size and shape of the mandible was analysed by landmark-based geometric morphometrics as the centroid size and principal components (PCs), respectively. The Ay allele at the agouti locus significantly reduced the mandible size in DDD/Sgn background, and substantially altered the mandible shape in both strain backgrounds. Single-QTL scans, by including the agouti locus genotype (Ay or non-Ay) as an additive covariate, identified three significant QTL for the centroid size on chromosomes 5, 6 and 17, along with four suggestive QTL on chromosomes 2, 12, 18 and 19. These QTLs explained 46.85% of the centroid size variation in F2 mice. When the F2Ay and F2 non-Ay mice were analysed separately, additional significant QTL were identified on chromosomes 12 and 15 in F2 non-Ay mice. Single-QTL scans also identified 15 significant QTL for the PC1, PC2 and PC3. When the agouti locus genotype was included as an interactive covariate, nine significant QTLs were identified. Unexpectedly, these agouti-interacting QTLs were identified for relatively minor PCs, for which no significant single-QTL were identified. Therefore, it was suggested that the alteration of the mandible shape in Ay mice was the consequence of interactions between the Ay allele and genes that themselves have relatively small phenotypic effect. Although further in vivo studies are required, we postulated Pkd1 as a possible candidate gene underlying QTL for the centroid size on chromosome 17.
Article ID 0088 Published: 30 August 2019 RESEARCH ARTICLE
Camelus dromedarius has played a pivotal role in both culture and way of life in the Arabian peninsula, particularly in arid regions where other domestic animals cannot be easily domesticated. Although, the mitochondrial genomes have recently been sequenced for several camelid species, wider phylogenetic studies are yet to be performed. The features of conserved gene elements, rapid evolutionary rate, and rare recombination make the mitochondrial genome a useful molecular marker for phylogenetic studies of closely related species. Here we carried out a comparative analysis of previously sequenced mitochondrial genomes of camelids with an emphasis on C. dromedarius, revealing a number of noticeable findings. First, the arrangement of mitochondrial genes in C. dromedarius is similar to those of the other camelids. Second, multiple sequence alignment of intergenic regions shows up to 90% similarity across different kinds of camels, with dromedary camels to reach 99%. Third, we successfully identified the three domains (termination-associated sequence, conserved domain and conserved sequence block) of the control region structure. The phylogenetic tree analysis showed that C. dromedarius mitogenomes were significantly clustered in the same clade with Lama pacos mitogenome. These findings will enhance our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Camelus, and provide more data for comparative mitogenomics in the family Camelidae.
Article ID 0087 Published: 30 August 2019 RESEARCH ARTICLE
Cytoplasmic male sterility (CMS) is widely used for hybrid seed production in cultivated Solanaceae species. However, there is very limited information about CMS-Rf genetic systems in potato (Solanum tuberosum). Studying the CMS-Rf systems in potato is both of theoretical and practical significance due to the emergence of a new revolutionary strategy of reinventing potato as adiploid inbred line-based crop to develop F1 hybrid seed potato breeding (Lindhout et al. 2011; Jansky et al. 2016). To search for potato Rf gene candidates, the comparative genetic approach was applied. Based on similarity to petunia Rf-PPR592 gene, 38 fragments were identified in five loci of the whole-genome nucleotide sequence of the accession DM 1-3 516 R44 S. tuberosum Phureja group (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The putative encoded mitochondrial proteins have 589–597 amino acid residues, similarto RF-PPR proteins of petunia and chili pepper and contain 14 or 15 PPR motifs. Primers have been developed flanking the most variable 782–865 bp regions of the selected loci, and polymorphism of the cloned fragments has been investigated in a subset of nine potato genotypes. The amplified fragments included seven or eight PPR motifs and lacked introns. The SNP frequencies ranged from 7.0 to 19.8% depending on the locus, while the ratio of nonsynonymous to synonymous substitutions varied between 0.9 and 2.1.Positions 1, 3 and 6 were the most variable in the studied PPR motifs. Our results demonstrated that the analysed sequences belong to the RFL-PPR gene subfamily and may be considered as Rf gene candidates in potato.
Article ID 0086 Published: 28 August 2019 REVIEW ARTICLE
Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.
Article ID 0085 Published: 23 August 2019 RESEARCH ARTICLE
In view of the documented association of solute carrier family 19 member 1 (SLC19A1) G80A (R27H) polymorphism with the risk for different types of cancers and systemic lupus erythematosus (SLE), we have reanalysed the case–control study on breast cancer to ascertain the conditions in which this polymorphic variant exerts the risk of breast cancer. Association statistics have revealed that this polymorphism exerts the risk for breast cancer under the conditions of low folate intake, and in the absence of well-documented protective polymorphism in cytosolic serine hydroxymethyltransferase. To substantiate this observation, we have developed a homology model of SLC19A1 using glycerol-3-phosphate transporter (d1pw4a) as a template where 73% of the residues were modelled at 90% confidence while 162 residues were modelled ab initio. The wild and mutant proteins shared same topology in S3, S5, S6, S7, S11 and S12 transmembrane domains. The topology varied at S1 (28–43 residue vs 28–44 residue), S2 (66–87 residue vs 69–87 residue), S4 (117–140 residue vs 117–139 residue), S8 (305–325 residue vs 305–324 residue), S9 (336–356 residue vs 336–355residue), and S10 (361–386 residue vs 361–385 residue) transmembrane domains between wild versus mutant proteins. S2 domain is shortened by three amino acid residues in themutantwhile in other domains the difference corresponds to one amino acid residue. The 3DLigandSite analysis revealed that the metallic-ligand-binding sites at 273Trp, 277Asn, 379Leu, 439Phe and 442Leu are although unaffected, there is a loss of active sites corresponding to nonmetallic ligand binding. Tetrahydrofolate and methotrexate have lesseraffinity towards the mutant protein than the wild protein. To conclude, the R27H polymorphism affects the secondary and tertiary structures of SLC19A1 with the significant loss in ligand-binding sites.
Article ID 0084 Published: 22 August 2019 RESEARCH ARTICLE
The six basic generations (two parents, F1, F2 and backcrosses) of 14 crosses developed from nine parents differing in fruits node−1 and fruit orientation were evaluated to decipher the genetics of three quantitative traits (average fruit weight, fruits plant−1 and green fruit yield plant−1) during the rainly season of 2016 and 2017. The magnitude and direction of the additive genetic effects [a], dominance genetic effects [d], magnitudes of additive genetic variance (σ2 A) and dominance genetic variance (σ2 D) varied with the genetic background of the crosses and traits. In the genetic background of crosses involving parents differing in fruit node−1, the inheritance of average fruit weight, fruits plant−1 and fruit yield plant−1 were controlled by the genes with both additive and ambidirectional dominant effects. On the contrary, genes with only additive effects controlled the inheritance of average fruit weight, fruits plant−1 and fruit yield plant−1 in most genetic backgrounds of crosses involving parents differing in fruit orientation and those differing in both fruits node−1 and fruit orientation. Further, the genes controlling the inheritance of all the traits are dispersed among the parents used in the investigation. These results are discussed in relation to strategies to be used in breeding chilli.
Article ID 0083 Published: 19 August 2019 PERSPECTIVES
During the last two decades, our understanding of the genetics of African elephant populations has greatly increased. Strong evidence, both morphological and genetic, supports recognition of two African elephant species: the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis). Among elephantids, phylogeographic patterns for mitochondrial DNA are highly incongruent with those detected using nuclear DNA markers, and this incongruence is almost certainly due to strongly male-biased geneflow in elephants. As our understanding of elephant population genetics has grown, a number of observations may be considered enigmatic or anomalous. Here, several of theseare discussed. (i) There are a number of within-species morphological differences purported to exist among elephants in different geographic regions, which would be difficult to reconcile with the low genetic differentiation among populations. (ii) Forest elephants have a higher effective population size than savanna elephants, with nuclear genetic markersmuch more diverse in the forest elephants than savanna elephants,yet this finding would need to be reconciled with thelife history of the two species. (iii) The savanna and forest elephants hybridize and produce fertile offspring, yet full genome analysis of individuals distant from the hybrid zone suggests that gene flow has been effectively sterilized for atleast ∼500,000 years. (iv) There are unexplored potentialramifications of the unusual mito–nuclear patterns among elephants. These questions are considered in light of highmale and low female dispersal in elephants, higher variance of reproductive success among males than females, and of habitat changes driven by glacial cycles and human activity
Article ID 0082 Published: 9 August 2019 RESEARCH ARTICLE
Thirty-nine wheat genotypes were studied to estimate their partial resistance levels to leaf rust at Behira governortae during three growing seasons, i.e. 2016/2017, 2017/2018 and 2018/2019. In these genotypes, partial resistance was characterized using final leaf rust severity (FRS %) and area under disease progress curve (AUDPC). Of the tested genotypes, only three wheat varieties;Giza 171, Misr 3 and Sohag 5 showed complete resistance. Further, 28 of the 39 genotypes had partial resistance as they revealed low and/or moderate values of FRS (%) and AUDPC (not exceeding 30% and 300, respectively). The other eight varieties were fast rusting, as they displayed the maximum values of FRS (%) and AUDPC. The four monogenic lines; Lr 34, Lr 46, Lr 67 and Lr 68 were identified in the wheat varieties using linked molecular markers; csLV34, Xgwm259, CFD71 and csGSR. Phenotypic results of the wheat varieties were confirmed by molecular marker analysis.
Article ID 0081 Published: 8 August 2019 REVIEW ARTICLE
Long noncoding RNA (lncRNA) H19, a well-known oncogenic lncRNA, is overexpressed in various cancers. Several studies have investigated the association between polymorphisms in lncRNA H19 and the risk of various cancer types; however, the findingswere inconsistent. In this study,we performed ameta-analysis to identify the precise association between H19 polymorphismsand cancer risk. Appropriate studies were retrieved from searching Web of Science, PubMed, Scopus, and Google scholar databases, updated 25 November 2018. The pooled odds ratios (ORs with 95% confidence intervals (CIs) were calculated to estimate the strength of the association between H19 polymorphisms and cancer risk. Our findings revealed that the H19-rs217727 C>T polymorphism is significantly associated with an increased risk of overall cancer in homozygous codominant (OR=1.28, 95%CI=1.04–1.57, P =0.020, TT vs CC), dominant (OR=1.20, 95% CI=1.04–1.37, P =0.010, CT+TT vs CC), recessive (OR=1.21, 95% CI=1.00–1.46, P =0.048, TT vs CT+CC), and allele (OR=1.16, 95%CI=1.05–1.28, P =0.003, T vs C) genetic models. No significant correlations were observed between H19: rs2839698 G>A, rs2107425 C>T, rs2735971 C>T, rs3024270 G>C, rs3741219 T>C, rs2839701 C>G, rs2735469 C>T, rs17658052 G>A, and rs3741216 T>A polymorphisms and overall cancer risk. Stratified analysis by cancer type proposed that the rs217727 variant is associated with increased risk of oral squamous cell carcinoma (OSCC) andlung cancer, whereas the rs2839698 variant is associated with increased risk of gastrointestinal cancer. Taken together, these findings support an association between H19 rs217727, and rs2839698 polymorphisms and cancer susceptibility. Larger and well-designed studies are necessary to further confirm these findings in detail.
Article ID 0080 Published: 7 August 2019 RESEARCH ARTICLE
Rice is believed to have originated from Indo-China, area between China and India, and then spread throughout the world. The Indochina region mainly includes countries like Thailand, Laos and Vietnam, which are the world’s major rice exporters. Rice varieties grown in this area are highly diverse due to their different environment, ecosystem and climatic conditions. The objective of this study was to evaluate the genetic relationship of Indochina rice varieties using intersimple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP) and insertion–deletion (InDel) markers. Forty-six rice varieties, including 16, 4,11 and 15 from Thailand, China, Laos and Vietnam, respectively were used in this study. Seventeen of the 20 ISSR primers showed 82.96% polymorphism. At the same time, 17 of the 30 primer pairs of SRAP marker showed clearDNA amplification, which resulted in 84.79% polymorphism. Ninety-seven of 133 InDel markers have about 99.47% polymorphism. Three markers showed average PIC score ranging from 0.20 to 0.26. When the analysis was conducted using UPGMA clustering method, it was found that the combined data from three markers gave a better result than each marker separately. The results from clustering analysis showed that all accessions can be grouped based on their location and can be categorized into two major groups. Useful results from this study could bring substantial benefits and ultimately help the rice breeders to develop elite rice varieties in future.
Article ID 0079 Published: 7 August 2019 RESEARCH ARTICLE
Cytoplasmic male sterility (CMS) is an important trait for large-scale hybrid seed production which avoids manual emasculation and undesired horizontal spread of pollen.Rearrangements in mitochondrial genome in terms of deletions and insertions are frequent causes leading to CMS. Mitochondrial ATP synthase is a multisubunit molecular machine which is involved in synthesis of ATP. In this study, three mutations in ATPase subunit 6 were identified and their cosegregation with male sterility was established using tobacco male sterile hybrids and Nicotiana suvaolensis. A breeder friendly Kompetitive allele specific polymerase chain reaction (KASP) SNP marker was developed for high throughput and quick genotyping. Introgression of this trait into selected germplasm lines (n = 9) was achieved based on foreground for CMS and background selection for recurrent parent using KASP marker and 50K custom tobacco SNP array, respectively. Analysis of genotyping data from SNP array revealed the presence of 88–99% of recurrent parent genome in BC3F1 plants. The selected BC3F1 plants exhibit CMS and are indistinguishable from the fertile recurrent parent (germplasm) in terms of plant morphology.
