Article ID 0077 Published: 9 October 2020 RESEARCH ARTICLE
Gloriosa superba is an economical source of pharmaceutical colchicine, which is a mitotic poison used to treat gout, cancer and inflammatory diseases. It is important to study the genetic variations in this plant, but the progress is impeded due to limited number of molecular markers. In this study, we developed the expressed sequence tag-derived simple sequence repeat (EST-SSR) markers from the transcriptome sequence of the leaf samples of three different ecotypes of G. superba. De novo assembly was performed on these sequencing data to generate a total of 65,579 unigenes and 38,200 coding sequences (CDSs). These CDSs were annotated using NCBI Nr protein database, gene ontology terms and KEGG pathways. Differential gene expression was studied to yield differences in these ecotypes at the molecular level. Finally, a total of 14,672 potential EST-SSRs were identified from these unigenes, among which the dinucleotide (5754, 39.22%) and trinucleotide (5421, 36.95%) repeats were most abundant types followed by mononucleotides (3213, 21.83%). The most frequent motifs were CT/GA (1392, 9.48%), AG/TC (1219, 8.31%), and GA/CT (1146, 7.82%) among the dinucleotide repeats and CCG/CGG (1487, 10.13%), AGG/CCT (1421, 9.68%), AGC/CTG (697, 4.75%) and AAG/CTT (621, 4.23%) among the trinucleotide repeats. Polymorphism study using a random set of 20 newly developed EST-SSRs revealed polymorphic information content value ranging from 0 to 0.5926 with an average of 0.4021. The large-scale ESTs developed in the current study will be useful as a genomic resource for further investigation of the genetic variations in this species.
Article ID 0076 Published: 7 October 2020 RESEARCH ARTICLE
The genus Phlogacanthus Nees belongs to the family Acanthaceae and is represented by herbs or shrubs species. The present work shows detailed karyomorphological studies in two species, Phlogacanthus quadrangularis (Hook.) Heine and Phlogacanthus guttatus Nees. Both the species grow as undergrowth vegetation. The conservation status of both the species are yet to be determined. The somatic chromosome counts of both the mentioned species are available for the first time, 2n = 40 for P. quadrangularis and 2n = 34 for P. guttatus. The karyomorphological observations showed that both plant species show dominance of sub-telocentric chromosomes with a few metacentric chromosomes. P. quadrangularis have telocentric chromosomes which is absent in the other species. The range of length ofchromosomes in P. quadrangularis is from 0.340 $\mu$m to 1.32 $\mu$m and that of P. guttatus is from 0.560 $\mu$m to 1.878 $\mu$m. The karyotype type of the two species are classified as 3B type. But the dispersion index (DI) value of both the species are different. P. guttatus shows higher value of DI than P. quadrangularis. Higher the DI value more specialized is the karyotype. By comparing the chromosome length, size, DI value and idiogram of both the species, it is concluded that the karyotype of P. guttatus is more asymmetric and advanced than karyotype of P. quadrangularis. The karyomorphological findings of the present study will aid in determining the importance and utility, ex-situ conservation, protection, preservation and regeneration of germplasm.
Article ID 0075 Published: 7 October 2020 RESEARCH ARTICLE
The best linear unbiased prediction (BLUP), derived from the linear mixed model (LMM), has been popularly used to estimate animal and plant breeding values (BVs) for a few decades. Conventional BLUP has a constraint that BVs are estimated from the assumed covariance among unknown BVs, namely conventional BLUP assumes that its covariance matrix is a $\lambda$K, in which $\lambda$ is a coefficient that leads to the minimum mean square error of the LMM, and K is a genetic relationship matrix. The uncertainty regarding the use of $\lambda$K inconventional BLUP was recognized by past studies, but it has not been sufficiently investigated. This study was motivated to answer the following question: is it indeed reasonable to use a $\lambda$K in conventional BLUP? The mathematical investigation concluded: (i) the use of a $\lambda$K in conventional BLUP biases the estimated BVs, and (ii) the objective BLUP, mathematically derived from the LMM, has the same representation as the least squares.
Article ID 0074 Published: 28 September 2020 RESEARCH NOTE
The broad spectrum of causal variants in the newly discovered GIPC3 gene is well reflected in worldwide studies. Except for one missense variant, none of the reported variants had reoccurred, thus reflecting the intragenic heterogeneity. We screened all the six coding exons of GIPC3 gene in a large cohort of 177 unrelated prelingual hearing impaired after excluding the common GJB2, GJB6 nuclear and A1555G mitochondrial variants. We observed a single homozygous pathogenic frameshift variant c.685dupG (p.A229GfsX10), accounting for a low incidence (0.56%) of GIPC3 variants in south Indian population. GIPC3 being a rare gene as a causative for deafness, the allelic spectra perhaps became much more diverse from population to population, thus resulting in a minimal recurrence of the variants in our study, that were reported by authors from other parts of the globe.
Article ID 0073 Published: 22 September 2020 RESEARCH ARTICLE
Cotton has received attention of geneticists since more than a century. Gossypium hirsutum, the predominantly cultivated cotton species worldwide, has a narrow genetic base. It is important to broaden its genetic base through introgression of novel alleles from related species. Here, we report the development and characterization of a backcross population derived from the hybridization of a 'synthetic' (derived by crossing and chromosomal doubling of nonprogenitor Gossypium species) and natural tetraploid upland cotton. 'Synthetic' was observed to be male-sterile and thus, was used as the female parent. A total of 7434 flowers were pollinated to obtain 1868 BC1F1 seeds by direct and reciprocal crosses. Characterization of the experimental plant material was conducted in the field for several morphological traits such as pubescence on the stem, leaf, petiole and bract, presence/absence of petal spot, petal margin colouration andstamen filament colouration. Genetic analysis revealed that petal margin colouration phenotype was governed by a single dominant gene,whereas the petal spot and filament colouration phenotypes manifested segregation distortion. None of the BC1F1 plants was devoid of trichomes thus demonstrating that presence of trichomes is dominant over their absence. Modern upland cotton cultivars are usually devoid of petal spot, petal margin colouration and stamen filament colouration. These floral anthocyanin pigmentation characteristics, if fixed in the cotton germplasm, may serve as diagnostic features for the identification of cultivars during DUS testing as well as in the maintenance breeding programmes.
Article ID 0072 Published: 12 September 2020 RESEARCH NOTE
We report a rare case of a 14-month-old male child who was referred for developmental delay. Clinical examination revealed a hypotonic infant with speech delay and no dysmorphic features. The banding cytogenetics revealed a small supernumerary marker chromosome. Upon silver staining, the marker showed the presence of satellite regions on either ends. Further, analysis using fluorescence in situ hybridization on marker chromosome revealed its origin from chromosome 15.
Article ID 0071 Published: 9 September 2020 RESEARCH ARTICLE
Genome sequence of Acinetobacter baumannii DS002 revealed the existence of seven contigs with features of indigenousplasmids. Of the seven contigs, three of them have shown size and sequence identity. They appeared to have been generated due to theunique recombination events leading to a large-scale recombination and sequence inversions. The rest of the indigenous plasmids haveshown significant size variations and contained the genetic repertoire required for the detoxification of formaldehyde and biosynthesis ofexopolysaccharides. Genetic modules encoding novel toxin–antitoxin systems were found in most of the plasmids to ensure their survival inthe host. In some instances, the toxin and antitoxin coding sequences were found on two different plasmids promoting the cosegregation ofthese two plasmids into the daughter cells.
Article ID 0070 Published: 20 August 2020 RESEARCH ARTICLE
This study was undertaken to measure the genetic diversity and population structure of 48 barley accessions introduced from ICARDA using 51 polymorphic simple sequence repeat (SSR) markers to select unique parents for breeding. The mean polymorphic information content was 0.491, suggesting high polymorphism for the selected SSR markers among the barley accessions. The populationstructure indicated a fine genetic base only with two major clusters. All accessions had 100% membership probability in their respective clusters. Analysis of molecular variance revealed that most (78%) of the variation was attributed between populations, while 22% was due to variation among individuals within populations. Neighbour-joining (NJ) tree was constructed using this distance matrix and two major clusters were observed in it. Cluster 1 had all hulled barley accessions and cluster 2 had all hulless barley accessions. Cluster 2 could befurther divided into three subclusters. Principal coordinates analysis results were similar to the NJ tree, where the hulled and hulless barley accessions were grouped into separate clusters. This study established the existence of considerable genetic diversity among the 48 tested accessions. The selected genetic resources will be useful for barley breeding in India and other countries.
Article ID 0069 Published: 16 August 2020 RESEARCH ARTICLE
Members of the bZIP transcription factor family play crucial roles in the regulation of plant development, biosynthesis of secondary metabolites, and response to abiotic and biotic stresses. To date, multiple bZIPs have been identified and investigated in numerous plant species. However, few studies have characterized bZIPs from Dimocarpus longan Lour. In this study, nine bZIPs from D. longan were identified from RNA-Seq data and further verified using the NCBI conserved domain search tool and Pfam database. Bioinformatics tools were used to systematically analyse the physicochemical properties, protein structures, multiple sequence alignment, motif compositions, evolutionary relationships, secondary structures, subcellular localization, phosphorylation sites, signal peptides, GO annotations and protein–protein interactions of the DlbZIPs. The expression patterns of the nine DlbZIPs were evaluated by qRT-PCR inroots and leaves and in response to varying durations of a 38°C heat treatment. DlbZIP3, DlbZIP5, DlbZIP6 and DlbZIP7 were differentially expressed between root and leaf tissues. All nine DlbZIPs responded to heat treatment in both roots and leaves, but their specific expression levels differed. DlbZIP4 and DlbZIP8 were highly expressed in roots after heat treatment, whereas DlbZIP1 and DlbZIP5 were highly expressed in leaves after heat treatment. These findings lay a foundation for increasing active secondary metabolite content and improving abiotic stress tolerance in D. longan using transgenic technology.
Article ID 0068 Published: 13 August 2020 RESEARCH ARTICLE
Ochlandra Thwaites, an economically exploited bamboo genus of the Western Ghats of India is severely affected by unsustainable extraction, natural habitat destruction and endangerment of species resources. This taxonomically challenging genus consists of a genetic mixture of 10 related polyploid species that are difficult to define and classify using traditional morphology. The present study investigated the probability of DNA barcoding using seven standard barcode regions recommended by CBOL as a supplementary tool to define true species boundaries. Distance (MEGA v.6.0) and sequence similarity (TaxonDNA) based approaches highlighted the discriminatory power of psbA–trnH intergenic spacer barcode region, but did not support true species entities. Neighbour-joining and Bayesian inference trees supported the existence of morphospecies complex in seven species of the genus owing to weak reproductive barriers amongnaturally coexisting species. Morphological affinities existing within genus might have stemmed from natural interspecific hybridization events and consequent reticulate evolution in morphospecies complex of genus Ochlandra.
Article ID 0067 Published: 6 August 2020 RESEARCH ARTICLE
The yellowtail rasbora (Rasbora tornieri) is a miniature ray-finned fish categorized under the genus Rasbora in the family of Cyprinidae. In this study, a complete mitogenome sequence of R. tornieri was sequenced using four primers targeting two halves of the mitogenome with overlapping flanking regions. The size of mitogenome was 16,573 bp, housing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organization was detected between this species and other members of Rasbora genus. The heavy strand encompassed 28 genes while the light strand accommodated the other nine genes. Most protein-coding genes execute ATG as start codon, excluding COI and ND3 genes, which utilized GTG instead. The central conserved sequence blocks (CSB-E, CSB-F and CSB-D), variable sequence blocks (CSB-1, CSB-3 and CSB-2) as well as the terminal associated sequence (TAS) were conserved within the control region. The maximum likelihood phylogenetic family tree revealed the divergence of R. tornieri from the basal region of the Rasbora clade, where its evolutionary relationships with other Rasbora members are poorly resolved as indicated by the low bootstrap values. This work acts as window for further population genetics and molecular evolution studies of Rasbora genus in future.
Article ID 0066 Published: 4 August 2020 RESEARCH NOTE
Brugada syndrome (BrS) is a rare genetic arrhythmic disorder with a complex model of transmission. At least 20 different genes have been identified as BrS-causal or susceptibility genes. Of these, SCN5A is the most frequently mutated. Coregulation of different mutations or genetic variants, including mitochondrial DNA (mtDNA), may contribute to the clinical phenotype of the disease. In thepresent study, we analysed the mitochondrial genome of a symptomatic BrS type 1 patient to investigate a possible mitochondrial involvement recently found in the arrhytmogenic diseases. No pathogenic mutation was identified; however, a high number of singlenucleotide polymorphisms were found (n=21) and some of them were already been reported in molecular autopsy case for sudden death.The results reported here further support our hypothesis on the potential role of mtDNA polymorphisms in mitochondrial dysfunction, which may represent a risk factor for arrhythmogenic disease.
Article ID 0065 Published: 21 July 2020 REVIEW ARTICLE
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approachesassociated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on diseasemediatedextinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
Article ID 0064 Published: 21 July 2020 RESEARCH ARTICLE
The developmentally active and cell-stress responsive hsrω locus in Drosophila melanogaster carries two exons, one omega intron, one short translatable open reading frame (ORFω), long stretch of unique tandem repeats and an overlapping mir-4951 near its 30´ end. It produces multiple long noncoding RNAs (lncRNAs) using two transcription start and four termination sites. Earlier cytogenetic studies revealed functional conservation of hsrω in several Drosophila species. However, sequence analysis in three species showed poor conservation for ORFω, tandem repeat and other regions while the 16 nt at 50 and 60 nt at 30 splice junctions of the omega intron, respectively, were found to be ultra-conserved. The present bioinformatic study using the splice-junction landmarks in D. melanogaster hsrω identified orthologues in publicly available 34 Drosophila species genomes. Each orthologue carries a short ORFω, ultra-conserved splice junctions of omega intron, repeat region, conserved 30-end located at mir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in the repeat sequences. Intriguingly, only the omega intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested in Chironomus and Ceratitis genera. Amidst the high sequence divergence, the conserved organization of exons, ORFω and omega intron in this gene’s proximal part and tandem repeats in distal part across the Drosophila genus is remarkable and possibly reflects functional importance of higher order structure of hsrω lncRNAs and the small omega peptide.
Article ID 0063 Published: 16 July 2020 RESEARCH NOTE
A relationship between the polymorphism in promoter region of the UGT1A1 gene and the development of jaundice has been demonstrated recently. This polymorphism leads to 30% of normal rate transcription initiation of UGT1A1 gene, thus decreasing the bilirubin glucuronidation. The combination of the G6PD deficiency and polymorphism in neonates and adults may causepronounced hyperbilirubinaemias. The aim of this study was to analyse the variations in the UGT1A1 gene promoter in Panamanians neonates with G6PD deficiency and its association with neonatal jaundice (NJ). We identified five different genotypes of TA repeats, in 17 neonates (42.5%) the normal variant TA6/TA6 and in the other 57.5% of the subjects: TA7/TA7 (12.5%), TA6/TA7 (40%), TA6/TA8 (2.5%) and TA6/TA5 (2.5%). Additionally 75% of the 16 newborns that showed NJ had an abnormal variant in the promotersequence, although, there was no significant difference (P = 0.068). The risk of jaundice in neonates with TA7 variant was thrice higher in subjects than with other alleles (P = 0.093, CI: 0.81–11.67). The TA7 allele frequency in this study (0.325) was consistent with the global frequency and similar to Caucasians. The results proved that there is no significant relationship between promoter polymorphism in UGT1A1 and NJ in G6PD deficient Panamanian newborns. Further studies with a greater number of subjects would determine the exact relationship between marked NJ and UGT1A promoter variations.
Article ID 0062 Published: 16 July 2020 RESEARCH ARTICLE
The aim of present study was to evaluate the linkage disequilibrium (LD) of p.R72P, PIN3 Ins16bp, p.P47S, p.R213R and r.13494g[a polymorphism of TP53 and their haplotypes association with oesophageal cancer risk in patients from Punjab, northwest India. A total of 466 samples, including 233 oesophageal cancer patients and 233 healthy individuals were analysed. Data analysis revealed the gender specific association. In female group, arginine–proline (RP) genotype (P = 0.08) and P allele (P = 0.07) of p.R72P polymorphism was marginally associated with increased risk of oesophageal cancer. A1A2 genotype (P = 0.06) and A2 allele (P = 0.07) of PIN3 Ins16bp polymorphism was marginally associated with decreased risk of oesophageal cancer in male group. A1A2–GA genotype combination (P = 0.04) of PIN3 and r.13494g[a polymorphisms was significantly associated with decreased risk of oesophageal cancer in male group. In female group, PP–GA genotype combination (P = 0.02) of p.R72P and r.13494g[a polymorphisms and RP–A1A1–GG genotype combination (P = 0.04) of p.R72P, PIN3 and r.13494g[a polymorphisms was significantly associated with increased risk of oesophageal cancer. We observed moderate LD between two intronic polymorphisms PIN3 Ins16bp and r.13494g[a (D´ = 0.90; r2 = 0.68). Haplotype analysis revealed that none of the haplotype combination was associated with oesophageal cancer risk when both the genders were considered. Stratification on the basis of gender showed that P-A2-P-A-A haplotype of p.R72P, PIN3 Ins16bp, p.P47S, p.R213R and r.13494g[a polymorphisms was marginally associated with reduced oesophageal cancer risk in male group (P = 0.08). Replication of these findings in independent cohorts may be insightful for the role of TP53 in oesophageal cancer pathogenesis.
Article ID 0061 Published: 16 July 2020 RESEARCH NOTE
Psoriasis-2 (PSORS2) is caused by the heterozygous mutation of the caspase recruitment domain 14 (CARD14) gene on chromosome 17q25. To evaluate the contribution of CARD14 variants in psoriasis of the Chinese Han population, we performed deep sequencing of the CARD14 gene in 372 Chinese Han patients with psoriasis. The exonic nucleotide variants were confirmed by Sanger sequencing in the affected individuals and 1114 controls. In 27 patients with psoriasis, we identified 15 variations, including three novel variants: c.381C[G (p.Cys127Trp), c.712A[G (p.Met238Val) and c.2260_2261delinsGG (p.Gln754Gly). These findings could enrich and update the Human Gene Mutation Database of CARD14 variants for psoriasis.