Article ID 0078 Published: 5 August 2019 RESEARCH NOTE
Article ID 0077 Published: 5 August 2019 RESEARCH ARTICLE
Although it is known that the parental carriers of chromosomal translocation are considered to be at high risk for spontaneous abortion and embryonic death, normal gestation and delivery remain possible. This study aims to investigate the genetic factors of a Chinese infant with multiple malformations and severe postnatal development retardation. In this study, the routine cytogenetic analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) analysis were performed. Conventional karyotype analyses revealed normal karyotypes of all family members. CMA of the DNA of the proband revealed a 8.3Mb duplication of 5q35.1-qter and a 6.9Mb deletion of 11q24.3-qter. FISH analyses verified a paternal tiny translocation between the long arm of chromosomes 5 and 11. Our investigation serves to provide important information on genetic counselling for the patient and future pregnancies in this family. Moreover, the combined use ofCMAand FISH is effective for clarifying pathogenically submicroscopic copy number variants.
Article ID 0075 Published: 31 July 2019 RESEARCH ARTICLE
To detect the genetic variation and relationships among different Salvia ecotypes/species, the gene targeted CAAT boxderived polymorphism (CBDP) markers were employed in terms of their efficiency. In this study, 25 CBDP primers amplified a total of 323 different polymorphic fragments that discriminate all 26 Salvia ecotypes/species and produced an informative and differentiated dendrogram and population structure. The CBDP markers were found to be effective in Salvia genetic diversity estimation with regard to the averages polymorphism (100%), polymorphism information content (PIC = 0.89), marker index (MI = 4.5) and the effective multiplex ratio (EMR = 5.01) which were higher than other reported markers on Salvia. The extent of heterozygosity (0.034≤H≤0.223) and Shannon index (0.042≤I≤0.278) indicated a high level of genetic variation among Salvia species. The species containing the highest basic chromosome number (X = 12) revealed the highest values for the number of different (Na) and effective (N e) alleles, Shannon index (I), and heterozygosity (H). Additionally, the tetraploid species showed high values of N a, Ne, I and H compared to the diploid species. Mean of gene differentiation (Gst) among Salvia species was 0.792, and the estimation of gene flow (Nm) was 0.13, indicating high genetic differentiation. Remarkably, similar results were obtained from the principal co-ordinate analysis (PCoA) as compared with the cluster analysis, in which all different Salvia species formed individual groups. In conclusion, because the CBDP markers are derived from the gene containing regions of the genome, consequently, the high genetic diversity among studied Salvia species would be more useful for crop improvement programmes, such as hybridization between species and QTL mapping. The potential of CBDPs for analysing the phylogeny and genetic diversity of Salvia species is another key result with practical implications.
Article ID 0076 Published: 31 July 2019 REVIEW ARTICLE
Spirometry based measurement of lung function is a global initiative for chronic obstructive lung disease (GOLD) standard to diagnose chronic obstructive pulmonary disease (COPD), one of the leading causes of mortality worldwide. Theenvironmental and behavioural risk factors for COPD includes tobacco smoking, air pollutants and biomass fuel exposure, which can induce one or more abnormal lung function patterns. While smoking remains the primary risk factor, only 15–20% smokers develop COPD, indicating that the genetic factors are also likely to play a role. According to the study of Global Burden of Disease 2015, ∼174 million people across the world have COPD. From a comprehensive literature search conducted using the ‘PubMed’ and ‘GWAS Catalogue’ databases, and reviewing the literature available, only a limited number of studies were identified which hadattempted to investigate the genetics of COPD and lung volumes, implying a huge research gap. With the advent of genomewide association studies several genetic variants linked to lung function and COPD, like HHIP, HTR4, ADAM19 and GSTCD etc., have been found and validated in different population groups, suggesting their potential role in determining lung volume and risk for COPD. This article aims at reviewing the present knowledge of the genetics of lung function and COPD.
Article ID 0074 Published: 29 July 2019 RESEARCH ARTICLE
The cassava grows well on low-nutrient soils because of its high-affinity to absorb nitrate. However, the molecular mechanisms by which cassava adapts itself to this environment remain elusive, although we have cloned a putative gene named MeNRT2.1 which has a crucial role in high-affinity nitrate transporter from cassava seeding. Here, the expression pattern of MeNRT2.1 was further assessed using the GUS activity driven by MeNRT2.1 promoter in Arabidopsis transformation plants. The GUS activity was monitored over time following the reduction of nitrate supply. The GUS gene expression not only peaked in roots after 12 h in 0.2mM nitrate media, but also stained stems and leaves. Arabidopsis plants with overexpression of MeNRT2.1 increased the biomass compared to the wild type on rich nitrogen (N-full) media. However, chlorate sensitivity analysis showed that Arabidopsis plants expressing MeNRT2.1 were more susceptable to chlorate than wild type. Significantly, after growing for 15 days on media containing 0.2mM nitrate concentration, wild-type plants became yellowor died, while the transgenic MeNRT2.1 Arabidopsis plants maintained normal growth. With significant increases in the amount of 15NO− 3 uptake in roots, the MeNRT2.1 plants also increased the contents of chlorophyll and nitrate reductase. Taken together, these results demonstrate that MeNRT2.1 has an important role in adaptation to low nitrate concentration as a nitrate transporter.
Article ID 0073 Published: 29 July 2019 RESEARCH ARTICLE
MANOJ KUMAR YADAV S. ARAVINDAN U. NGANGKHAM S. R. PRABHUKARTHIKEYAN U. KEERTHANA S. RAGHU D. PRAMESH A. BANERJEE S. ROY P. SANGHAMITRA T. ADAK PRIYANKA PRIYADARSHINEE MAYABINI JENA M. K. KAR P. C. RATH
Rice blast is one of the most serious diseases in the world. The use of resistant cultivars is the most preferred means to control this disease. Resistance often breaks down due to emergence of new races; hence identification of novel resistance donors is indispensable. In this study, a panel of 80 released varieties from National Rice Research Institute, Cuttack was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular marker-trait association with blast resistance. The polymorphism information content of 36 loci varied from 0.11 to 0.37 with an average of 0.34. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant and moderately resistant NRVs into different groups. Analysis of molecular variance result demonstrated maximum (97%) diversity within populations and minimum (3%) diversity between populations. Among tested markers, two markers (RM7364 and pi21_79-3) corresponding tothe blast resistance genes (Pi56(t) and pi21) were significantly associated and explained a phenotypic variance of 4.9 to 5.1% with the blast resistance. These associated genes could be introgressed through marker-assisted to develop durable blast resistant rice varieties. The selected resistant NRVs could be good donors for the blast resistance in rice crop improvement research.
Article ID 0072 Published: 19 July 2019 RESEARCH ARTICLE
Presummer, summer, and autumn bolls (PSB, SB and AB, respectively) in cotton are related to both maturity and yield. Therefore, studying their genetic basis is important for breeding purposes. In this study, we developed an association analysis panel consisting of 169 upland cotton accessions. The panel was phenotyped for PSB, SB and AB across four environments and genotyped using a Cotton SNP80K array. Single-nucleotide polymorphisms (SNPs) associated with these three traits were identified by a genomewide association study. A total of 53,848 high-quality SNPs were screened, and 91 significant trait-associated SNPs were detected. Of the 91 SNPs 33 were associated with PSB, 21 with SB and 37 with AB. Three SNPs for PSB (TM10410, TM13158 and TM21762) and five for AB (TM13730, TM13733, TM13834, TM29666 and TM43214) were repeatedly detected in two environments or by two methods. These eight SNPs exhibited high phenotypic variation of more than 10%, thus allowing their use formarker-assisted selection. The candidate genes for target traits were also identified. These findings provide a theoretical basis for the improvement of early maturity and yield in cotton breeding programmes.
Article ID 0071 Published: 16 July 2019 RESEARCH ARTICLE
Myotonia congenita (MC) is a Mendelian inherited genetic disease caused by the mutations in the CLCN1 gene, encoding the main skeletal muscle ion chloride channel (ClC-1). The clinical diagnosis of MC should be suspected in patients presenting myotonia, warm-up phenomenon, a characteristic electromyographic pattern, and/or family history. Here, we describe the largest cohort of MC Spanish patients including their relatives (up to 102 individuals). Genetic testing was performed by CLCN1 sequencing and multiplex ligation-dependent probe amplification (MLPA). Analysis of selected exons of the SCN4A gene, causing paramyotonia congenita, was also performed. Mutation spectrum and analysis of a likely founder effect of c.180+3A>T was achieved by haplotype analysis and association tests. Twenty-eight different pathogenic variants were found in the CLCN1 gene, of which 21 were known mutations and seven not described. Gross deletions/duplications were not detected. Four probands had a pathogenic variant in SCN4A. Two main haplotypes were detected in c.180+3A>T carriers and no statistically significant differences were detected between case and control groups regarding the type of haplotype and its frequencies. A diagnostic yield of 51% was achieved; of which 88% had pathogenic variants in CLCN1 and 12% in SCN4A. The existence of a c.180+3A>T founder effect remains unsolved.
Article ID 0070 Published: 16 July 2019 RESEARCH ARTICLE
Somatic embryos (SE) of habanero pepper (Capsicum chinense Jacq.) represent persistent deformations in the shoot apical meristem (SAM), which inhibits their capacity to form organs and subsequently plants. In dicotyledonous plants, SAM is formed in the apex, between cotyledons and it plays a central role in postembryonic shoot organ formation. Based on the previous knowledge on the role of some families of gene in the formation, organization and maintenance of the SAM, the expression patterns of WUS, WOX2, NAM, STM, PIN1 and PIN7 genes were analysed, which would allow us to elucidate the possible implication of these genes in SAM deformations in the SE of C. chinense. The results show that the expression patterns of STM and PIN1 in the SE were completely opposite to the respective expression pattern obtained in zygotic embryos (ZE). Moreover, NAM and PIN7 showed an over accumulation of transcripts in SE, compared with ZE. This is the first time in the genus Capsicum that alterations in the expression pattern of key genes of the SE development are reported, as well as its possible implication in the persistent deformations of the SAM.
Article ID 0068 Published: 10 July 2019 RESEARCH ARTICLE
The hard clam (Meretrix petechialis) is a commercially important shellfish in China. To provide valuable insights into management and conservation of M. petechialis, we investigated the genetic variation and population structure of M. petechialis by analysing samples from nine geographical populations. In this study, the genetic diversity and differentiation of nine populations of M. petechialis were assessed using the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. A total of 90 COI sequences were obtained and each COI sequence was 699 bp in length. Fifty-one haplotypes were identified with 10 haplotypes sharedamong populations. The haplotype diversity was highest in Fujian, Panjin and Jiangsu (0.9778 ± 0.0540) and lowest in Dalian (0.7778 ± 0.1374). The nucleotide diversity was highest in Panjin (0.453401 ± 0.240463) and lowest in Jiangsu (0.006213 ± 0.004141). Neutral test (Fu’s Fs) and mismatch distribution analysis revealed that the hard clam experienced a population expansion event. Analysis of molecular variance (AMOVA) indicated that 91.7% of the genetic variance was within populations and 0.52% of the variance was among populations, demonstrating significant genetic differentiation among populations (P < 0.05). The neighbour-joining tree showed that the haplotypes were not clustered according to the geographical location, but some haplotypes from the same or neighbouring locations grouped together. The results obtained in this study provide useful information on the genetic diversity and population structure of M. petechialis and shed light on the management and protection of resources of M. petechialis in the northwestern Pacific.
Article ID 0067 Published: 10 July 2019 RESEARCH ARTICLE
This study aims to analyse the potential relationship between single-nucleotide polymorphism (SNPs) in trace element related metabolic genes GSTM3, GSTP1, GPX1 and NKG2D and the risk of gastric cancer. A case–control study was conducted in the hospital of Xianyou, Fujian, China. In this study, a total of 299 patients with histopathological diagnosis in gastric cancer and 295 healthy control subjects were involved. Association between the SNPs in trace element-related metabolic genes and gastric cancer risk was analysed using the unconditional logistic regression model. No relationship was found between the SNPs of GSTM3 and GPX1 genes and gastric cancer risk. However, the risk of gastric cancer is related to the SNPs of NKG2D gene (rs1049174). Patients who carry the rs1049174 GG genotype have a higher incidence of the gastric cancer and a multivariate odds ratio (OR) of 1.85 (95% confidence intervals (CI): 1.02–3.38). Through haplotype analysis, two haplotypes (i.e. A_rs1746123-T_rs10431294-G_rs1049174 and T_rs1746123-T_rs10431294-C_rs1049174), OR of 0.29 (95% CI: 0.15–0.56) and 0.33, (95% CI: 0.22–0.50), respectively, were found to have lower incidence of gastric cancer. Meanwhile, another two haplotypes (T_rs1746123-C_rs10431294-C_rs1049174 and T_rs1746123-T_rs10431294-G_rs1049174), OR of 1.81 (95% CI: 1.40–2.34) and 3.09 (95% CI: 2.30–4.16), respectively, were found to have a higher incidence of gastric cancer. Further, no influence of the haplotype on the risk of cardia gastric cancer was found. However, the haplotype T_rs1746123-T_rs10431294-C_rs1049174 had lower incidence of noncardia gastric cancer by 46%. Our data showed that polymorphisms of trace element-related metabolic genes are important in gastric cancer pathology.
Article ID 0069 Published: 10 July 2019 RESEARCH ARTICLE
Genetic information of polymerase chain reaction (PCR)-based markers, one of the main tools of genetics and genomics research in wheat, have been well documented in wheat. However, the physical position in relation to these markers has not yet been systematically characterized. Aim of this study was to characterize the physical information of thousands of widely usedmolecular markers.We first assigned 2705 molecular markers to wheat physical map, of which 86.1% and 84.7% were the best hits to chromosome survey sequencing (CSS) project (CSS-contigs) and International Wheat Genome Sequencing Consortium Reference Sequence v1.0 (IWGSC RefSeq v1.0), respectively. Physical position of 96.2% markers were predicated based on BLAST analysis, were in accordance with that of the previous nullisomic/aneuploidy/linkage analysis. A suggestive high-density physical map with 4643 loci was constructed, spanning 14.01 Gb (82.4%) of the wheat genome, with 3.02Mb between adjacent markers. Both forward and reverse primer sequences of 1166 markers had consistent best hits to IWGSC RefSeq v1.0 based on BLAST analysis, and the corresponding allele sizes were characterized. A detailed physical map with 1532 loci was released, spanning 13.93 Gb (81.9%) of the wheat genome, with 9.09Mb between adjacent markers. Characteristic of recombination rates in different chromosomal regions was discussed. In addition, markers with multiple sites were aligned to homoeologous sites with a consistent order, confirming that a collinearity existed among A, B and D subgenomes. This study facilitates the integration of physical and genetical information of molecular markers, which could be of value for use in genetics and genomics research such as gene/QTL map-based cloning and marker-assisted selection.
Article ID 0066 Published: 28 June 2019 RESEARCH ARTICLE
Iron (Fe) and zinc (Zn) deficiencies are wide spread in South Asia and Africa. Biofortification of food crops is a viable means of addressing micronutrient deficiencies. Lentil is an important pulse crop that provides affordable source of proteins, minerals, fibre and carbohydrates for micronutrient deficient countries. An association mapping (AM) panel of 96 diverse lentil genotypes fromIndia and Mediterranean region was evaluated for three seasons and genotyped using 80 polymorphic simple-sequence repeat (SSR) markers for identification of the markers associated with grain Fe and Zn concentrations. A Bayesian model based clustering identified five subpopulations, adequately explaining the genetic structure of the AM panel. The linkage disequilibrium (LD) analysis usingmixed linear model (MLM) identified two SSR markers, GLLC106 and GLLC108, associated with grain Fe concentration explaining 17% and 6% phenotypic variation, respectively and three SSR markers (PBALC 364, PBALC 92 and GLLC592) associated with grain Zn concentration, explaining 6%, 8% and 13% phenotypic variation, respectively. The identified SSRs exhibited consistentperformance across three seasons and have potential for utilization in lentil molecular breeding programme.
Article ID 0065 Published: 17 June 2019 RESEARCH NOTE
Mucopolysaccharidosis type I (MPSI) is a rare autosomal recessive disorder caused bymutations in alpha-L-iduronidase (IDUA) gene. IDUA contributes to the degradation of the glycosaminoglycans, including heparan sulphate and dermatan sulphate. Deficient activity of IDUA generates accumulation of glycosaminoglycans in lysosomes leading to MPS I. Here, we identified twoboys with MPS I caused by a compound heterozygote of a reported c.265C > T (p.R89W) missense mutation in exon 2 and a novel c.1633G > T (p.E545*, 109) nonsense mutation in exon 11 of IDUA gene in a Chinese family. R89 is close to the active site and its replacement will affect the structure and function of IDUA. Besides, termination from E545 deletes one of the prominent domainsand alters the spatial structure of IDUA. In conclusion, our study demonstrates a previously unrecognized mutation in IDUA gene and this report adds to the mutational spectrum observed.
Article ID 0064 Published: 14 June 2019 RESEARCH NOTE
Plasmodium knowlesi contributes to the majority of human malaria incidences in Malaysia. Its uncontrollable passage among the natural monkey hosts can potentially lead to zoonotic outbreaks. The merozoite of this parasite invades host erythrocytes through interaction between its erythrocyte-binding proteins (EBPs) and their respective receptor on the erythrocytes. The regionII of P. knowlesi EBP, P. knowlesi beta (PkβII) protein is found to be mediating merozoite invasion into monkey erythrocytes by interacting with sialic acid receptors. Hence, the objective of this study was to investigate the genetic diversity, natural selection and haplotype grouping of PkβII of P. knowlesi isolates in Malaysia. Polymerase chain reaction amplifications of PkβII were performed on archived blood samples from Malaysia and 64 PkβII sequences were obtained. Sequence analysis revealed length polymorphism, and its amino acids at critical residues indicate the ability of PkβII to mediate P. knowlesi invasion into monkey erythrocytes. Low genetic diversity (π = 0.007) was observed in the PkβII of Malaysia Borneo compared to PeninsularMalaysia (π = 0.015). The PkβII was found to be under strong purifying selection to retain infectivity in monkeys and it plays a limited role in the zoonotic potential of P. knowlesi. Its haplotypes could be clustered into Peninsular Malaysia and Malaysia Borneo groups, indicating the existence of two distinct P. knowlesi parasites in Malaysia as reported in an earlier study.
Article ID 0063 Published: 8 June 2019 PERSPECTIVES
Article ID 0062 Published: 7 June 2019 RESEARCH NOTE
The aetiology of developmental dyslexia (DD) is complex; although candidate genes have been suggested, the molecular mechanism and risk factors remain unknown. The KIAA0319 gene is functionally related to neuronal migration and axon growth, and several studies have examined associations between KIAA0319 polymorphisms with DD, but the results remain inconsistent. The sample size affects the results of meta-analysis. The aim of this meta-analysis was to clarify the effect of KIAA0319 polymorphisms on dyslexia susceptibility according to the available evidence. All eligible case–control and transmission/disequilibrium test (TDT) studies published until March 2018 were identified by searchingMedline, PubMed, Embase, Web of Science and Chinese Biomedical Database, limited to Chinese and English language papers. Pooled odds ratios and 95% confidence intervals were calculated using STATS package v12.0. A total of 11 related studies, including 3130 cases of dyslexia and 3460 healthy control subjects, as well as four TDT studies with 842 families were included in our meta-analysis. The results indicated that the polymorphisms rs4504469, rs2038137, rs2179515, rs3212236, rs6935076, rs9461045, rs2143340 and rs761100 have no association between the polymorphisms and dyslexia risk. Three subgroup meta-analyseswere performed according to the study design, country and population. The stratified analysis revealed that the KIAA0319 rs4504469 minor allele was a risk allele t in the TDT subgroup, rs3212236 minor allele was a risk allele t in the UK subgroup and rs6935076 minor allele was a risk allele t in the Canada subgroup. Further studies with larger sample sizes that assess gene–gene and gene–environment interactions are required. The sample size of our study is larger than that of the previous studies, and the results are different from those of the previous studies.We have synthesized all the current studies on KIAA0319 and obtained reliable results.
Article ID 0061 Published: 6 June 2019 RESEARCH ARTICLE
Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity
Being an economical and nutritional crop, Capsicum appeases people’s peppery taste and is found to bewidely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.
Article ID 0060 Published: 5 June 2019 RESEARCH ARTICLE
Schizophrenia (SZ) is a debilitating mental illness with a multigenic aetiology and significant heritability. Despite extensive genetic studies, the molecular aetiology has remained enigmatic. A recent systems biology study suggested a protein–protein interaction network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominant during adolescence, often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan Atlas data allowed us to re-examine the genes present in the SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and nonpsychiatric Exome Aggregation Consortium database allowed us to identify the variants of criticality. The expression of the SZ candidate genes responsible for cognition and disease onset was studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by theprevious interactome study to 10 proteins. These proteins belonging to 81 biological pathways are targeted by 34 known Food and Drug Administration-approved drugs that have distinct potential for the treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to celecoxib pharmacodynamics, Gα signalling and cGMP-PKG signalling pathwaysthat are not known to be specific to SZ aetiology.
Article ID 0059 Published: 4 June 2019 RESEARCH ARTICLE
Several studies including genomewide association studies (GWASs) in diverse ethnic populations have reported a significant association of genetic variant rs10937405 of TP63 with nonsmall cell lung cancer (NSCLC). However, no data are available from any Indian population on the association of this variant with NSCLC. Using TaqMan genotyping chemistry, we conducted a case–control study involving 190 NSCLC cases and 400 ethnic, age-matched controls to explore the association of rs10937405 genetic variant with NSCLC in patients from north India. Our data support that the rs10937405 variant is also significantly associated with the NSCLC and is a risk factor in the north Indian populations to develop NSCLC. However, unlike most other studies, the wild-type allele T appears to be the risk allele, as its frequency was significantly higher in the cases than controls (0.439 in cases versus 0.383 in controls. OR=1.95 (1.23–3.09 at 95% CI); P value (adjusted)= 0.004). Genetic association was also observed by applying different genetic models. The present study provides important information of the genetic aetiology of NSCLC and strengthens GWAS findings, highlighting the role of TP63 in lung cancer risk.
Article ID 0058 Published: 3 June 2019 RESEARCH ARTICLE
Screening of trait-associated molecular markers can be used to enhance the efficiency of selective breeding. Previously, we produced the first high-density genetic linkage map for the mandarin fish (Siniperca chuatsi) and identified 11 quantitative-trait loci significantly associated with growth, of which one is located within the growth hormone (GH) gene. To investigate the GH gene polymorphisms and their correlation with growth, the complete sequence was cloned and 32 single-nucleotide polymorphisms (SNPs) and one simple-sequence repeat (SSR)were identified. Of which, eight SNPs (G1–G8) and the SSR (GH-AG)were selected for genotyping and correlation analysis with growth traits in a random population. The results showed that the four novel polymorphicloci (G1, G2, G3 and GH-AG) were significantly correlated with growth traits of mandarin fish (P < 0.05). Of these, G1, G3 and GH-AG showed highly significant correlations with multiple growth traits (P < 0.01) and the combined SNP analysis showed that G1–G3 formed four effective diplotypes (D1–D4), among which D1 was highly significantly greater than D4 (P < 0.01) for some important growth traits. In conclusion, our results show that the four polymorphic loci G1–G3 and GH-AG within the mandarin fish GH gene are significantly correlated with growth traits and could be used as candidate molecular markers for selective breedingof superior varieties of mandarin fish.
Article ID 0056 Published: 1 June 2019 RESEARCH NOTE
The 16p12.2 chromosome band contains three large segmental duplications: BP1, BP2 and BP3, providing a substrate for recombination and recurrent chromosomal rearrangements. The ‘16p12.2 microdeletion’ is a recurrent deletion comprised between BP2 and BP3, associated with variable clinical findings. We identified a heterozygous 16p12.2 microdeletion spanning between BP1 and BP2 in a child evaluated for short stature and mild dyslexia. Unexpectedly, the mother carried the same deletion in the homozygous state and suffered from severe hearing loss. Detailed family history revealed consanguinity of the maternal grandparents. The 16p12.2 microdeletion is a rare condition and contains only three genes: METTL9, IGSF6 and OTOA of which the OTOA is considered responsible for DFNB22 hearing loss (MIM: 607039) under its homozygous condition. A number of OTOA mutations have been described, whereas very few cases of a 16p12.2 microdeletion similar to that observed in our family have been reported. In conclusion, we describe a rare ‘distal 16p12.2microdeletion’ widening the phenotypic spectrum associated with the recurrent 16p12.2 microdeletion and support the causative role of OTOA microdeletion in hearing impairment.
Article ID 0057 Published: 1 June 2019 RESEARCH ARTICLE
Ceratitis capitata is one among the most destructive and economically important agricultural pests worldwide. Despite its economic significance, the population structures of this pest have remained relatively unexplored in the eastern Mediterranean basin. Using two mitochondrial markers, the present study aimed to examining the population genetic structure and diversity of C. capitata populations in Turkey, the region that covers a large part of the eastern Mediterranean area. Our results revealed that the Turkish Mediterranean fruit fly populations are characterized by low levels of genetic diversity and limited population differentiation. For comparison purposes, wemerged the sequences identified in the present study with the previously reported sequences from acrossthe world into the data matrix. The haplotype network showed that, unlike the African samples the Mediterranean samples and samples from the new world (America, Pacific region and Australia) did not show any clear pattern of geographical structuring, which indicates that the Mediterranean basin, particularly the eastern Mediterranean region populations, may have played a moreimportant role in the colonization of C. capitata populations to the new world. The results also revealed a close genetic relationship between the Turkish and Iranian populations, suggesting that the Iranian C. capitata populations probably originated from Turkey.