Article ID 0060 Published: 2 July 2020 RESEARCH ARTICLE
In heterozygote state, we interogressed three chromosomal segments of Drosophila koepferae in D. buzzatii. The effect of each introgression was evaluated in the fertility of the segmental males, quantifying the amount of offspring produced. Through specific crosses method, we generated Drosophila segmental isolines carrying specific chromosomal introgression segments. The introgressions were monitored cytogenetically by the method of molecular markers of chromosomal asynapsis. The statistical analysis showed that none of the three segments evaluated, introgressed individually or in pairs, as well as cis or trans, do not produce sterility in the segmental males, as determined by the normal productions of offspring. Additional introgressions using other larger segments show that when the introgressions reach a minimum size of 31.15%, they produce sterility. It is concluded that the hybrid sterility genes present in the three segments evaluated did not act in strong epistasis, but show a pattern of gradual additive behaviour by requiring a minimum threshold size to produce sterility. Finally, we also isolated the smallest introgressing segment that has been reported for these species (2.19%), and for the first time we have managed to place it in homozygous state (data not shown), so we are now in the process of evaluating the ability to these segments in homozygous state.
Article ID 0059 Published: 2 July 2020 RESEARCH ARTICLE
MITHLESH KUMAR MANUBHAI PATEL RAVINDRASINGH CHAUHAN CHANDRESH TANK SATYANARAYAN SOLANKI PRAVINBHAI PATEL HITENDRA BHADAURIA RAMAN GAMI KAREN PACHCHIGAR NISHIT SONI PRANAY PATEL ANUJ SINGH NITIN PATEL RAMESH PATEL
The present study was undertaken to delineate genotype–environment interactions and stability status of 16 genotypes of ashwagandha (Withania somnifera (L.) Dunal) in context to the 12 characters, namely plant height, number of primary branches, number of secondary branches, days to flowering, days to maturity, number of berries, number of seeds/berry, root length, root diameter, root branches, dry root yield and total alkaloid content (%). Experiment was carried out in a randomized complete block design with three replicationsover three different locations (S. K. Nagar, Jagudan and Bhiloda) in north Gujarat for three years (2016–17, 2017–18 and 2018–19). Pooled analysis of variance revealed that the mean squares due to genotypes and genotype 9 environment interaction along with linear and nonlinear components were highly significant (P<0.01) for most of the traits under study. Stability parameters for component traits through Eberhart and Russell model showed that genotypes that can be used directly in breeding programme are SKA-4 for early flowering, SKA-21 for early maturity and SKA-1, SKA-4, SKA-6 and SKA-17 for shorter plant height. Further, SKA-21 could be used for improving number of primary branches per plant, SKA-11 and SKA-17 for number of secondary branches per plant, SKA-19 for number of berries per plant, SKA-6, SKA-21, SKA-27 and AWS-1 for root branches and SKA-17 for root length as these genotypes were found to be moststable across the environments for mentioned traits. The result revealed that some reliable predictions about genotype 9 environment interaction and its unpredictable components were involved significantly in determining the stability of genotypes. Hence, the present investigation can be exploited for the identification of more productive genotypes in specific environments, leading to significant increase in root productivity of ashwagandha.
Article ID 0058 Published: 30 June 2020 RESEARCH ARTICLE
Eukaryotic and prokaryotic cell genomes exhibit multiple microsatellites. In this study, we characterized microsatellites in genomes and genes of Nanorana parkeri and Xenopus laevis. This characterization was used for gene ontology (GO) analysis of coding sequences (CDS). Compared to the genome of . parkeriN, the genome of X. laevis is larger and contains more number of microsatellites, but the diversity of both species are similar. Trinucleotide repeats in the genome of N. parkeri and dinucleotide and tetranucleotide repeats inthe genome of X. laevis were the most diverse. In both the species, diversity of microsatellites was highest in intergenic regions, followed by intron and exon regions, and lowest in coding regions. Microsatellites in CDS are thus subject to higher selective pressure. Many microsatellites are concentrated upstream and downstream of genes in both species, suggesting suppression of repeats in the middle of protein–CDS. Repeats are enriched in regions near gene termini purely due to the biophysical constraints of protein structure. In GO analysis, two and five unique GO terms, only found in N. parkeri and X. laevis, respectively, indicate advantageous mutations during species evolution. Biological process, cellular component and molecular function ontology reflected in the GO analysis predicted that the microsatellites located in CDS can alter protein function and may provide a molecular basis for species adaptation to new and changing environments.
Article ID 0057 Published: 19 June 2020 RESEARCH ARTICLE
Both cowpea and yard-long bean belong to Vigna unguiculata ssp. unguiculata but have diverged through human induced evolution in sub-Saharan Africa and Asia, respectively. To map the quantitative trait loci (QTLs) for yield associated traits and derive new lines that may combine the attributes of both types, we developed a F2:3 mapping population derived from a cross between cowpea line TVu2185 and yard-long bean line TVu6642. Using DArT markers, a total of 30 QTLs accounting for 1.8–13.0% phenotypic variation was detected for pod and seed traits. Some novel major QTLs for peduncle number per plant (qPeN2.2), pod length (qPoL3), seed breadth (qSB4), length (qSL7.2) and thickness (qST9) identified on chromosomes 2, 3, 4, 7 and 9, respectively, are particularly interesting and need to be validated. Moreover, we confirmed previously reported QTLs for pod length (qPoL8) and 100-seed weight (qSW8) on chromosome 8 and for seed number per pod (qSN9.2) on chromosome 9 suggesting usefulness for marker-assisted-selection purpose. Notably, some QTLs for these traits were clustered especially on chromosomes 5, 7, 8, 9 and 10 indicating the presence of the same QTL or linked loci in these regions. Moreover, the involvement of epistasis was observed for trait expressions, but compared with the main effect QTLs, the phenotypic effects of epistatic-QTLs detected were much less. The present QTL analysis may provide a useful tool for breeders to formulate efficientbreeding strategy for introgression of the desirable alleles for yield related traits in cowpea using molecular markers.
Article ID 0056 Published: 19 June 2020 RESEARCH ARTICLE
Development of mutants and their effective utilization to incorporate desirable traits in tomato would be a sound improvement strategy to develop so called ‘smart’ tomato variety of the coming century. Initially we developed three induced mutants from two varieties, ‘Patharkuchi’, a local adapted cultivar and an introduced variety ‘Berika’, and then three crosses (Berika 9 P Mut-5, Berika 9 P Mut-11, Patharkuchi 9 B Mut-1) were made to involve in these two varieties and their respective mutants. Six generations (P1, P2, F1, F2, BC1 and BC2) of three crosses were utilized to study the genetic control of yield and quality traits, and to study the genetic basis of formation of dark green fruit. The nature and magnitude of gene action controlling the inheritance of 27 quantitative traits differed from one cross to another and from one trait to another, mostly conditioned by nonadditive gene action and duplicate epistasis. The prevalence of duplicate epistasisin three crosses for most of the traits revealed that the pace of progress through conventional selection process would be hindered as this kind of epistasis might result in decreased variation in F2 and subsequent generations. Recurrent selection in biparental progenies would be helpful for exploiting this type of nonallelic interaction through generation of high frequency of desirable recombination and concentration of genes having cumulative effects in the population. We also observed complex genetic behaviour of some of the traits revealing significant epistatic components. Inheritance study of ‘dark green fruit’ (dg1) of Berika 9 P Mut-5 cross revealed a single recessive gene governing the trait and expressed when the mutant gene was in homozygous recessive condition (designated as dg-1/dg-1).
Article ID 0055 Published: 15 June 2020 RESEARCH NOTE
The number of gene mutations involved in the hereditary spastic paraplegias is rapidly growing due to the expansion of the frontiers of genomic research by next-generation DNA sequencing platforms. Nevertheless, a comprehensive genetic diagnosis method remains yet unavailable for these diseases. In the current research, an 8-year-old boy with short stature and developmental delay impairment, from a nonconsanguineous family, was referred to our genetic lab. Firstly, based on the physician recommendation, the patient was evaluated by tandem mass spectrometry (MS/MS) for the quantitative examination of amino acids, and then the patient was genetically investigated by karyotype analysis and whole-exome sequencing (WES) technique. Subsequently, targeted Sanger sequencing was applied to confirm the presence of the candidate variant in all the members of the family and screening the other patients for Troyer syndrome. Analysis of inherited metabolic disorders by tandem MS/MS showed the state of all the family members as normal and also karyotyping indicated no chromosomal aberration in the patient. Further investigation by WES technique indicated a homozygous missense variant in the SPG20 gene, c.1006C[T. Targeted sequencing result of the mutation confirmed homozygote state for the affected case and a heterozygote genotype for his parents. The mutation was classified as pathogenic. Detection of novel variants especially pathogenic variantin the SPG20 gene was associated with Troyer syndrome, which encodes a multifunctional protein termed Spartin, assist in improving genotype–phenotype correlation of genetic variants and may facilitate initial diagnosis of Troyer syndrome.
Article ID 0054 Published: 9 June 2020 RESEARCH NOTE
Droughtmaster is a tropical breed of beef cattle that can survive in hot climates and easily adapt to torrid environments. These traits are important in livestock breeding. In this study, we genotyped five single-nucleotide polymorphisms (SNPs) of the AHSA2 gene from 190 cattle belonging to three different breeds (Droughtmaster, Angus and Simmental) by using snapshot technology. This work aimed to identify the valuable molecular marker of heat resistance in cattle. Results showed that Droughtmaster exhibited higher expected heterozygosity and polymorphic information content compared with the two other breeds. The AHSA2-1 locus deviated from the Hardy–Weinberg equilibrium in the Droughtmaster breed (P < 0.05). Two SNPs in Droughtmaster diverged significantly from Angus and Simmental. The SNPs were identified as AHSA2-3 and AHSA2-4, which were closely linked to the three breeds based on pair-wise FST. AHSA2-4 involved a missense mutation. In summary, the GG genotypes in AHSA2-3 and AHSA2-4 may be candidate genotypes associated with heat resistance traits and may serve as valuable genetic markers for breeding of heat-tolerant beef cattle in the future.