Article ID 0055 Published: 1 June 2019 RESEARCH NOTE
Restorer line F6 (Oryza sativa L. ssp. indica) has been widely used in hybrid rice breeding systems in southern China. However, line F6 is susceptible to drought stress, which restricts its utilization in many areas. Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) has strong drought stress resistance, but the molecular factors responsible for drought resistance in DXWR remain unknown. In this study, we used the combination of phenotypic selection and molecular marker-assisted selection (MAS) to improve the drought stress resistance of line F6 by introgression of qSDT12-2, a large effect drought stress-related quantitative trait locus identified in DXWR. Molecular MAS was carried out using linked marker RM1226, which is associated with qSDT12-2. Genomic background assessmentwas performed using 112 polymorphic markers. Finally, a stable drought stress-resistant backcross inbred line (BIL) was developed from a BC5F5 population, termed BIL627. Genetic constitution analysis revealed that the genome of BIL627 is almost identical (99.1%) to that of the restorer line F6. Further, BIL627 showed no yield penalty and no decrease in restorationability under normal conditions. Taken together, our findings reveal the intrinsic value of using genetic resources present in wild species of Oryza to improve undesirable traits found in cultivated rice.
Article ID 0054 Published: 30 May 2019 RESEARCH NOTE
Neuronal migration disorders (NMDs) are a heterogeneous group of conditions caused by the abnormal migration of neuroblasts in the developing brain and nervous system, resulting in severe developmental impairment, intractable epilepsy and intellectual disability (Spalice et al. 2009). To date, many genes have been identified as the leading cause of migration defects, i.e. agyria/pachygyria, polymicrogyria, heterotopias, agenesis of the corpus callosum and agenesis of the cranial nerves (Spalice et al. 2009). Here, we present a patient with early infantile epileptic encephalopathy (Ohtahara syndrome) with seizure onset on the first dayof life, severe developmental delay and an abnormal brain MRI with excessive folding of small, fused gyri and bilateral perisylvian polymicrogyria, suggestive of neuronal migration disorder. To clarify the unknown aetiology, we conducted whole-exome sequencing, which detected a de novo missense variant (c.5308A>T; p.(Met1770Leu)) in the SCN2A gene. This is a report of SCN2A gene variant identified in a patient with neuronal migration disorder which could further expand the phenotypic spectrum of these genetic disorders.
Article ID 0053 Published: 23 May 2019 RESEARCH ARTICLE
In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated thatthere is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had α-turns and β-turns, and α-amphipathic regions up to 129, 138–156 and 151–155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima’s D value was negative (−2.404165), indicative of negative selection pressure.
Article ID 0052 Published: 21 May 2019 RESEARCH ARTICLE
NAC transcription factors (TFs) are master regulators of environmental stresses exerting a crucial role in plant growth and development. However, the studies on NAC TFs from Bambusa emeiensis are scarce. In this investigation, a novel gene from B. emeiensis encoding NAC protein was cloned and characterized. The gene was isolated based on the amino acid sequence data of stress-responsive SNAC1 of rice, named ‘BeSNAC1 (accession no. MG763922)’. The full-length sequence of 1681 bp was found to contain an open-reading frame of 912 bp that encode a protein of 303 amino-acid residues. The multiple protein sequence alignments unveiled that BeSNAC1 contains a typical NAC domain. Additionally, the phylogenetic analysis showed that the corresponding protein belonged to the SNAC group, as it cladded with SNAC1, HvSNAC1, TaNAC2, SbSNAC1 and ZmSNAC1 proteins. Transactivation and subcellular localization assay disclosed that BeSNAC1 is a transcriptional activator localized in the cell nucleus.Moreover, the time-dependent expression pattern of BeSNAC1 was profiled under abscisic acid (ABA), polyethylene glycol 6000 (PEG-6000), NaCl, H2O2 and Na2SO4 treatments via a quantitative real-time polymerase chain reaction. The results revealed that the expression of BeSNAC1 was significantly upregulated in all treatments, a significant difference was observed under H2O2, NaCland ABA (P 0.001) and PEG and Na2SO4 (P < 0.01) treatments, respectively. Conclusively, our findings provide evidence that ‘BeSNAC1’ is a nuclear protein that might act as part of the transcription regulation complex and is involved in the ABA signalling pathway and abiotic stress tolerance mechanisms in B. emeiensis.
Article ID 0051 Published: 14 May 2019 RESEARCH NOTE
Mutations in several genes, including SERPRINF1 and COL1A1, have been associated with the development of osteogenesis imperfecta (OI). Here, we reported the co-occurrence of a rare heterozygous variant (c.167C>G p.Ala56Gly) in SERPRINF1 and a novel heterozygous mutation (c.1634G>A p.Gly545Asp) in COL1A1 in a foetus with a severe form of OI. Bioinformatics modelling revealed that the effect of the mutation on SPERINF1 is neutral. In contrast, the mutation in COL1A1 is deleterious. It is predicted to cause distortion of the α (1) chain of the type I collagen and results in structural instability of the protein. Therefore, a novel dominant variant of COL1A1 likely underlies the severe foetal pathology observed, although we do not exclude the possibility that the heterozygous mutations in SERPINF and COL1A1 may interact and co-ordinately cause pathogenesis. This novel COL1A1 mutation is recommended to be included in the diagnostic panels for OI.
Article ID 0049 Published: 13 May 2019 RESEARCH NOTE
Northern snakehead, Ophiocephalus argus Cantor, is an endemic freshwater fish in China. However, wild stocks of O. argus are dwindling sharply. Further, water conservancy projects, environmental pollution and human activities have caused the decrease of wild stocks, which has attracted much attention. Here, we have investigated the genomic information of O. argus using IlluminaHiseq 4000 sequencing. The transcriptomes of O. argus were sequenced by Illumina technology. A total of 67,564 sequences from 79,500,964 paired-end reads were generated, 33,710 unigenes were annotated based on protein databases (NCBI nonredundant (NR) databases). In total, 7182 unigenes had the clusters of orthologous group (COG) classifications, 33,710 unigenes were assigned to 59 gene ontology (GO) terms. Further, a total of 21,464 simple sequence repeats (SSRs) from 67,564 unigenes and 113,518 single nucleotide polymorphism (SNP) sites among 335 Mclean reads were yielded for O. argus based on a transcriptome-wide search. The new transcriptome data which is presented in this study for O. argus will provide valuable information for gene discovery and downstream applications, such as phylogenetic analysis, gene-expression profiling and identification of genetic markers (SSRs andSNP).
Article ID 0050 Published: 13 May 2019 RESEARCH ARTICLE
Panicle traits are the most important agronomic characters which directly relate to yield in rice. Panicle length (PL) being one of the major components of rice panicle structure is controlled by quantitative trait loci (QTLs). In our research, conducted at Research Farm of SKUAST-J, crosses of parental lines K343 and DHMAS were made for generating F2 mapping population, which were then transplanted into the field using augmented design-I. The F2 population was used for phenotypic evaluation, development of linkage map and identification of QTLs on the chromosomes by using SSR markers. A total of 450 SSR markers were used for screening both the parents of which 53 highly polymorphic markers were selected and used for genotyping of 233 genotypes of F2population. Linkage map was generated using MAPMAKER/EXP3.0 software, seven linkage groups were found distributed on 11 chromosomes of rice. QTLs were detected using QTL Cartographer (v2.5) software. Based on 1000 permutation tests, a logarithm of odds (LOD) threshold value 2.0 and 3.0 was set. Composite interval mapping was used to map QTLs in populations derived from bi-parental crosses. The phenotypic data, genotypic data and the genetic linkage map generated identified total three QTLs of which one was identified for PL qPL2, located at 85.01 cM position with 2.1 LOD value and in between the marker intervals RM324–RM208, this QTL explained the phenotype variation by 4.36%. The other two QTLs were identified for spikelet density (SD) qSD3.1 and qSD3.2, located at 28.91 and 39.51 cM, respectively, both with a flanking marker RM6832 on chromosome 3. The LOD value and phenotypic variation explained for qSD3.1 and qSD3.2 was 3.00 and 3.25; 9.70 and 12.34% respectively. The reported QTLs identified in the study suggested a less diversity in the parents used and also the rejection of not so useful markers from the used set of markers for PL and SD.
Article ID 0048 Published: 9 May 2019 RESEARCH ARTICLE
Despite the ubiquitous occurrence of heat-shock protein 60 (Hsp60) and their role in maintenance of cell activity and integrity, this protein remains poorly characterized in many of the symbiotic soil mycorrhizal fungi such as Rhizophagus irregularis. Thus, in the current study, an attempt has been made to elucidate the evolutionary history, time of divergence followed by estimation of population genetic parameters of hsp60 using R. irregularis as a model organism. Sequence alignment reported here identified several close homologues for hsp60 (gene) and Hsp60 (protein) from diverse taxa, while the output from protein-based phylogenetic tree indicates that mitochondrial Hsp60 of R. irregularis shares close evolutionary relationship with classical α-proteobacteria. This is perhaps the first line of evidence elucidating the likelihood of hsp60 from fungal taxa sharing a close evolutionary relationship with classical α-proteobacteria as a common ancestor. Comprehensive analysis of mitochondrial hsp60 from selected fungal taxa from the evolutionary point of view explains the possibility of gene duplication and or horizontal gene transfer of this gene across various fungal species. Synteny relationships and population genetics credibly explain high genetic variability associated with fungal hsp60 presumably brought by random genetic recombination events. The results presented here also confirm a high level of genetic differentiation of hsp60 among all the three fungal populations analysed. In this context, the outcome of the current study, basedon computational approach, stands as a testimony for explaining the possibility of increased genetic differentiation experienced by hsp60 of R. irregularis.
Article ID 0046 Published: 9 May 2019 RESEARCH ARTICLE
Finger millet (Eleusine coracana (L.) Gaertn.), an important C4 species is known for its stress hardiness and nutritional significance. To identify novel drought responsive mechanisms, we generated transcriptome data from leaf tissue of finger millet, variety GPU-28, exposed to gravimetrically imposed drought stress so as to simulate field stress conditions. De novo assembly basedapproach yielded 80,777 and 90,830 transcripts from well-irrigated (control) and drought-stressed samples, respectively. A total of 1790 transcripts were differentially expressed between the control and drought-stress treatments. Functional annotation and pathway analysis indicated activation of diverse drought-stress signalling cascade genes such as serine threonine protein phosphatase 2A (PP2A), calcineurin B-like interacting protein kinase31 (CIPK31), farnesyl pyrophosphate synthase (FPS), signal recognition particle receptor α (SRPR α) etc. The basal regulatory genes such as TATA-binding protein (TBP)-associated factors (TAFs) werefound to be drought responsive, indicating that genes associated with housekeeping or basal regulatory processes are activated underdrought in finger millet. A significant portion of the expressed genes was uncharacterized, belonging to the category of proteins of unknown functions (PUFs). Among the differentially expressed PUFs, we attempted to assign putative function for a few, using anovel annotation tool, Proteins of Unknown Function Annotation Server. Analysis of PUFs led to the discovery of novel drought responsive genes such as pentatricopeptide repeat proteins and tetratricopeptide repeat proteins that serve as interaction modules in multiprotein interactions. The transcriptome data generated can be utilized for comparative analysis, and functional validation of the genes identified would be useful to understand the drought adaptive mechanisms operating under field conditions in finger millet, as has been already attempted for a few candidates such as CIPK31 and TAF6. Such an attempt is needed to enhance the productivity of finger millet under water-limited conditions, and/or to adopt the implicated mechanisms in other related crops.
Article ID 0047 Published: 9 May 2019 RESEARCH ARTICLE
Whole-genome resequencing provides the opportunity to explore the genomic variations and pave way for further functional assays to map the economical trait loci. In this study, we sequenced the genomes of mixed chicken samples from a full-sib family, with feathered and unfeathered legs at an average effective depth of 4.43×, using Illumina Hiseq 2000 instruments. Over 2.1 million nonredundant short indels (1–71 bp) were obtained. Among them, 16,375 common indels that were polymorphic between the comparison groups were revealed for further analysis. The majority of the common differential indels (76.52%) were novel. Follow-up validation assays confirmed that 80% randomly selected indels represented true variations. The indels were annotated based on the chicken genome sequence assembly. As a result, 16,375 indels were found to be located within 2756 annotated genes, with only 33 (0.202%) located in exons. By integrated analysis of the 2756 genes with gene function and known quantitative trait loci, we identified a total of 24 promising candidate genes potentially affecting feathered-leg trait, i.e. FGF1, FGF4, FGF10, FGFR1, FRZB, WNT1, WNT3A, WNT11, PCDH1, PCDH10, PCDH19, SOX3, BMP2, NOTCH2, TGF-β2, DLX5, REPS2, SCN3B, TCF20, FGF3, FSTL1, WNT7B, ELOVL2 and FGF8. Our findings provide a basis for further study and reveal key genes for feathered-leg trait in chickens.
Article ID 0044 Published: 8 May 2019 RESOURCES
Rapid molecular assays for species and sex identification of swamp deer and other coexisting cervids in human-dominated landscapes of the Terai region and upper Gangetic plains, northern India: implications in understanding species distribution and population parameters
Burgeoning pressures of habitat loss is a major cause of herbivore decline across India, forcing them to coexist with humans in non-protected areas. Their conservation in such landscapes is challenging due to paucity of ecological and demographic information. The northern subspecies of swamp deer, Rucervus duvaucelii duvaucelii, is one such herbivore that lives across human dominated landscapes in Terai region and upper Gangetic plains of north India. Here, we describe species-specific molecular markers and a cervid-specific molecular sexing assay for swamp deer and four other coexisting cervids sambar, chital, barking deer and hog deer. Our markers show species-specific band patterns and a high success rate of 88.21% in large number of field collected referencesamples for all species. Faecal pellets from pilot swamp deer survey samples from upper Ganges basin show 93.81% success rate, and only 5.5% misidentification based on morphological characteristics. Our cervid-specific molecular sexing multiplex assay accurately ascertained 81.15% samples to respective sexes. These molecular approaches provide an easy, quick and cheap option to generate critical information on herbivore population parameters and aid their conservation in this mosaic of protected and non-protected grassland habitats.
Article ID 0045 Published: 8 May 2019 RESEARCH ARTICLE
Hypoplastic right heart syndrome(HRHS) is characterized by hypoplastic right ventricle (RV); Numerous transcriptional cascades in the second heart field (SHF) regulateRVdevelopment. The relationship of SHF gene variants with humanHRHS remains unknown. The whole lengths of 17 SHF genes were sequenced in 16 HRHS, and the selected single-nucleotide variants (SNVs) were then genotyped in HRHS, other congenital heart disease (CHD) and healthy control. Luciferase assay was performed to verify the effect of FOXC2: rs34221221A>GandTBX20: rs59854940C>Gat the transcription level. There were 151 (12.86%) novel SNVs after sequence analysis, of which three were in exons (one was synonymous SNV and two were nonsynonymous SNVs), two in promoter, and most SNVs (89.95%) were in intronic regions. Genotype analyses revealed that the minor alleles of FOXC2: rs34221221 A>G and TBX20: rs59854940 C>G could increase HRHS risk (P<0.05), but not in other CHD or healthy control. Luciferase assay showed that the minor G allele in rs34221221 significantly increased FOXC2 transcription while in rs59854940 it decreased TBX20 transcription significantly. Novel variants of SHF gene associated with HRHS were identified. Minor alleles in two variants from FOXC2 and TBX20 could increase the risk of HRHS.
Article ID 0041 Published: 4 May 2019 RESEARCH ARTICLE
Yak (Bos grunniens) is a unique bovine species and considered as lifeline of highlanders. The male subfertility in yak is a matter of concern that causes huge economic loses. The spermatogenesis and male reproduction machinery are critically governed by Y-linked genes which tend to acquire necessary information in the course of evolution. The Y-linked fertility genes are present in multiple copies with testis-limited expression. To understand this novel complexity, 12 male-specific region of Y chromosome (MSY) genes have been studied in the yak. Targeted genes are amplified in male and female genomic DNA and confirmed the male derived specificity. Moreover, testis and sperm-specific expressions of MSY genes are distinct among different tissues. The quantitative polymerase chain reaction results validate the expression pattern of these genes in various tissues with predominant expression intestis and sperm. The sequencing of resultant yak MSY genes gives significant result and shows similarity with cattle (Bos indicus), but few nucleotide mismatches define the proposition of infertile male in the F1 hybrid of cattle and yak. The identified MSY genes can be used to establish male-specific characteristics and to differentiate male and female yak genotypically. Further, these genes may act as valuable resources to understand the capacity of spermatogenesis, embryogenesis, cellular growth, azoospermia and malesubfertility in the yak.
Article ID 0043 Published: 4 May 2019 RESEARCH ARTICLE
The Hazaras are a distinct ethnic group from central Afghanistan and northwestern Pakistan of Mongoloid descent. Here, we sought to dissect the genetic admixture history of the Pakistani Hazaras and investigated their likely affiliation to ancient and extant West Eurasian populations. Our results indicated that the likely proportion of West Eurasian ancestry was low in the Hazaras and could be attributed putatively to a combination of Steppe populations from Early/Middle Bronze Age or Middle/Late Bronze Age and the Neolithic Iranians. Our results expand upon the current understanding and provide an improved resolution into the population history of the Pakistani Hazaras.
Article ID 0042 Published: 4 May 2019 RESEARCH ARTICLE
Diagnosis and treatment of velocardiofacial syndrome (VCFS) with variable genotypes and phenotypes are considered to be very complicated. Establishing an exact correlation between the phenotypes and genotypes of VCFS is still a challenging. In this paper, 88 Chinese VCFS patients were divided into five groups based on palatal anomalies and one or two of other four common phenotypes, and copy number variations (CNVs) were detected using multiplex ligation-dependent probe amplification (MLPA), array comparative genomic hybridization (aCGH) and quantitative polymerase chain reaction. The findings showed that palatal anomalies and characteristic malformation of face were important indicators for 22q11.2 microdeletion, and there was difference inthe phenotypic spectrum between the duplication and deletion of 22q11.2. MLPA was a highly cost-effective, sensitive and preferred method for patients with 22q11.2 deletion or duplication. Our results also firstly reported that all three patients who simultaneously exhibited palatal anomalies and cognitive disorder, without other phenotypes, have Top3b duplication, which strongly suggested thatTop3b may be a pathogenic gene for these patients. Further, the findings showed that patients with palatal anomalies and congenital heart disease or immune deficiency, with or without other uncommon phenotypes, exhibited heterogeneity in CNVs, including 4q34.1-qter, 6q25.3, 4q23, Xp11.4, 13q21.1, 17q23.2, 7p21.3, 2p11.2, 11q24.3 and 16q23.3, and some possible pathogenic genes, including BCOR, PRR20A, TBX2, SMYD1, KLKB1 and TULP4 have been suggested. For these patients, aCGH, whole genomic sequencing,combined with references and phenomics database to find pathogenic gene,may be choices of priority. Taking these findings together, we offered an alternative method for diagnosis of Chinese VCFS patients based on this phenotypic strategy.
Article ID 0040 Published: 27 April 2019 RESEARCH NOTE
The Hardy–Weinberg equilibrium (HWE) model states that allele and genotype frequencies in a population will remain constant for generations in the absence of evolutionary effects. A goodness-of-fit test can be used to test if a population is significantly different from the expectations of HWE. Pearson statistics are commonly used in goodness-of-fit tests for testing the HWE. In this paper, a simulation study is carried out to evaluate the performance of power divergence statistics under different sample sizes, effect sizes and minor allele frequencies. A real genotype dataset is also analysed to compare the results of several power divergence test statistics.
Article ID 0039 Published: 26 April 2019 REVIEW ARTICLE
The process of development of quantitative trait locus (QTL) involves interactions between many factors, both environmental and genetic, in which many genes interact often in no additive pathways together and with environment. Integration of the mathematical, statistical and biological aspects of these subjects has made important and interesting results. In this review, mathematical methods offered to study the QTL × environment interactions. The topic is circumscribed, going from basic selection equations to models of evolution of QTLs. Discrete and continuous time mathematical models and subsequently, QTL modelling were introduced with and without environmental interactions. The mathematical models derived here showed that the gradients of mean fitness which have revealed in studies by many researchers had a basic role in mathematical genetics, evolutionary aspects of biometrical genetics and QTL analysis. QTL × environment interactions were studied mathematically including fitness components too. It was revealed that QTL × environment interactions in fitness could generate a balancing selection. Also, QTL analysis could be used to calculate the geometry of the phenotype landscape. In this paper, models applied in biometrical genetics corresponds to QTL analysis and matched with results from other researchers. The originality of this synthesis is the evolutionary modelling of QTL × environment interactions which can be used to investigate the extinction or stability of a population. Also to emphasize that although some scientific subjects like Brownian motion, quantum mechanics, general relativity, differential geometry, and evolutionarybiometrical genetics were apparently different subjects, but the mathematical models were the backbone of these branches of science. This implies that such matters in nature have probably common and elegant basis. The perspective of the subject of this paper in future will be a new and interesting branch of interdisciplinary science.
Article ID 0037 Published: 16 April 2019 RESEARCH ARTICLE
Evaluation of sequence variations in the internal transcribed spacer (ITS) region of 19 accessions, comprising of 11 accessions of Chenopodium quinoa, eight accessions of Chenopodium album and 165 retrieved sequences of different species of Chenopodium belonging to subfamily Chenopodioideae revealed a higher intraspecific genetic diversity in Himalayan C. album than that in C. quinoa. ITS and amplified fragment-length profiles of the accessions suggest the existence of accessions of Himalayan C. album as heteromorphs of the same species rather than a heterogenous assemblage of taxa. While the evolutionary relationship reconstructed from variations in 184 sequences of ITS region from species belonging to Chenopodiaceae, Amaranthaceae, Polygonaceae and Nelumbonaceae established a paraphyletic evolution of family Chenopodiaceae, it also revealed a monophyletic evolution of Chenopodieae I. The reconstruction also established five independent lineages of the subfamily Chenopodioideae with C. album as a sister clade of C. quinoa within the tribe Chenopodieae I. The results also indicate a much younger age for Himalayan chenopods (C. album) than the reported crown age of Chenopodieae I.
Article ID 0038 Published: 16 April 2019 RESEARCH NOTE
Stanniocalcin-1 (STC1) is secreted by the variety of tissues having a major role in the regulation of calcium ions in the involuting mammary gland. The present work aims to sequence and structural characterization as well as expression profiling of STC1 gene in buffalo. Polymorphism identified in the 3-untranslated region (UTR) was analysed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) genotyping in riverine and swamp buffaloes. Expression profiling of STC1 was performed in different lactation stages of mammary gland and peripheral blood mononuclear cells to study the impact of 3'-UTR polymorphism on its expression. Different polymorphic sites were detected in the entire coding and noncoding regions of riverine and swamp buffaloes, including two INDELs. An identified polymorphic nucleotide locus A324G, having target sites for two miRNAs, namely bta-miR-2382 and bta-miR-1343, reported in cattle, was genotyped by PCR-RFLP to reveal variable allelic distribution among swamp and riverine buffaloes. Gene expression profiling across buffalo mammary tissues representing different lactation stages showed maximum expression of the STC1 gene in the involuting mammary gland. Ruminants’ specific genetic variation has been observed in STC1 and its implication in buffalo mammary gland involution as well as coregulation of gene expression throughmiRNA binding in the 3'-UTR is suggested.
Article ID 0036 Published: 11 April 2019 RESEARCH NOTE
The Chinese softshell turtle exhibits ZZ/ZW sex determination. To identify the sex of embryos, juvenile and adult individuals, we designed two pairs of polymerase chain reaction primers, SB1-196, which amplifies a fragment of 196 bp in the female and the other, CK1-482, which amplifies the 482-bp fragment in both the sexes. It is validated in 24 adult turtles of known sex, sampled from three different locations. This one-step sexing technique is rapid and easy to perform and is reported for the first time.
Article ID 0035 Published: 8 April 2019 RESEARCH NOTE
Noncoding somatic mutations have been demonstrated to play important role in tumourigenesis. Here we show that there exists an acute myeloid leukaemia associated noncoding somatic mutation at 3′ terminal of conserved HOXA cluster. The mutation was identified in the bone marrow blasts but not peripheral blood mononuclear cells or buccal cells of two M3 (acute promyelocytic leukaemia, APL) type patients from 45 acute myeloid leukaemia patients. The mutation also existed in a pair of twins one of them developed acute myeloid leukaemia M4 (acute myelomonocytic leukaemia) type. The mutation resides in about 2-kb downstream of HOXA1 gene where a functional retinoic acid response element is located and also bound by histone demethylase KDM3B. Reporter assay showed that the mutation results in the upregulation of transcriptional activity and unresponsiveness to retinoic acid receptor. To sum up, we identified a new acute myeloid leukaemia associated noncoding somatic mutation.