Article ID 0053 Published: 9 June 2020 RESEARCH NOTE
At present, more than 200 countries and territories are directly affected by the coronavirus disease-19 (COVID-19) pandemic. Incidence and case fatality rate are significantly higher among elderly individuals (age>60 years), type 2 diabetes and hypertension patients. Cellular receptor ACE2, serine protease TMPRSS2 and exopeptidase CD26 (also known as DPP4) are the three membrane bound proteins potentially implicated in SARS-CoV-2 infection. We hypothesised that common variants from TMPRSS2 and CD26 may play critical role in infection susceptibility of predisposed population or group of individuals. Coding (missense) and regulatory variants from TMPRSS2 and CD26 were studied across 26 global populations. Two missense and five regulatory SNPs were identified to have differential allelic frequency. Significant linkage disequilibrium (LD) signature was observed in different populations. Modelled protein–protein interaction (PPI) predicted strong molecular interaction between these two receptors and SARS-CoV-2 spike protein (S1 domain). However, two missense SNPs, rs12329760 (TMPRSS2) and rs1129599 (CD26), were not found to be involved physically in the said interaction. Four regulatory variants (rs112657409, rs11910678, rs77675406 and rs713400) from TMPRSS2 were found to influence the expression of TMPRSS2 and pathologically relevant MX1. rs13015258 a 50 UTR variant from CD26 have significant role in regulation of expression of key regulatory genes that could be involved in SARS-CoV-2 internalization. Overexpression of CD26 through epigenetic modification at rs13015258-C allele was found critical and could explain the higher SARS-CoV-2 infected fatality rate among type 2 diabetes.
Article ID 0052 Published: 4 June 2020 RESEARCH ARTICLE
In the present investigation, phenotypic evaluation of blast disease reaction was conducted at Ponnampet and Mandya districts of Karnataka, India, which indicated that the rice varieties such as IR64, Jaya, KMP153, IR30864, Mandya Sona-1, Mandya Sona-2, KCP-1, Dodda Byra, and Malgudi Sanna were susceptible to both leaf and neck blasts. Further, the rice varieties that were resistant to leaf blast such as KMP200, DHMAS70Q164-1b, Karibatta, Coimbatore Sanna and others showed susceptible reaction to neck blast only. In contrast, the varieties such as JyothixBR2655, Punkutt Kodi, Sirsi, 222 and Gangadale which were resistant to neck blast were found to be susceptible to leaf blast also. Only one variety, BR2655 showed resistance to both leaf and neck blast diseases. The genotypic studies using simple sequence repeat markers showed that the analysis of the distribution of resistance genes and genotyping of the selected rice varieties, and traditional rice varieties from different ecological regions with allele specific markers helped to identify 20 major blast resistance genes. The individual gene frequencies of the 20 major rice blast resistance genes varied from 10.34 to 100%. Less and more frequency of resistance gene distribution occurred in Pi9 and Pizt gene, respectively. The result of this study would help to create strategies for improving rice blast resistance through genetic studies and plant–pathogen interaction.
Article ID 0051 Published: 4 June 2020 RESEARCH ARTICLE
In male, the prostate cancer (PCa) is one of the most frequent neoplasias and the second cause of cancer deaths worldwide. In 2015, more than 6000 men died in Mexico due to this disease. In this regard, prostate cancer associated gene 3 (PCA3) has become an interesting target in PCa as is found highly overexpressed. Moreover, TAAA tandem repeats have been suggested to be associated with the regulation of PCA3 expression and, in turn, to be related with the development of the disease. The aim of the study was to understand thegenetic basis of the disease in search for a better diagnosis. Expression levels of PCA3 gene were analysed in tissue of 13 patients diagnosed with PCa and six patients diagnosed with a benign prostatic disease (BPD). The absolute expression of PCA3 was quantified by real-time PCR. Genotype for TAAA tandem repeats was measured using automatic sequencing and the results were analysed to determine whether an association existed between them. We identified three alleles: 4, 5, 6 and four genotypes: 4/5, 5/5, 5/6, 6/6. Our analysis identified amutation in the nucleotide 76764237 of the PCA3 gene that generates an extra TAAA tandem repeat. The nucleotide mutation is present in 61.53% of PCa and 66.66% of BPD patients. Our study revealed the presence of a mutation in the PCA3 gene that generates an extra TAAA tandem. We observed no association between the absolute expression of PCA3 messenger and the number of TAAA repetitions.
Article ID 0050 Published: 4 June 2020 RESEARCH ARTICLE
Smith–Magenis syndrome (SMS, OMIM: 182290) is a multiple congenital anomalies and intellectual disability syndrome due to a 3.45 Mb microdeletion involving 17p11.2 and is estimated to occur about one in 25,000 births. Up to now, the ultrasound findings of the foetus with SMS and their external genital defects in patients are rarely reported. This case indicates that foetus with SMS may presentpolyhydramnios and ventriculomegaly in the second trimester. The newborn male patient had an abnormal phenotype in which he has micropenis and his anus is close to the perineal body. The identification of this case may further expand the phenotypic spectrum of this genetic disorder.
Article ID 0049 Published: 3 June 2020 RESEARCH ARTICLE
Transaminases are an industrially important class of enzyme, due to their ability to catalyse amination reactions for production of chiral amines, and are key building blocks of small molecule pharmaceuticals. We analysed the genome of strain GS115 of the methylotrophic yeast Komagataella phaffii, formerly known as Pichia pastoris, to identify the transaminase genes and propose a systematic nomenclature based on both phylogeny and structuro-functional features. K. phaffii is an increasingly attractive industrial host cell due to its ability to grow to high biomass, up to 60% wet cell weight by volume, using methanol as carbon source and inducer of transgene expression. Thirty-nine UniProt database hits were reduced to 19 on the basis of sequence similarity and hidden Markov model. Of the 19 genes, the open-reading frames of three (KpTam I-II.1b, KpTam I-II.7 and KpTam V.2) had strong homology with no characterized proteinand four (KpTam III.1a, KpTam III.1b, KpTam III.2a and KpTam III.2b) had relatively high sequence similarity to x-type transaminases, a subtype that typically accepts the broadest range of substrates. Comparison with Saccharomyces cerevisiae S288C suggested functions for KpTam I-II.1b and KpTam I-II.7. K. phaffii GS115 was originally generated by mutagenesis of K. phaffii CBS7435 and comparison revealed that one transaminase gene may have been deleted during this mutagenesis. These insights can advance fundamental understanding of yeast biology and can inform industrial screening and engineering of yeast transaminases.
Article ID 0048 Published: 2 June 2020 REVIEW ARTICLE
Several recent investigations show that HOX transcript antisense intergenic RNA (HOTAIR) play an important role in the pathogenesis of different cancers. HOTAIR polymorphisms has been widely studied in the context of association between with the risk of cancer pathogenesis. However, there is no certain conclusion about the role of HOTAIR polymorphisms in different cancer initiation and progression. Our team has selected eligible studies up to 1 May 2019, from several electronic databases, including Web of Science, PubMed, Scopus, and Google Scholar databases. We have included total number of 102 case–control investigations extracted from 41 eligible articles for the current meta-analysis. We calculated pooled odds ratio (ORs) with their corresponding 95% confidence intervals (CIs) using either fixed-effect or random-effect models for quantitative evaluation of the strength for the association between HOTAIR gene polymorphisms and the risk of cancer. Our current meta-analysis investigation showed that HOTAIR rs4759314 polymorphism particularly increased the overall risk of cancer in different models including homozygous, recessive and allele genetic. HOTAIR rs920778 significantly raised the cancer risk only in recessive genetic model. HOTAIR rs12826786 polymorphism was associated with cancer development in heterozygous, homozygous, dominant, recessive and allele genetic models. Also, an increase in cancer risk was observed with rs874945 polymorphism of HOTAIR gene in heterozygous, dominant and allele genetic models. The rs12427129 polymorphism showed correlation with cancer susceptibility only in recessive model. Subgroup analysis based on cancer type suggested that rs4759314 polymorphism significantly increased the risk of gastric and cervical cancers, and the rs920778 polymorphism increased the risk of gastrointestinal, cervical and gastric cancers. In summary, this study found that HOTAIR polymorphisms are significantly associated with cancer development.
Article ID 0047 Published: 30 May 2020 RESEARCH NOTE
IQSEC2 is an X-linked gene highly expressed at the excitatory synapses where it plays a crucial role in a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor trafficking and synaptic plasticity. To date, several males and females with severe to profound intellectual disability have been reported harbouring frameshift and nonsense variants in this gene, whereas a milder phenotype has been recognized in females carrying missense pathogenic variants. Here, we report two novel IQSEC2 variants in four females with psychiatric features and otherwise variable cognitive impairment. A female (case 1) with severe verbal language learning disorder and a psychotic episode (precipitated by exposure to anti-contraceptive pill) harboured a de novo pathogenic frameshift variant (c.1170dupG,p.Gln391Alafs*5), whereas the female proband of family 2, displaying severe psychomotor regression and complex psychiatric features carried a missense variant of uncertain significance (c.770G[A,p.Ser257Asn) that was maternally inherited. Skewed X-inactivation was noted in the carrier mother. The maternal aunt, affected by schizophrenia, was found to bear the same IQSEC2 variant. We discuss the variable clinical presentation of IQSEC2 spectrum disorders and the challenging genotype–phenotype correlation, including the possible role of environmental factors as triggers for decompensation. Our report highlights how psychiatric features may be the main clinical presentation in subtle IQSEC2 phenotype, suggesting that the prevalence of IQSEC2 mutations in patients with psychiatric disorders may be underestimated.
Article ID 0046 Published: 29 May 2020 RESEARCH ARTICLE
Diabetes mellitus and its complications are major international health problems in which there are many limitations to the orthodox approaches in the treatment. Sodium glucose cotransporter 2 (SGLT2) inhibitors are a new class of diabetic medications, with a different mechanism of action that may reduce risk of cardiovascular complications. To evaluate the effect of SGLT2 inhibitor monotherapy on cardiovascular complications in patients with type-2 diabetes and to compare its effect with the first-line therapy, metformin. Eighty rats divided into four groups were used: nondiabetic, diabetic nontreated, diabetic + met and diabetic + dapa. At the end, the arterial blood pressure and cardiac performance were assessed. Glycemic index, lipid profile, total antioxidant capacity, malondialdehyde, tumour necrosis factor a were measured. DNA changes were assessed from the hearts and aortae. Aortic tissue changes recorded using haematoxylin and eosin, Masson trichrome and iNOS immune stain. Glycemic index, lipid profile, oxidative stress and inflammatory parameters were significantly improved in both metformin and dapagliflozin treated groups with significant improvement in blood pressure and cardiac performance. Also, there were noticeable significant reduction in DNA fragmentation in aortic and cardiac tissues and reduction in collagen deposition and iNOS expression in aortic tissue. Dapagliflozin treatment results’ significantly surpassed improvement of metformin treatment nearly in all parameters. Total genomic DNA extraction proved that SGL2 inhibitor (dapagliflozin) has superior glycemic control and cardiovascular protective effect over metformin especially in type-2 diabetes with high fat intake.
Article ID 0045 Published: 27 May 2020 RESEARCH ARTICLE
Rice blast disease, caused by Magnaporthe oryzae, is one of the most importance diseases of rice production worldwide. The keyrole of defense mechanism to combat this fungus in rice follows the gene-for-gene concept, which a plant resistant (R) gene product recognizes a fungal avirulent (AVR) effector and triggers the hypersensitive response. However, the AVR genes have been shown to be rapidly evolving resulting in high level of genetic diversity. The aims of this study were to examine the nucleotide sequence variation of AVR-Pita1 gene in Thai rice blast isolates and to identify the severity of blast disease using isogenic line of Pita gene. Seventy-six rice blast isolates collected from different parts of Thailand were used. Gene specific primers for AVR-Pita1 gene coding sequence were designed and used for identifying the genetic diversity of AVR-Pita1 gene by PCR amplification and sequencing. The obtained sequences were analysed for genetic variation and genetic relationship. Our results revealed the association between the sequence variations of AVR-Pita1 and selective forces from Pita gene. This phenomenon demonstrated the coevolution between rice blast resistant gene in rice and avirulent gene in blast fungus. The information about variation and evolutionary mechanisms of AVR gene obtained from this study can be used in rice blast resistant breeding programme.
Article ID 0044 Published: 20 May 2020 RESEARCH ARTICLE
Powdery mildew (Blumeria graminis f. sp. Tritici, (Bgt)) is an important worldwide fungal foliar disease of wheat (Triticum aestivum) responsible for severe yield losses. The development of resistance genes and dissection of the resistance mechanism will therefore be beneficial in wheat breeding. The Bgt resistance gene PmAS846 was transferred to the hexaploid wheat lines N9134 from Triticum dicoccoides, and it is still one of the most effective resistance genes. Here, by RNA sequencing, we identified three co-expressed gene modules using pairwise comparisons and weighted gene co-expression network analysis during wheat–Bgt interactions compared with mock-infected plants. Hub genes of stress-specific modules were significantly enriched in spliceosomes, phagosomes, the mRNA surveillance pathway, protein processing in the endoplasmic reticulum, and endocytosis. Induced module genes located on chromosome 5BL were selected to construct a protein–protein interaction network. Several proteins were predicted as the key hub node, including Hsp70, DEAD/DEAH box RNA helicase PRH75, elongation factor EF-2, cell division cycle 5, ARF guanine-nucleotide exchange factor GNOM-like, and protein phosphatase 2C 70 protein, which interacted with several disease resistance proteins such as RLP37, RPP13 and RPS2 analogues. Gene ontology enrichment results showed that wheat could activate binding functional genes via an mRNA transcription mechanism in response to Bgt stress. Of these node genes, GNOM-like, PP2C isoform X1 and transmembrane 9 superfamily member 9 were mapped onto the genetic fragment of PmAS846 with a distance of 4.8 Mb. This work provides the foundations for understanding the resistance mechanism and cloning the resistance gene PmAS846.
Article ID 0043 Published: 16 May 2020 REVIEW ARTICLE
The relationship between the long noncoding RNA (lncRNA) expression and oesophageal cancer prognosis has been widelystudied, but less consensus has been reached. We conducted this study to evaluate the relationship between the expression of lncRNAs and the prognosis and clinical pathology of oesophageal cancer. We conducted a systematic search of PubMed, EMBASE and Cochrane Library until 25 January 2019. Studies that evaluated the associations of a specific lncRNA with survival and/or clinicopathology of oesophageal cancer were included. Pooled hazard ratios (HRs), odds ratios (ORs), and corresponding 95% confidence intervals (CIs) were calculated using fixed or random-effect models. Sensitivity analysis was used to verify the stability of results. Publication bias was detected usingBegg tests and adjusted utilizing the trim-and-fill method if a bias existed. A total of 51 studies comprising 6510 patients and regarding 41 lncRNAs were included in the present systematic review and meta-analysis. The results showed that dysregulation of lncRNAs was associated with overall survival, disease-free survival, and progression-free survival. The expression of lncRNAs was related to some certain clinicopathological parameters of oesophageal cancer, including tumour size, T classification, lymph node metastasis, tumour nodemetastasis (TNM) stage and differentiation. Among these findings, lncRNA AK001796, CASC9, HOTAIR, MALAT1 and UCA1 wereidentified and were expected to be ideal biomarkers for the prognosis and clinicopathology of oesophageal cancer. Although significant publication bias was observed in some studies, the results were not changed after adjustment using the trim-and-fill method. Abnormal lncRNA-expression profiles could serve as a promising indicator for prognostic evaluation of patients with oesophageal cancer. The combination of these lncRNAs will contribute to clinical decision-making in the future.
Article ID 0042 Published: 15 May 2020 RESEARCH ARTICLE
Tay–Sachs disease (TSD), a deficiency of b-hexosaminidase A (Hex A), is a rare but debilitating hereditary metabolic disorder. Symptoms include extensive neurodegeneration and often result in death in infancy. We report an in silico study of 42 Hex A variants associated with the disease. Variants were separated into three groups according to the age of onset: infantile (n=28), juvenile (n=9) and adult (n=5). Protein stability, aggregation potential and the degree of conservation of residues were predicted using a range of in silico tools. We explored the relationship between these properties and the age of onset of TSD. There was no significant relationship between proteinstability and disease severity or between protein aggregation and disease severity. Infantile TSD had a significantly higher mean conservation score than nondisease associated variants. This was not seen in either juvenile or adult TSD. This study has established that the degree of residue conservation may be predictive of infantile TSD. It is possible that these more highly conserved residues are involved in trafficking of the protein to the lysosome. In addition, we developed and validated software tools to automate the process of in silico analysis of proteins involved in inherited metabolic diseases. Further work is required to identify the function of well-conserved residues to establish an in silico predictive model of TSD severity.
Article ID 0041 Published: 14 May 2020 RESEARCH ARTICLE
CmFT homologous gene in muskmelon was obtained by homologous cloning, introducing CmFT gene by Agrobacterium mediated transformation. The results of subcellular localization showed that CmFT protein was expressed in cytoplasm and nucleus. qRTPCR results showed that the expression levels of AtLFY, AtFT, AtCO, AtFLC, AtSOC1 and AtAP1 were upregulated in the 35S::MeFT Arabidopsis line. The CmFT gene was introduced into wild-type Arabidopsis by Agrobacterium-mediated transformation, and the growth status of T2 transgenic Arabidopsis thaliana and wild-type A. thaliana was observed. The results showed that wild-type Arabidopsis began to bolt on the 25th day after sowing, we can initially confirm that the FT gene of melon can promote the early flowering of melon in thegrowth and development of melon.
Article ID 0040 Published: 14 May 2020 RESEARCH ARTICLE
Chromosomal behaviour during megasporogenesis and microsporogenesis has been studied in ornamental Delphinium ajacis L. Meiosis in female sex cell initiates later than male. The floral buds which carry egg mother cell (EMC) at diplotene stage has pollen mother cells (PMCs) at tetrad stage of meiosis suggesting protandry. Although the 16 chromosomes formed regular eight bivalents in both the sex cells, they differed in overall chiasma frequency which was 32.95% higher in EMCs and found to be 18.52 ± 2.12 per cell. In PMCs, the average chiasma frequency recorded was 13.93 ± 1.40 per cell. Interestingly, this variation in chiasma frequency was largely confined to the two large bivalents which shared 42.61% chiasma per EMC. The use of Q–Q plot, Box plot and Whisker plot showed departure in the chiasma frequency distributions in EMCs and PMCs from the normal distribution pattern. The difference in chiasma frequency in the two sex cells was significant at all levels as indicated by the low P values of 3.094 × 10-11 obtained from nonparametric test, i.e. Wilcoxon rank-sum test. It is suggested that the two different mechanisms of recombination are operational in the two sex cells, and the sex differences of chiasma frequency could have arisen due to differential epigenetic modifications of the chromatin which pattern the double-strand breaks, and the position and frequency of crossing over visible as chiasmata.