Article ID 0034 Published: 8 April 2019 RESEARCH ARTICLE
AZUBEL RAMíREZ-VELAZCO THANIA ALEJANDRA AGUAYO-OROZCO LUIS FIGUERA HORACIO RIVERA LUIS JAVE-SUÁREZ ADRIANA AGUILAR-LEMARROY LUIS A. TORRES-REYES CARLOS CÓRDOVA-FLETES PATRICIO BARROS-NÚÑEZ SATURNINO DELGADILLO-PÉREZ INGRID PATRICIA DÁVALOS-RODRíGUEZ JOSÉ ELÍAS GARCíA-ORTIZ MARÍA G. DOMÍNGUEZ
Williams–Beuren syndrome (WBS) has a prevalence of 1/7500–20000 live births and results principally from a de novo deletion in 7q11.23 with a length of 1.5 Mb or 1.8 Mb. This study aimed to determine the frequency of 7q11.23 deletion, size of the segment lost, and involved genes in 47 patients with a clinical diagnosis of WBS and analysed by fluorescence in situ hybridization (FISH); among them, 31 had the expected deletion. Micro-array comparative genomic hybridization (aCGH) confirmed the loss in all 18 positive-patients tested: 14 patients had a 1.5 Mb deletion with the same breakpoints at 7q11.23 (hg19: 72726578–74139390) and comprising 24 coding genes from TRIM50 to GTF2I. Four patients showed an atypical deletion: two had a 1.6Mb loss encompassing 27 coding genes, from NSUN5 to GTF2IRD2; another had a 1.7 Mb deletion involving 27 coding genes, from POM121 to GTF2I; the remaining patient presented a deletion of 1.2 Mb that included 21 coding genes from POM121 to LIMK1. aCGH confirmed the lack of deletion in 5/16 negative-patients by FISH. All 47 patients had the characteristic facial phenotype of WBS and 45 of 47 had the typical behavioural and developmental abnormalities. Our observations further confirm that patients with a classical deletion present a typical WBS phenotype, whereas those with a high (criteria of the American Association of Pediatrics, APP) clinical scorebut lacking the expected deletion may harbour an ELN point mutation. Overall, the concomitant CNVs appeared to be incidental findings.
Article ID 0033 Published: 23 March 2019 REVIEW ARTICLE
The Juglans plants are economically important as they provide nuts, wood and garden trees. They also play an important ecological role by supplying food for wild insects and animals. The decoding of genome sequences has fundamental values for understanding the evolution of Juglans plants and molecules, and is also a prerequisite for molecular breeding. During the last three years, the rapid development of sequencing technology has made walnut research into the genome era. Here, we reviewed the progress of genome sequencing of six Juglans species, the resequencing of four Juglans populations as well as the genome sequencing of the closely related species Pterocarya stenoptera. The analysis of the Juglans regia genome uncovers a whole genome duplication (WGD) event. Based on the molecular dating of the divergence time of six Juglans species, we proposed this WGD event was associated with Cretaceous–Palaeogene (K-Pg) boundary occurred ∼65 million years ago. Genomic sequences also provide clear details for understanding the evolution and development of GGT and PPO genes involved in fruit development. The decoding of these genomes has made it easier for us to understand and enhance the use of walnuts. We expect that the functional genomics research of walnut will also develop rapidly in the near future.
Article ID 0032 Published: 13 March 2019 RESEARCH ARTICLE
Chronic periodontitis (CP) is the common form of inflammatory oral disease. Matrix metalloproteinases (MMPs) play a pivotal role in the progression of CP by degrading gingival tissue and its remodelling. Here, we conducted a case–control study to investigate a possible association of single-nucleotide polymorphism of MMP genes and their interaction with CP in the Indian population. A total of 357 DNA samples of venous blood was isolated, of which 157 were identified as CP patients and 200 were healthy individuals. Genotyping of six MMP genes (MMP1, MMP3, MMP7, MMP8, MMP12 and MMP13) was done using polymerase chain reaction following Sanger’s method of sequencing. Statistical analyses were performed by SPSS v16.0, R package (SNPassoc). Gene–gene interactions were evaluated by MDR 3.0.2. The frequency of 6A allele of MMP3 −11715A-6A gene polymorphisms (36%) and G allele of MMP8 +17G-C gene polymorphisms (34%) were higher in the CP population compared with the healthy population (19% and 24%, respectively). A significant association of T allele of MMP8 −799C-T gene promoter polymorphism was found with CP (OR = 2.95, 95%CI = 2.16 − 4.04, P < 0.0001). Genotypic frequency of MMP12 −82A-G polymorphism is associated with CP risk while its allelic distribution is not (OR = 1.32, 95%CI = 0.93 − 1.88, P = 0.129). Gene–gene interactions show the best cross validation consistency model, i.e. MMP1 −519A-G X MMP7 −181A-G X MMP8 −799C-T polymorphismswith a value of 9/10. This gene–gene interaction shows that the significant association of MMP8 −799C-T polymorphism with CP increased susceptibility. Allelic distribution of MMP8+17G-C and MMP3−11715A-6A polymorphisms revealed their protective role towards decreased risk of CP. MMP1 −519A-G and MMP7 −181A-G polymorphisms show combinatorial synergistic effect on CP risk.
Article ID 0031 Published: 9 March 2019 RESEARCH ARTICLE
Calmodulin-binding transcription activators (CAMTAs) are a family of transcription factors that play an important role in plants’ response to the various biotic and abiotic stresses. The common bean (Phaseolus vulgaris L.) is one of the most important crops in the world and plays a pivotal role in sustainable agriculture. To date, the composition of CAMTA genes in genomes of Phaseolus species and their role in resistance to drought stress are not known. In this study, five PhavuCAMTA genes were characterized in common bean genome through bioinformatics analysis, the morphological and biochemical response of 23 Ph.vulgaris genotypes to different levels of drought stress were evaluated and the expression patterns of PhCAMTA1 in the leaf tissues of sensitive and tolerant genotypes were analysed. Gene structure, protein domain organization and phylogenetic analyses showed that the CAMTAs of Phaseolus were structurally similar and clustered into three groups as other plant CAMTAs. Genotypes showeda differential response to drought stress. Thus, the plant height, number of nodes and flower, total chlorophyll and total protein content, and activity of antioxidant enzymes (ascorbate peroxidase and catalase) in plants significantly influenced by genotype and drought stress interaction. Moreover, the resistant and susceptible genotypes were identified according to three-dimensional plots and the expression patterns of PhavuCAMTA1 gene were studied using real-time quantitative polymerase chain reaction. The results of the present study serve as the basis for future functional studies on the Phaseolus CAMTA family.
Article ID 0028 Published: 9 March 2019 RESEARCH ARTICLE
To better understand the role of integrin subunit alpha 9 (ITGA9) gene polymorphism in epithelial ovarian cancer (EOC), we investigated the distribution of ITGA9 gene polymorphisms (rs2212020 and rs189897) and revealed whether these polymorphisms were associated with a curative effect in EOC. It was found that rs2212020 and rs189897 were correlated significantly with EOC incidence. The frequency of the C allele of rs2212020 was significantly higher in EOC patients than in the control group (P = 0.009, χ2 = 6.857). The population with the C allele of rs2212020 had a higher EOC risk than the population with the T allele (hazard ratio = 1.97, 95.0% CI = 1.178−3.299). Further, our results showed that the CC genotype was a risk factor for EOC. Regarding the association between ITGA9 and the sensitivity to platinum-based chemotherapy in EOC, there were no statistically significant differences in the frequencies of the rs189897 and rs2212020 polymorphisms between the chemosensitivegroup and the control group. In multivariate analysis, the patients with the TT genotype of rs189897 had longer progression free survival (PFS) than the patients without this genotype (P = 0.010, OR = 2.491). The AT genotype of rs189897 was a risk factor for PFS in EOC. These findings suggested that rs189897 and rs2212020 could play important roles in EOC diagnosis and prognosis.
Article ID 0029 Published: 9 March 2019 REVIEW ARTICLE
Nonalcoholic fatty liver disease (NAFLD) is characterized by the accumulation of fat in the liver without any history of chronic alcohol consumption. It encompasses a wide spectrum of diseases that range from simple steatosis to nonalcoholicsteatohepatitis. NAFLD is strongly associated with obesity, insulin resistance / type-2 diabetes mellitus and the metabolic syndrome. NAFLD is a complex disorder; environmental and genetic factors interact with NAFLD manifestation and determine its progression. In this review, an attempt was made to provide current information on the genetic variants of NAFLD in Asian populations. Literature search was performed by using PubMed, Medline and Google Scholar database. Candidate gene, validation and genomewide association studies (GWASs) were included in this review. A total of 41 studies fulfilled inclusion criteria of which 12 candidate gene studies exclusively focussed on the PNPLA3 gene and 17 other studies on other important candidate genes such as NCANCILP2, PPARG,AGTR1, FABP1, APOC3 etc. reported significant association with NAFLD. Eight validation studies identified associations of variants on PNPLA3, LYPLAL1, TM6SF2, ADIPOR2, STAT3, GCKR, SAMM50 etc. with NAFLD. Thus, so far, four GWASs have been conducted in Asian population that reported PNPLA3, SAMM50, PARVB and GATAD2A genes which were significantly associated with NAFLD. Findings indicate that PNPLA3, APOC3, PPARG, NCAN and GCKR genes emerge out to be the important biological markers associated with NAFLD.
Article ID 0027 Published: 9 March 2019 RESEARCH ARTICLE
Creation of genetic variability and development of varieties having higher yield potential depends on information about nature of gene action. The present investigation was undertaken to decipher the nature of gene action and allied genetic parameters involved in the inheritance of yield and yield-related component traits in opium poppy (Papaver somniferum L.). The biparental inbreeding progenies derived from four segregating base populations of crosses NB-1Kr40-3/3×NB-1Kr30+0.2-2/1, NB-5Kr40-7/2×58/1, NB-1Kr30+0.2-2/1×58/1 and NB-Kr40-3/3×NB-5Kr40-7/2 of opium poppy were analysed to study the gene actions involved in the inheritance of yield and component traits. Additive component of variance played a predominant role in North Carolina design (NCD)-I, while both additive and dominance genetic components were found important in NCD-III design. The presence of additive as well as nonadditive components of variance suggested that one or two generations of intermating in further generations followed by selection may lead to development of novel genotypes.
Article ID 0030 Published: 9 March 2019 RESEARCH ARTICLE
Long noncoding RNAs (lncRNAs) are important regulators of biological processes, and regulate genomic imprinting in cis and/or trans to induce monoallelic expression with parent-origin-specific pattern. DLK1–DIO3 domain is one of the largest imprinted clusters in mammals, and maternally expressed noncoding RNAs of this region is related to the pluripotency of the embryonic stem cells. Previously, we sequenced the cDNA of two maternally expressed noncoding RNAs, MEG8 and MEG9, and mapped a lncRNA (LINC24061) between the two genes in the cattle DLK1–DIO3 domain on chromosome 21. In this study, we identified LINC24065, a novel long intergenic noncoding RNA (lincRNA), which was also located between MEG8 and MEG9. We identified four variants of LINC24065 (LINC24065-v1, LINC24065-v2, LINC24065-v3 and LINC24065-v4) that were a result of alternative splicing from 18 exons. LINC24065-v1 and LINC24065-v2 showed tissue-specific expression patterns in adultbovine tissues, and LINC24065-v3 and LINC24065-v4 were detected in all eight analysed tissues (heart, liver, spleen, lung, kidney, skeletal muscle, adipose and brain). Using single-nucleotide polymorphism (SNP)-based method, LINC24065 was identified to have monoallelic expression in adult tissues, suggesting that it is imprinted in cows. These results provide a foundation for further investigation about whether LINC24065 plays a role in regulating imprinting of the DLK1–DIO3 domain.
Article ID 0026 Published: 4 March 2019 RESEARCH NOTE
Yellow catfish (Pelteobagrus fulvidraco) is an important aquaculture species which is widely distributed, especially in the Yangtze River of China. To facilitate its conservation and stock improvement, 273 yellow catfish samples from the Yangtze River (seven populations) and Baiyangdian (BYD) Lake were genotyped using eight microsatellites in combination with capillary electrophoresis. A total of 250 alleles were detected at eight loci in eight populations showing high allelic (Na= 31.25 ± 7.38) and genetic diversity (He = 0.888–0.944). Both FST and clustering analyses revealed the presence of subtle population differences between the species of Yangtze River and the BYD lake. Mantel tests suggest that genetic distance is significantly correlated with geographical distance (R = 0.9294 and P < 0.05). The results of genetic diversity and population structure will help in conservation and improvement of yellow catfish.
Article ID 0025 Published: 4 March 2019 RESEARCH ARTICLE
The expression of four genes involved in milk regulation and production in bovine milk and tissue samples profiled using quantitative PCR to identify differential gene expression. Our goal focussed on the differential mRNA expression of milk genes (KCN, PRL, BLG and PIT-1) in milk samples and different tissues from four different breeds of ecologically adapted and geographically separated cattle species. The mRNA expression identified the four milk genes understudiedmost upregulated in mammary gland and milk samples as compared with other tissues. The expression of PIT-1 gene in the brain identified to have influenced the expression of PRL and K-CN in the mammary and milk samples. Among the four genes, PRL had the highest mRNA expression (144.19-fold change) in Holstein followed by K-CN with 100.89-fold change, while the smallest relative expression for most genes in this study are in the range from 0.79 to 7.35-fold difference. White Fulani cattle was identified to have a higher expression for K-CN, PRL and BLG compared with Angus and Ndama cattle, while Holstein cattle is on top of the list on the basis of the gene expression and gene regulation for all the four genes in this study. Also, White Fulani and Holstein are in the same cluster based on their mRNA expression for milk genes. Our data showed the first evidence of the molecular identification of indigenous White Fulani cattle ofhaving potential for higher milk production.