Article ID 0039 Published: 11 May 2020 RESEARCH ARTICLE
Chimpanzees (Pan troglodytes), with a dwindling population size, are distributed across sub-Saharan Africa. They are classified into two biogeographical clusters comprising of four subspecies: a western African cluster that includes P. t. verus and P. t. ellioti and a central/eastern African cluster that includes P. t. troglodytes and P. t. schweinfurthii. While the genetic distinctness of Nigeria-Cameroonian chimpanzees (P. t. ellioti) from western chimpanzees has been known for a while, the fine structures within P. t. ellioti population has remained under-studied. In this study, we developed the first ever ancestry informative marker (AIMs) panel that can detect the fine population structure within Nigeria-Cameroonian chimpanzees with high resolution. We compared four commonly used AIMs determining strategies, namely Infocalc algorithm, Wright’s FST, smart principal component analysis (SmartPCA) and ADMIXTURE to first identify the best approach and then developed an AIMs panel of 435 SNPs employing the consensus of the four approaches (n = 129),with additional supplements from the best two approaches (Infocalc and ADMIXTURE). To the best of our knowledge, we have developed the first-ever AIMs panel for chimpanzees, which can greatly aid in their planned reintroduction to the natural habitat, maintaining their genetic integrity through planned captive breeding, and in tracking illegal trading across the globe.
Article ID 0038 Published: 30 April 2020 RESEARCH ARTICLE
Zokor (Myospalacinae) is one of the subterranean rodents, endemic to east Asia. Due to the convergent and parallel evolution induced by its special lifestyles, the controversies in morphological classification of zokor appeared at the level of family and genus. To resolve these controversies about taxonomy and phylogeny, the phylogenetic relationships of 20 species of Muroidea and six species of zokors were studied based on complete mitochondrial genome and mitochondrial Cytb gene, respectively. Phylogeny analysis of 20 species of Muroidea indicated that the zokor belonged to the family Spalacidae, and it was closer to mole rat rather than bamboo rat. Besides, by investigating the phylogenetic relationships of six species of zokors, the status of two genera of Eospalax and Myospalax was affirmed because the two clades differentiated in phylogenetic tree represented two types of zokors, convex occiput type and flat occiput type, respectively. In addition, the two origins in Eospalax were found diverged at 3.71 million years ago (Ma) based on estimation of divergence time. It is suggested that the climate and ecology changes caused by the Qinghai-Tibet Plateau uplift event in 3.6 Ma led to the inner divergence of Eospalax. The intraspecific phylogenetic relationships of partial zokors were well resolved, the two clades of Eospalax cansus represented two geographical populations, respectively, and the divergent pattern of Eospalax baileyi was characterized by allopatric divergence spatially. In this study, we explored the taxonomic status and phylogenetic relationships of Myospalacinae at the molecular level. These works would be significant to understanding the evolutionary process and to clarify the mechanism of differentiation ofMyospalacinae.
Article ID 0037 Published: 29 April 2020 PERSPECTIVES
Coronavirus disease 2019 was first reported from Wuhan district of China and has spread to 210 countries across the world claiming over 97,602 human lives as on 10 April 2020 by 21:06 pm. Currently, there is no specific treatment for this virus and the treatment is mainly relied on controlling symptoms. Here we discuss our current understanding of SARS-CoV-2 with respect to its receptor recognition and how this knowledge could be useful in treatment using clinically known inhibitory drugs. We have also discussed the diagnosis, treatment and preventive measures that are currently being employed for controlling further spread of the virus.
Article ID 0036 Published: 25 April 2020 RESEARCH NOTE
The Amorphophallus genus is a perennial herb which belongs to the family Araceae. There are more than 170 species in this genus, which is widely distributed in tropical and subtropical areas. As a kind of food and medicine Amorphophallus has been used for more than 2000 years in China. Because of the high content of konjac glucomannan (KGM) and dietary fiber, it has attracted more attention worldwide. In this article, the DNA contents of A. konjac, A. albus and A. bulbifer in China, A. albus, A. paeoniifolius and A. muelleri in Indonesia were estimated by using flow cytometry. In the samples of China, the DNA contents were 12.95 ± 0.73 pg/2C in A. konjac, 10.51 ± 0.05 pg/2C in A. albus and 17.61 pg/2C in A. bulbifer, and for Indonesia, 14.16 ± 0.48 pg/2C in A. albus (flowering), 8.49 ± 0.2 pg/2C in A. paeoniifolius and 17.84 ± 1.46 pg/2C in A. muelleri were used. Interspecific variation was found significantly (P<0.01), suggesting that DNA content might be a parameter that can be used to differentiate the species. Intraspecific variation has also been found significantly (P<0.01), whether in the same region or between two regions. As far as we know, this is the first report ongenome size estimation of the A. konjac, A. albus and A. muelleri using flow cytometry. Understanding the genome size of Amorphophallus species will help to sequence the genome and analyse the genetic diversity, evolutionary relationship and geographical variation pattern of Amorphophallus species.
Article ID 0035 Published: 22 April 2020 RESEARCH ARTICLE
Meta-analysis provides a systematic access to the previously studied microarray datasets that can recognize several commonsignatures of stresses. Three different datasets of abiotic stresses on rice were used for meta-analysis. These microarray datasets were normalized to regulate data for technical variation, as opposed to biological differences between the samples. A t-test was performed to recognize the differentially-expressed genes (DEGs) between stressed and normal samples. Gene ontology enrichment analysis revealed the functional distribution of DEGs in different stressed conditions. Further analysis was carried out using software RICE NET DB and divided into three different categories: biological process (homoiothermy and protein amino acid phosphorylation), cellular component (nucleus and membrane), and molecular function (zinc ion binding ad DNA binding). The study revealed that 5686 genes were constantly expressed differentially in Oryza sativa (2089 upregulated and 3597 downregulated). The lowest P value (P = 0.003756) among upregulated DEGs was observed for naringenin, 2-oxoglutrate 3-dioxygenase protein. The lowest P value (P = 0.002866816) among the downregulated DEGs was also recorded for retrotransposon protein. The network constructed from 48 genes revealed 10 hub genes that are connected with topological genes. These hub genes are stress responsive genes that may also be regarded as the marker genes for drought stress response. Our study reported a new set of hub genes (reference genes) that have potentially significant role in development of stress tolerant rice.
Article ID 0034 Published: 20 April 2020 RESEARCH ARTICLE
MADS-box genes interact with TB1 to regulate plant organ morphogenesis. In rice, OsMADS57 interacts with OsTB1 to control OsD14 transcription. In this study, we aimed to determine the relationships among these genes in barley. We identified a natural mutant of HvTB1 (HvTB1x) formed by a C→A transition at position 230, which resulted in a premature stop codon. We cloned the HvMADS57 and HvD14 genes and studied their expression in the tb1 mutant. The results showed that tHvMADS57 is a MIKCc-type MADS-box gene, and the expression levels of both HvMADS57 and HvD14 were significantly reduced in the tb1 mutant when compared to those in the wildtype gene. These results indicate that, HvMADS57 regulates plant growth and development by interacting with HvTB1 to suppress the transcription of HvD14 in barley which is similar to the relationships among the orthologs of these genes in rice.
Article ID 0033 Published: 20 April 2020 RESEARCH ARTICLE
Nephrotic syndrome (NS) is considered as a primary disease of the kidney that represents a heterogeneous group of glomerulardisorders occurring mainly in children. It is generally divided into steroid-sensitive and steroid-resistant forms, depending upon the patient’s response to steroid therapy. Among the genes involved, the NPHS2 gene has been reported as the causative gene in steroid resistant form of nephrotic syndrome. In the present study, heterozygosity rate, allelic frequency and linkage of rs2274625 and rs3829795 markers were investigated in the NPHS2 gene region. To determine the SNP alleles, tetra-primer ARMS PCR was used. After genotyping rs2274625 and rs3829795 polymorphic markers in 120 unrelated individuals and nine trios families, the data were analysed using various computerprograms such as UCSC Genome Browser, dbSNP and SNPper. Based on the statistical analysis of the results, for rs2274625 marker, allele frequency for C and T alleles was 97% and 3%, respectively. For rs3829795 marker allele frequency for G and A alleles was 55% and 45%, respectively. The values of heterozygosity index for the examined markers were 5% for rs2274625 and 45/8% for rs3829795. Consequently,two informative haplotypes, CG/CA, were identified in the NPHS2 gene region through combination of these two markers. Thesehaplotypes can serve as appropriate tools for the identification of heterozygous carriers and linkage analysis of nephrotic syndrome disease in the Iranian families with an affected child.
Article ID 0032 Published: 20 April 2020 RESEARCH NOTE
Pallister–Killian syndrome (PKS) is a rare genetic developmental disorder characterized, by intellectual disability, seizures,streaks of hypo- or hyperpigmentation and characteristic dysmorphic features. PKS is characterized by the presence of cytogenetic abnormality in form of a supernumerary isochromosome 12p, in a tissue limited mosaicism. The isochromosome 12p is usually not detected in karyotype done from peripheral blood. Presence of patchy pigmentary skin lesions suggest the possibility of mosaicism and karyotype from skin is done which clinches the diagnosis. We describe an infant with severe hypotonia in whom trisomy 12p was detected bychromosomal microarray performed on peripheral blood. The karyotype from blood was normal and combining this information with three copies of 12p in microarray suggests the possibility of tetrasomy12p in mosaic form. The infant did not have any skin patchy pigmentary changes and malformations and hence, the diagnosis of PKS was not clinically suspected. Cytogenetic microarray is the first test for evaluation of cases with developmental delay and intellectual disability, PKS diagnosis may come as a surprise in unsuspected caseswithout characteristic skin pigmentary abnormality and malformations.
Article ID 0031 Published: 19 April 2020 RESEARCH ARTICLE
miRNAs are important regulators of plant gene expression. There are few studies on the regulation of miRNAs in Lonicera edulis. We used high-throughput sequencing technology to analyse miRNAs in L. edulis, aiming to identify miRNAs and elucidate their function in L. edulis. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in L. edulis. A total of 51,819,072 small RNA tags with sizes ranging from 18 to 30 nt were obtained, indicating that L. edulis have a large and diverse small RNA population. Bioinformatic analysis identified 507 mature miRNAs, and 16 predicted novel miRNAs that are likely to be unique toL. edulis. Three miRNAs related to anthocyanin biosynthesis were locked by gene ontology (GO) analysis and target gene analysis. The selected three miRNAs are relatively high in the expression of L. edulis. Some of the previous studies have studied these types of miRNAs involved in the anthocyanin metabolism pathway in fruits. Among them, expression profiles of three conserved miRNAs were validated by stem loop qRT-PCR. Further, the potential target genes of conserved and novel miRNAs were predicted and subjected to GO annotation.Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were potentiallyinvolved in a wide range of metabolic pathways and developmental processes. In particular, different families of miRNAs can directly or indirectly regulate anthocyanin biosynthesis. In recent years, the research on miRNAs has become more and more clear, but the research onmiRNAs involved in the regulation of anthocyanin synthesis of L. edulis is still lagging. This study provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.
Article ID 0030 Published: 19 April 2020 RESEARCH NOTE
Niemann–Pick disease type C (NPC) is a progressive lysosomal storage disorder caused by mutations in the NPC1 (in 95% of cases) or NPC2 (in *5% of cases) genes, inherited in an autosomal recessive manner. We report the case of a 38-year-old woman with learning disorder from her first year of schooling, and could notice slow progressed cognitive impairment, social withdrawal, apathy, handwriting alterations, deterioration of language skills and dysphagia. Brain magnetic resonance imaging showed severe cerebellar atrophy, hypoplasia of the corpus callosum, asymmetric lateral ventricular enlargement, and severe enlargement of frontal and parietal subarachnoid spaces. Next generation sequencing for NPC genes (NPC1 and NPC2) detected compound heterozygous mutations in NPC1 gene, including c.1553G[A (p.Arg518Gln), paternally inherited, and c.1270C[T (p.Pro424Ser) maternally inherited. The first mutation has been already described in literature and correlated to NPC, while the second mutation is still unknown. Moreover, filipin test and quantification of plasma oxysterols confirmed NPC diagnosis. We can suggest the missense mutation c.1270C[T (p.Pro424Ser) as a new causative mutation of NPC.
Article ID 0029 Published: 10 April 2020 RESEARCH ARTICLE
Ornithine transcarbamylase deficiency is an X-linked disease with a wide range of clinical severity and manifestation age both in males and females. Here, we describe a case which is caused by a novel c.78-1G[A splice site mutation, which on mRNA level leads to a 1-bp deletion and a frameshift (c.78delG (p.C27Vfs*11)) in OTC exon 2 in a young girl. The same mutation has been detected in a mosaicstate in her asymptomatic father.
Article ID 0028 Published: 10 April 2020 RESEARCH ARTICLE
Many studies on forensic entomology have focussed on Diptera and lack the Hymenopteras population. Nonetheless, hymenopterans are part of the entomofaunal colonization of a corpse. Morphologically, it is difficult to identify and distinguish between them. In this study, using mitochondrial DNA knowledge, the molecular analysis was performed to classify the recovered species of hymenoptera collected from rabbit carcass, quickly and accurately. A molecular identification method with a 251-bp fragment of the 16S ribosomal gene RNA (16S rRNA) from a single ant species was evaluated. The maximum likelihood method analysis has recovered a generally well-supported phylogeny, with most taxa and species groups currently being recognized as monophyletic. The aculeate consistsof some Hymenoptera’s best known. Their sister group has traditionally been considered in Ichneumonoidea. In addition, Trigonaloidea was found as the aculeates’ sister group and Crabronidae in Apoidea forming the Formicidae’s sister group. These results will play an important role in the implementation of the Saudi database forensically relevant ants.
Article ID 0027 Published: 7 April 2020 RESEARCH NOTE
Karyotyping is one among the culling parameter used for taking up culling decisions. Cytogenetic screening of breeding bulls has been recommended to screen for chromosomal abnormalities before semen production in artificial insemination. The chromosomal analysis of a Holstein Friesian crossbred bull revealed the presence of acrocentric Y-chromosome, which was further confirmed by CBGbanding. The shape of the Y-chromosome determining that male line used for crossbreeding was from indigenous origin. Karyotyping is a best and reliable technique for the identification of crossbred calves born to the indigenous bulls.
Article ID 0026 Published: 19 March 2020 RESEARCH ARTICLE
Intracellular double-stranded RNA (dsRNA) is a chief sign of replication for many viruses. Pattern recognition receptors(PRRs) of the innate immune system detected the dsRNA and initiate the antiviral responses. Retinoic acid-inducible gene I (RIG-I), a member of PRRs, plays an essential regulatory role in dsRNA-induced signalling. In this study, the full-length complementary DNA (cDNA) of duck RIG-I (duRIG-I) was cloned using the reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of the cDNA ends (RACE). The cDNA of duRIG-I contained 97-bp 5'UTR, 141-bp 3'-UTR and 2802 bp complete open-reading frame (ORF) encoding 933 amino acids. Multiple sequence alignments showed that duRIG-I shared high similarity with RIG-I from other vertebrates. Quantitative real-time PCR (qRT-PCR) analysis revealed that duRIG-I mRNA was expressed in all tested tissues, with high levels in the liver, heart, spleen, kidney and thymus, while lower in the duodenum. duRIG-I could be induced by treatment with poly(I:C). Further, overexpression of duRIG-I significantly activated the transcription of poly(I:C)-induced IFN-b, IRF7, TRIF, Mx, STAT1 and STAT2 mRNA, and duRIG-I knockdown showed the opposite results. Overall, our results suggested that duRIG-I could be an important receptor for mimicking antiviral state in duck, which warrant further studies to show the possible mechanism.
Article ID 0025 Published: 19 March 2020 RESEARCH NOTE
Goat is the most preferred domesticated animal in Indian subcontinent. However, the climatic change-induced heat stresscauses a formidable challenge for maintaining optimum productivity. G protein subunit alpha i3 (GNAI3) is one of the genes that may have significant role in heat tolerance mechanism in goats. The caprine GNAI3 gene was searched for homology analysis and its three dimensional protein structure was predicted followed by its validation through in silico approach. Nucleotide sequence-based phylogenetic tree analysis showed that the caprine GNAI3 gene has close evolutionary relationship with that of Ovis aries. Homology modelling of caprine GNAI3 protein was done in MODELLER 9.18 (P1), PHYRE2 (P2), GENO3D (P3) and SWISS MODEL (P4). The modelled structures were further validated after observing the Ramachandran and hydrophobicity plots. In the best of three dimensional protein structure (P4 as produced by SWISS MODEL), 330 (98.8%), three (0.9%) and one (0.3%) amino acid residues were found in favoured region, allowed region and outlier region, respectively. Degree of hydrophobicity of the generated protein structures revealed the presence of alternate hydrophobic and hydrophilic regions. The ligand receptor interaction site of the predicted 3D model was traced out using Discovery Studio 3.5. STRING database revealed protein interactions with Plcb1, Plcb2, Plcb3 and other proteins of G family such as Gnb1, Gnb2, Gnb3,Gnb4, Gng2, Gng4 and Gpsm1. KEGG pathway maps revealed interaction with eNOS, iNOS, VEGF and MAPK, which are reported to be transcribed in response to heat stress. Thus, caprine GNAI3 can be used as a possible biomarker for studying heattolerance mechanism in goats.