Article ID 0000 Published: March 2019 Editorial
Article ID 0022 Published: 28 February 2019 RESEARCH NOTE
A parental diagnosis was performed for an unborn foetus of a healthy couple, who was due for ultrasound detection of multiple malformations and abnormal amniotic fluid karyotypes. For an accurate diagnosis, routine G-banding analysis and nextgeneration sequencing (NGS)were carried out. Finally, conventional cytogenetic analysis suggested that the foetus had a karyotype of47,XX,+mar/46,XN,meanwhileNGSalso revealed a partial tetrasomy of 27.84Mbfrom4q26-q31.21 (117,385,735–145,225,759), and G-banding analysis excluded the couple to have carried the 4q26-q31.21 duplication. We have identified a de novo mosaic small supernumerary marker chromosomes (sSMC) derived from 4q26-q31.21 in a foetus with hemivertebra, polydactyly, abnormal ears, and heart and ventricular septal defect.
Article ID 0023 Published: 28 February 2019 REVIEW ARTICLE
Genes encoding structurally independent phosphotriesterases (PTEs) are identified in soil bacteria. These pte genes, often identified on mobilizable and self-transmissible plasmids are organized as mobile genetic elements. Their dissemination through lateral gene transfer is evident due to the detection of identical organophosphate degradation genes among soil bacteria with little orno taxonomic relationship. Convergent evolution of PTEs provided selective advantages to the bacterial strain as they convert toxic phosphotriesters (PTs) into a source of phosphate. The residues of organophosphate (OP) compounds that accumulate in a soil are proposed to contribute to the evolution of PTEs through substrate-assisted gain-of-function. This review provides comprehensiveinformation on lateral transfer of pte genes and critically examines proposed hypotheses on their evolution in the light of the short half-life of OPs in the environment. The review also proposes alternate factors that have possibly contributed to the evolution and lateral mobility of PTEs by taking into account their biology and analyses of pte genes in genomic and metagenomic databases.
Article ID 0024 Published: 28 February 2019 RESEARCH ARTICLE
Understanding the genetic basis of biochemical traits of different cauliflower genotypes is essential for planning the effective breeding strategies in genetic improvement. To determine the mode of inheritance of dry matter content and biochemical traits, we made crosses using four genotypes of cauliflower, and obtained F1, F2, BC1 and BC2 populations. The six generations obtained were replicated thrice and evaluated in a randomized block design. The generation mean analysis of data showed the presence of duplicate epistasis in dry matter content which suggested the adoption of reciprocal recurrent selection and biparental mating for the improvement of the trait. However, in case of vitamin C, complementary type of epistasis was reported in three crosses, which indicated the exploitation of heterosis breeding of enhancing vitamin C. It can be concluded that the role of gene action was in general more complex for the traits studied. The nature and magnitude of gene effects varies character-wise as well as cross-wise. Hence, for the improvement of dry matter content and biochemical traits in a particular cross, a specific breeding strategy has to be implemented.
Article ID 0021 Published: 28 February 2019 RESEARCH NOTE
This study evaluates a family with two siblings having severe growth retardation and facial dysmorphism, born to consanguineous normal healthy parents. Affymetrix CytoScan 750K microarray showed a 34-Mb pericentric homozygous region on chromosome 6 for both siblings. CUL7 was one of the 141 genes present in this region. Sanger sequencing of CUL7 gene detected a 2-bp novel deletion in the 15th exon (c.2943_2944delCT of the cDNA). This deletion leads to a frameshift and a premature termination signal much upstream of the wild-type termination signal, leading to a nonsense mediated decay of the mRNA. CUL7 protein plays an important role in formation of 3M complex, ubiquitination, microtubule dynamics and cell cycle regulation. Mutations in CUL7 gene is known to cause a rare 3M syndrome. Information about the novel mutation has been accepted in the ClinVar database with rs1064792895.
Article ID 0016 Published: 26 February 2019 RESEARCH NOTE
Insulin-like growth factor receptor (IGF-1R) deficiency is a rare form of short stature, and is difficult to clinically diagnose. Targeted next-generation sequencing (NGS) allows for the rapid and inexpensive assessment of short stature. We identified mutations in the pedigree of a Chinese boy with severe short stature using targeted NGS; we then assessed the clinical characteristicsand evaluated the efficacy of growth hormone therapy. NGS analysis revealed a novel heterozygous missense mutation in exon3 (c.926C>T, p.S309L) of the type-I IGF-1R gene in the proband, which was inherited from the mother. The proband, mother and grandfather suffered from severe growth failure. After recombinant human growth hormone therapy, the patient’s growth rate increased. The novel missensemutation in IGF-1R (c.926C > T, p.S309L) is associated with severe short stature in Chinese individuals. Targeted NGS may enable efficient diagnosis and genetic consultation of children with short stature.
Article ID 0019 Published: 26 February 2019 RESEARCH ARTICLE
Stem gall (Protomyces macrosporus Unger), a serious disease that affects leaves, petioles, stems and fruits of coriander (Coriandrum sativum L.) causing heavy loss in yield. Genetic improvement of coriander for stem gall disease is indispensable. Coriander cultivars of stem gall resistance (ACr-1) and susceptible (CS-6) leaf samples were utilized and transcriptome sequenced using Illumina NextSeq500 platform. After trimming low-quality reads and adapter sequences, a total of 49,163,108 and 43,746,120 high-quality reads were retained and further assembly resulted validated transcripts of 59,933 and 56,861. We have predicted 52,506 and 48,858 coding sequences (CDS) of which 50,506 and 46,945 were annotated using NCBInr database. Gene ontology analysis annotated 19,099 and 17,625 terms; pathway analysis obtained 24 different functional pathway categories; signal transduction, transport, catabolism, translation and carbohydrate metabolism pathways etc. were dominated. Differentially expressed genes analysis predicted 13,123 CDS commonly expressed of which 431 and 400 genes were significantly upregulated and downregulated, respectively, in which Rgenes, stress inducible transcription factors such as ERF, NAC, bZIP, MYB, DREB and WRKY and antifungal related genes were predicted. The real-time PCR analysis of HSP20 gene expression in resistance showed upregulation by 10-fold over susceptible sample and 18s used as a housekeeping gene for normalization. The present results provide an insights into various aspects underlying the development of resistance to stem gall in coriander.
Article ID 0020 Published: 26 February 2019 RESEARCH ARTICLE
Elevated C-reactive protein (CRP) serves as an independent biomarker for acute and chronic inflammation, and is also associated with metabolic diseases. Genomewide loci regulating CRP level in Indian population, a high-risk group for metabolic illness, is unexplored. Therefore, we aimed to discover common polymorphisms associated with plasma CRP level in 4493 Indians of Indo-European origin using genomewide association study. Genomewide strong associations of two known intronic variants in hepatocyte nuclear factor-1 α gene (HNF1A)were identified among Indian subjects. We also detected prior associations of several variants in/near metabolic and inflammatory process genes: APOC1, LEPR, CRP, HNF4A, IL6R and APOE with modest associations. This study confirms that Indians from Indo-European origin display similar core universal genetic factors for CRP levels.
Article ID 0015 Published: 26 February 2019 RESEARCH ARTICLE
Antheraea assamensis Helfer, popularly known as Muga silkworm, the golden silk producer of northeast India is economically important and unique among the Saturniid silkworms. In this study, the genetic diversity and phylogeny of semidomesticated and wild morphs of Muga silkwormcollected from different geographical locations of northeast India were investigated based on the sequences of five mitochondrial loci, i.e. 12S rRNA, 16S rRNA, CoxI, Cytb and CR. All the five mitochondrial loci showed a strong bias towards higher ‘A’ and ‘T’ contents. Transitional substitutions were found to be more than the transversional substitutions. The rate of nucleotide substitution and average genetic divergence were found to be highest in CR sequences and lowest in 12S rRNA gene sequences among the morphs of Muga silkworm. The morphs collected from same geographical area had identical 12S rRNA, 16S rRNA, CoxI and Cytb gene sequences. Moreover, the 12S rRNA and 16S rRNA gene sequences of somesemi-domesticated and wild morphs collected from different geographical locations were also found to be similar. In the phylogenetic trees generated based on themitochondrial loci, mixing of semi-domesticated and wild morphs was observed as they shared the same group. The information generated in this study will help in formulating strategies to conserve the natural biodiversity present among these unique silkworms in northeast India. In addition, this will be useful in identifying diverse morphs of Muga silkworm, which will help in effective breeding programmes to improve its productivity.
Article ID 0017 Published: 26 February 2019 RESEARCH NOTE
The medically important Indian red scorpion, Hottentotta tamulus, is one of the most poisonous scorpions of Indian subcontinent. We studied the haplotype diversity in eight populations of H. tamulus based on mitochondrial cytochrome oxidase subunit I (COI) partial gene sequence. Analyses revealed 22 haplotypes with a haplotype diversity of 0.941 and nucleotide diversity of 0.023. For the first two codon positions both transition and transversion types of substitutions were equally likely and the test for neutrality was not rejected. However, codon substitution pattern indicated that the gene has experienced purifying selection. Model-based clustering method indicated that the eight populations form three groups that correspond to high, moderate and low rainfall areas, indicating that there is biogeographical separation of haplotypes. Populations from three groups formed distinct clades in maximum likelihood analysis and median joining genetic network and were statistically supported by low within group and high among group variation in analyses of molecular variance. We provide the first account of haplotype diversity in Indian red scorpions and their biogeographical separation.
Article ID 0018 Published: 26 February 2019 RESEARCH ARTICLE
In this study, we show that NAC-like transcription factor (TF) has 90% sequence similarity with cDNA of the OsNac5 gene present in the NCBI database. Phylogenetic analysis of the NAC gene family was performed with inclusion of the highly diverse C-terminal sequences. We report that this gene is also found to be orthologous to Glycine max NAC8, NAC2, Triticum aestivum NAC6 and paralogous to OsNAC6. mRNA was purified from five recombinant inbred lines (RILs) and parents of rice at three different stages of grain filling under aerobic conditions, with grain protein content (GPC) spanning from 4 to 14%. TheNAC-like TF encoding a protein was found to be upregulated at the S2 stage in the leaf (3.9-fold) and panicle (1.84-fold) of parent HPR14 and in five RILs (1.9 to 4.51-fold in leaves and 0.47 to 3.2-fold in panicles). Expression analysis of the NAC-like TF encoding a protein for the rice gene was found to be upregulated at the S2 stage in the leaf and panicle of parental line HPR14 and RILs with high protein content.
Article ID 0011 Published: 21 February 2019 RESEARCH NOTE
Munida isos is a deep sea squat lobster species that is widely distributed across the New Zealand and east Australian region, and is often associated with deep sea vulnerable marine ecosystems. To investigate its population genetic structure and patterns of regional connectivity, microsatellite loci were developed for M. isos from two genomic libraries using the Illumina HiSeq 2500 sequencing platform. Twenty-six loci amplified consistently in M. isos from the Tasman Sea, among which 20 were polymorphic and selectively neutral. Evidence of null alleles was observed at eight loci. Most loci exhibited moderate to high levels of polymorphism, with an average polymorphic information content value of 0.482. The mean number of alleles per locus was 7.45, with a mean expectedheterozygosity of 0.520. Thirteen loci exhibited significant deviation from Hardy–Weinberg equilibrium, while only one locus pair was in linkage disequilibrium after false discovery rate correction for multiple testing (P < 0.05). Cross-species amplification tests revealed that the transferability of 14 loci (70%) was positive for the two congeners M. endeavourae and M. gracilis. The accessibility to new polymorphic microsatellite loci will facilitate population genetic studies and aid in developing conservation and management strategies for vulnerable marine ecosystems.
Article ID 0010 Published: 21 February 2019 RESEARCH NOTE
Microduplications of the X chromosome are a rare cause of X-linked intellectual disability (XLID), a clinically and genetically heterogeneous spectrum of disorders. In the present study, a 950-kb Xp22.12 microduplication including the RPS6KA3 gene was detected in affected members of a family, including the proband (male), his mother and one maternal uncle. Four female carriers had major depression and one of them also had mild intellectual disability. The present and previous cases with overlapping microduplications suggest that Xp22.12 microduplications can be included in the neuropsychiatric copy number variations.
Article ID 0013 Published: 21 February 2019 RESEARCH ARTICLE
Homeobox proteins (HOXs) comprise a large family in eukaryotes and share a highly conserved DNA-binding motif, the homeodomain (HD). HOXs play an important role in the regulation of plant growth, development and stress response. However, systematic analysis and expression profiling of these genes have not been reported in Malus domestica. In this study, a total of 207 HOXs of M. domestica (MdHOXs) were identified and classified into 11 distinct subfamilies, and an unclassified group according to their functional domains. The MdHOXs were localized in all 17 chromosomes with various densities and a majority of them tended to form gene clusters. Analysis of the Ka/Ks ratios suggested that the duplicated genes of MdHOXs mainly underwent purifying selection with restrictive functional divergence after the duplication events. The expression of MdHOXs has organ specific characteristics and were divided into seven different groups. Stress-related cis-acting elements were prevalent in the upstream sequence of MdHOXs by systematic analysis. To explore the response to abiotic stress, eight MdHOXs were randomly selected to investigate their expression using quantitative real-time polymerase chain reaction. Transcription levels of MdHOXs were upregulated in the leaves and roots under cold, osmotic, high salinity or exogenous ABA treatments, which suggested that they may take part in the plant response to abiotic stress. These results provided basic information of HOXs in apple and will further contribute to the functional research of MdHOXs, especially the response to abiotic stress.
Article ID 0012 Published: 21 February 2019 RESEARCH ARTICLE
The deep water penaeoid shrimp is an important commercial crustacean resource along the Indian coast. The molecular and morphological information of this group from the Indian coast is scarcely known. In this study, we investigated the identification and phylogenetic relationships of the deep water penaeoid shrimps using three mitochondrial (cytochrome oxidase subunit I (COI), cytochrome b, 16S rRNA) genes, which were compared with 54 morphological characters and further used to evaluate character evolution. Our study revealed remarkable molecular divergence (3.3–33.0%) in nine species from three genera of Solenoceridae, four species from three genera of Penaeidae and one species from Aristeidae using COI. Phylogenetic analysis using maximum likelihood and Bayesian approaches revealed that all species from these families are monophyletic. The present analysis revealed the existence of subgroups in the genus Solenocera suggesting the slow reduction of postrostral carina which corresponds to the increase in distributional depth during the evolutionary process which further indicates the origin of the genus in the continental shelf and extending up to the continental slope. In addition, we generated the DNA barcode database involving these species which can help further to investigate the detailed evolution and biogeography of these valuable crustacean resources.
Article ID 0009 Published: 21 February 2019 RESOURCES
Ionizing radiations (IRs) are widespread damaging stresses to plant growth and development. However, the regulatory networks underlying the mechanisms of responses to IRs remains poorly understood. Here, a set of publicly available transcriptomic data (conducted by Van Hoeck et al. 2015a), in which Lemna minor plants were exposed to a series of doses of gamma, beta and uranium treatments was used to perform gene coexpression network analysis. Overall, the genes involved in DNA synthesis and chromatin structure, light signalling, photosynthesis, and carbohydrate metabolism were commonly responsive to gamma, beta and uranium treatments. Genes related to anthocyanin accumulation and trichome differentiation were specifically downregulated, andgenes related to nitrogen and phosphate nutrition, cell vesicle transport, mitochondrial electron transport and ATP synthesis were specifically upregulated in response to uranium treatment. While genes involved in DNA damage and repair, RNA processing and RNA binding were specifically downregulated and genes involved in calcium signalling, redox and degradation of carbohydrate metabolism were specifically upregulated responding to gamma radiation. These findings revealed both dose-dependent and typespecific networks responding to different IRs in L. minor, and can be served as a useful resource to better understand the mechanisms of responses to different IRs in other plants.
Article ID 0014 Published: 21 February 2019 RESEARCH ARTICLE
Cupressus gigantea and C. torulosa are ecologically and economically important endemic species of the conifer family Cupressaceae on the Qinghai-Tibetan plateau. C. gigantea was previously classified as a subspecies of C. torulosa because of their similar morphological characteristics and close distribution. In this study, 401 individuals were sampled from 16 populations of the two Cupressus species. The specimens were genotyped using 10 polymorphic microsatellite loci through fluorescence polymerase chain reaction (PCR). The genetic diversity of C. gigantea and C. torulosa populations was generally low, with the highest genetic diversity detected in the population LLS of C. gigantea. Distance-based phylogenetic and principal co-ordinates analyses indicated a clear genetic structures for the 16 populations of the two Cupressus species. Moreover, Mantel test results showed indistinctive correlations between population-pairwise Fst values and geographic distances, as well as between genetic distances and geographic distances in C. gigantea and C. torulosa, respectively. AMOVA suggested that genetic variation mostly resided within populations. Sixteen naturalpopulations were evidently clustered into two major groups in the constructed neighbour-joining tree. The results demonstrated that C. gigantea and C. torulosa are different Cupressus species. The genetic information provided important theoretical references for conservation and management of the two endangered Cupressus species.
Article ID 0008 Published: 13 February 2019 RESEARCH ARTICLE
Insulin is a commonly used measure of pancreatic β-cell function but exhibits a short half-life in the human body. During biosynthesis, insulin release is accompanied by C-peptide at an equimolar concentration which has a much higher plasma half-life and is therefore projected as a precise measure of β-cell activity than insulin. Despite this, genetic studies of metabolic traits haveneglected the regulatory potential of C-peptide for therapeutic intervention of type-2 diabetes. The present study is aimed to search genomewide variants governing C-peptide levels in genetically diverse and high risk population for metabolic diseases—Indians. We performed whole genome genotyping in 877 healthy Indians of Indo-European origin followed by replication of variants with P ≤ 1 × 10−3 in an independent sample-set of 1829 Indians. Lead-associated signals were also tested in-silico in 773 Hispanics. To secure biological rationale for observed association, we further carried out DNA methylation quantitative trait loci analysis in 233 Indians and publicly available regulatory data was mined. We discovered novel lncRNA gene AC073333.8 with the strongest association with C-peptide levels in Indians that however missed genomewide significance. Also, noncoding genes, RP1-209A6.1 and RPS3AP5; protein gene regulators, ZNF831 and ETS2; and solute carrier protein gene SLC15A5 retained robust association with C-peptide after meta-analysis. Integration of methylation data revealed ETS2 and ZNF831 single-nucleotide polymorphisms as significant meth-QTLs in Indians. All genes showed reasonable expression in the human lung, signifying alternate important organs for C-peptide biology. Our findings mirror polygenic nature of C-peptide where multiple small-effect size variants in the regulatory genome principally govern the trait biology.
Article ID 0007 Published: 12 February 2019 RESEARCH NOTE
Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker. Thus, an attempt was made to use the gene as an advanced molecular marker of sexing of the yak to improve breeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. The test is further refined with qPCR validation by quantifying the DNA copy number of the Amelogenin gene in male and female. We observed a high level of sequence polymorphisms of AMELX and AMELY in yak considered as novel identification. These tests can be further extended into several other specialized fields includingforensics, meat production and processing, and quality control.
Article ID 0006 Published: 12 February 2019 RESEARCH ARTICLE
The aim of the present study was to evaluate the diagnostic yield of prenatal cytogeneticmicroarray (CMA) in structurally normal and abnormal foetuses and record the acceptance rate of CMA for prenatal diagnosis over a course of five year. In 128 structurally normal and abnormal foetuses, CMA was performed along with foetal karyotype, after exclusion of aneuploidy by quantitative fluorescence polymerase chain reaction. The microarray was able to detect the pathogenic variants in 5.5% cases; the diagnostic yield in structurally abnormal foetuses was 8.8% and 4.7% in foetuses with a high aneuploidy risk. Balanced and unbalanced translocations, and low level mosaicism were detected. Reanalysis of variants of uncertain significance identified pathogenic variant. The study shows higher diagnostic yield in structurally abnormal cases, the importance of foetal karyotype and reanalysis in microarray. The acceptance rate of prenatal CMA increased five-fold over a period of five year.
Article ID 0005 Published: 7 February 2019 RESEARCH NOTE
Gitelman syndrome is an autosomal recessive salt-wasting tubulopathy caused by mutations in the SLC12A3 gene. A female and a male sibling from two unrelated Greek-Cypriot families presenting with a severe salt-wasting tubulopathy dueto compound heterozygous mutations of a novel duplication and a previously reported missense mutation in the SLC12A gene are described. Sanger sequencing was used to identify possible mutations in the SLC12A3 gene. For the detection of duplications/conversions and deletions in the same gene, Multiplex ligation probe amplification (MLPA) analysis was performed. Direct sequencing and MLPA analysis of the SLC12A3 gene identified two compound heterozygous mutations in both unrelated probands. Both probands were identified to carry in compound heterozygosity the known p.Met581Lys and a novelheterozygous duplication of exons 9-14 (E9_E14dup). The diagnosis of Gitelman syndrome was made through clinical assessment, biochemical screening and genetic analysis. The identification of the novel SLC12A3 duplication seems to be characteristic of Greek-Cypriot patients and suggests a possible ancestral mutational event that has spread in Cyprus due to a possible founder effect. Testing for Gitelman syndrome probable variants can be performed before proceeding to a full gene sequencing dropping the diagnostic cost. In addition, this report adds to the mutational spectrum observed.
Article ID 0004 Published: 7 February 2019 RESEARCH NOTE
Dipentodon is a monotypic genus of Dipentodontaceae and the only species, Dipentodon sinicus, is scattered in southwest China as well as adjacent Myanmar, northeast India and northern Vietnam. This species was evaluated as vulnerable in ‘China Species Red List’. Here, we assembled and characterized the complete chloroplast (cp) genome of D. sinicus using Illumina sequencing data for the first time. The complete cp genome was 158,795 bp in length, consisting of a pair of inverted repeats of 26,587 bp, a large single-copy region of 87,233 bp and a small single-copy region of 18,388 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that D. sinicus is a member of Huerteales, consistent with its position in the latest classification of flowering plants (AGP IV).
Article ID 0003 Published: 31 January 2019 RESEARCH ARTICLE
Antitumour necrosis factor-alpha (TNF-α) therapy is used as a clinical intervention for rheumatoid arthritis (RA) but differences exist in response to the treatment which makes the candidature of the screening of TNF-α alteration(s) at genetic and expression levels an important agenda prior to treatment. This study aims to determine the associative role of TNF-α –308G/A polymorphism and differential expression of TNF-α in the pathogenesis of RA. A case–control study where a total of 126 RA patients were enrolled based on ACR-EULAR (2010) criteria, along with 160 community matched age and sex controls over a period of three years. The differential expression level of TNF-α mRNA and protein level was studied and TNF-α –308G/A polymorphism was screened by T-ARMS PCR assay. All statistical analysis was performed using SPSS software. mRNA expression level of TNF-α was upregulated in RA cases (avg. 15.85 ± 9.52 fold) compared to control. TNF-α protein level was found to be higher in RA cases (28.62±7.17 pg/mL) compared to control (23.14±6.91 pg/mL). TNF-α –308 variant GA genotype was higher in RA (46.03%) than in control (25%). The presence of TNF-α –308 variant A allele was associated with increased risk of RA susceptibility (odds ratio (OR) = 2.559 at 95% confidence interval (CI), P< 0.001) but not severity (OR = 1.617 at 95% CI, P = 0.571). The presence of –308 variant genotype was associated with a higher TNF-α mRNA and protein expression. The presence of TNF-α –308A allele is associated with increased risk of RA susceptibility and differential TNF-α expression, and has prognostic significance. Association of higher TNF-α pro-inflammatory cytokine levels with northeast Indian patients makes them suitable subjects for anti-TNF-α therapy.
Article ID 0002 Published: 31 January 2019 RESEARCH NOTE
Microsatellite markers from a fresh water yellow catfish, Pseudobagrus fulvidraco, were developed by whole-genome sequencing in the Ion S5 system. Of the 40 chosen sets of microsatellite markers, with tetra-repeat and penta-repeat motifs, from a total 19,743 sequence, only 13 markers were successfully applied in 78 individual fish sampled to detect genomic variability from four natural populations of Korea. On an average, the number of alleles per marker was 6.7. The observed heterozygosity varied from 0.048 to 0.810. Twelve microsatellite markers conformed to Hardy–Weinberg equilibrium and none exhibited significant linkage disequilibrium. In yellow catfish, genetic differentiation among four natural populations was further supported by FST (P < 0.05) and STRUCTURE analysis. The microsatellite markers identified could facilitate genetic diversity and population structure studies and thus aid in conservation of the yellow catfish.
Article ID 0001 Published: 30 January 2019 RESEARCH ARTICLE
The aim of this study was to determine whether the polymorphism of aldosterone synthase (CYP11B2) –344C/T and angiotensin-converting enzyme (ACE) insertion/deletion (I/D) were associated with the response of blood pressure (BP) to telmisartan treatment. After a two-week single-blind placebo run-in period, 148 patients with mild-to-moderate primary hypertension received monotherapy of telmisartan with 80 mg/day and then were followed up for eight weeks. Polymorphisms of CYP11B2 –344C/T and ACE I/D gene were determined through polymerase chain reaction-restriction fragment polymorphism analysis. The relationship between these polymorphisms and changes in BP was monitored and evaluated after eight weeks of treatment. With respect tothe polymorphism of CYP11B2 –344C/T, the reduction in diastolic BP was significantly greater in patients carrying the C allele (CC+CT) compared with those carrying the TT genotype. There was no significant differences between ACE I/D polymorphism and BP reduction after treatment. We concluded that the aldosterone synthase –344C/T polymorphism was related to the antihypertensive treatment with telmisartan in hypertensive patients.
Volume 98, 2019
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