Article ID 0023 Published: 12 March 2020 RESEARCH ARTICLE
Laccases (LACs) are versatile enzymes that catalyze oxidation of a wide range of substrates, thereby functioning in regulation of plant developmental processes and stress responses. However, with a few exceptions, the function of most LACs remains unclear in plants. In this study, we newly identified 4, 12, 22, 26, 27, 28 and 49 LAC genes for Physcomitrella patens, Amborella trichopoda, Zeamays, Ricinus communis, Vitis vinifera, Triticum aestivum and Glycine max, on the basis of exhaustive homologous sequence searches. In these plants, LACs differ greatly in sequence length and physical properties, such as molecular weight and theoretical isoelectric point (pI), but majority of them contain a signal peptide at their N-terminus. The originality of LACs could be traced back to as early as the emergence of moss. Plant LACs are clearly divided into seven distinct classes, where six ancient LACs should be present prior to the divergence of gymnosperms and angiosperms. Functional divergence analysis reveal that functional differentiation should occur among different groups of LACs because of altered selective constraints working on some critical amino acid sites (CAASs) within conserved laccase domains during evolution. Soybean and maize LACs have significantly different exon frequency (6.08 vs 4.82), and they are unevenly distributed and tend to form gene clusters on some chromosomes. Further analysis shows that the expansion of LAC gene family would be due toextensive tandem and chromosomal segmental duplications in the two plant species. Interestingly, *81.6% and 36.4% of soybean and maize LACs are potential targets of miRNAs, such as miR397a/b, miR408d, or miR528a/b etc. Both soybean and maize LACs are tissue specifically and developmental-specifically expressed, and are in response to different external abiotic and biotic stressors. These results suggest a diversity of functions of plant LAC genes, which will broaden our understanding and lay solid foundation for further investigating their biological functions in plants.
Article ID 0022 Published: 6 March 2020 RESEARCH ARTICLE
Major histocompatibility complex (MHC) polymorphisms are associated with animal and human diseases. However, only a few studies have reported an association between MHC polymorphisms and mycoplasma ovipneumonia (MO). In the present study, three resistance/susceptibility genotypes associated with MO were identified by polymerase chain reaction-restriction fragment length polymorphism genotyping, assessing the clinical and pathological features, and examining the immune factors. The current results showed that MvaI bb and HaeIII ee were dominant genotypes in the susceptible Hu population, while MO-resistant populations, Dorper and D 9 H hybrids, were dominated by the MvaI cc and HaeIII dd genotypes, suggesting that MvaI cc and HaeIII dd genotypes might be associated with the trait of MO resistance. Further, the clinical symptoms and pathological morphology in the susceptibility group infected with MO were more severe than those in the resistant groups infected similarly. The data on the changes in the immune factor responses were utilized to deduce the molecular mechanism underlying the MO resistance/susceptibility. The results showed that the susceptible genotypes promote the inflammatory responses by inducing a high expression of TNFa, IFNc, IL-4, IL-6, and IL-1b, while the resistant genotypes inhibit the inflammatory response by increasing the expression of IL-2 and IL-10 significantly. This finding would provide the theoretical guidance for propagating sheep breeds that are highly resistant to MO.
Article ID 0021 Published: 6 March 2020 RESEARCH ARTICLE
Lentil is one of the most important food legume species, however its genetic and genomic resources remained largely uncharacterized and unexploited. In the past few years, a number of genetic maps have been constructed and marker resources have been developed in lentil. These resources could be exploited for understanding the extent and distribution of genetic variation in genus Lens andalso for developing saturated and consensus genetic maps suitable for quantitative trait loci (QTL) mapping and marker-assisted selection.The present study aims to enrich polymerase chain reaction-based linkage map of F10 recombinant inbred lines (RILs) population of 94 individuals derived from cross WA8649090 9 Precoz and identification of QTLs linked to early plant vigour traits. Of the 268 polymorphic markers (93 simple sequence repeats (SSR), three inter-simple sequence repeats (ISSRs) and 172 random amplified polymorphic DNA (RAPDs)), 265 (90 SSRs, three ISSRs and 172 RAPDs) were mapped on seven linkage groups, varying in length between 25.6 and 210.3 cM, coverage of 809.4 cM with an average marker spacing of 3.05 cM. The study also reported assigning of 24 new cross-genera SSRs of Trifolium pratense on the present linkage map. The RILs along with the parents were screened for shoot length, root length, seedling length, dry weight, number of leaves and number of branches based on two replications under polyhouse conditions. A QTLhotspot consisting of six QTLs for shoot length (cm), root length (cm) and seedling length (cm) was observed between a map distances of56.61 and 86.81 cM on LG1.
Article ID 0020 Published: 6 March 2020 RESOURCES
Temminck’s ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck’s ground pangolin using next-generation sequencing. The markers were also optimized for crossamplification in other African species. All the markers amplified successfully in Temminck’s ground pangolin with allelic polymorphisms observed in 87% of the markers in giant pangolin (S. gigantea) whereas 60% of the markers were amplified polymorphic loci in both whitebellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Analysis of diversity estimates showed moderate levels of variability in Temminck’s ground pangolin (Na = 5; Ho = 0.559), giant pangolin (Na = 4.909; Ho = 0.514) and white-bellied pangolin (Na= 2.686; Ho = 0.541) with lower values being observed in black-bellied pangolin (Na = 3; Ho = 0.242). This study provides data of the first available STR markers which was amplified in all four African pangolin species that can now be used in conservation genetic and evolutionary aspects of population histories.
Article ID 0019 Published: 6 March 2020 Research Article
Oil palm (Elaeis guineensis Jacq.) is a perennial vegetable and a high oil-yielding crop (4–6 t/ha). There is a large scope for increasing the oil yield by selecting elite planting material for breeding programme in germplasm evaluation, characterization and utilization. In the present study, a diverse range of 150 oil palm genotypes were characterized using 12 quantitative variables with 54genomic microsatellite markers. A wide variation was observed in the morphological traits among indigenous populations. Highly significantand positive correlations were observed between vegetative dry matter (VDM) and total dry matter (TDM) (0.862), and height and height increment (0.838). The first two principal component analyses explained 67.7% of total variation among morphological traits. The genotypes IC0610001-59 (Pune-2) and IC0610001-60 (Pune-2) were found highly promising based on less height increment, more TDMwith high yield. For the mapping study, general linear model (GLM) approach, quantitative-trait loci (QTL) for annual height increment, number of bunches, bunch yield and bunch index were linked to simple-sequence repeat (SSR) loci mEgCIR3649 with phenotypic variance of 15.08, 10.43, 11.74, 15.39. TDM and VDM were linked to mEgCIR0192 (27.34 and 24.19%), mEgCIR3684 (16.84 and 18.30%), SPSC00163 (18.8 and 15.39%) and mEgCIR0555 (16.47 and 18.81%), with at a significant threshold (P) level of B0.001 and by mixed linear model (MLM) approach. TDM was linked to mEgCIR0555 with phenotypic variance of 20.72%, bunch yield and bunch index were linked to mEgCIR2813 at phenotypic variance of 17.11% and 12.88%, respectively, at a significant threshold (P) level of B0.01.
Article ID 0018 Published: 2 March 2020 RESEARCH ARTICLE
In human gamete development, the important period is spermatogenesis, which is organized by specific genes on Y chromosome. In some cases, the infertile men have shown microdeletions on Y chromosome, which seemed as if the structural chromosome variance is linked to the reduction of sperm count. This study aimed to determine the frequency and patterns of Y chromosome microdeletions in azoospermia factor (AZF) of Iraqi infertile males. Here, 90 azoospermic infertile males as a study group and 95 normal fertile males as control group were investigated for the microdeletion of AZF loci using numerous sequence-tagged sites. Of these 90 infertile male patients, 43 (47.8%) demonstrated Y chromosome microdeletions, in which AZFb region was the most deleted section inazoospermia patients (33.3%) followed by deletions in the AZFc region (23%), while there were no microdeletion in the AZFa region. The largest microdeletion involved in both AZFb and AZFc was detected in six azoospermic patients (6.7%). The present study demonstrated a high frequency of Y chromosome microdeletions in the infertile Iraqi patients which is not reported previously. The high frequency of deletions may be due to the association of ethnic and genetic factors. PCR-based Y chromosome screening for microdeletions has a potential to be used in infertility clinics for genetic counselling and assisted reproduction.
Article ID 0017 Published: 21 February 2020 RESEARCH ARTICLE
The phylogenetic relationships among the major groups of Pulmonata were studied by the information derived from a concatenated dataset consisting of mitochondrial (16S and COI) and nuclear (18S and 28S) markers. Heterobranchia are recovered as monophyletic. Euthyneura as paraphyletic due to the emergence of taxa from Opisthobranchia and lower Heterobranchia. The major groupsof Pulmonata, namely Stylommatophora, Veronicellidae, Onchidiidae, Otinoidea, Siphonarioidea and Hygrophila are recovered as monophyletic. Monophyly of Basommatophora was not confirmed due to the variable position of Siphonarioidea and Amphiboloidea. Evolutionary divergence times for different taxa were also estimated using a relaxed molecular clock method in Bayesian evolutionary analysis by sampling trees (BEAST). The common ancestor of Heterobranchia and Caenogastropoda was originated in the Silurian periodand the common ancestors of Euthyneura and Pulmonata were originated in the Carboniferous and lower Triassic periods, respectively.
Article ID 0016 Published: 10 February 2020 RESEARCH NOTE
Trinket cattle are the inhabitant of a small island called Trinket, which is one of the picturesque islands of Andaman. This herd is thought to be of Danish leftover during their dynasty in Nicobar archipelago. When the island was abandoned by foreign invaders, indigenes utilized the animals for the purpose of meat. As a result, the cattle became semi-feral in nature. After the Great Sumatra earthquake and tsunami of Indian Ocean in 2004, Trinket island was left abandoned by indigenes and the cattle became totally feral in nature. To trace the genetic root of the cattle, this study has been undertaken based on the sequence information of the mitochondrial D-loop and cytochrome b gene. The genomic DNA was extracted from the blood samples of the Trinket cattle and was used for amplification of mitochondrial markers, and the sequence information was generated by Sanger sequencing. The analysis of sequence information revealed that the Trinket cattle belongs to Bos indicus (I) haplotype, sub-haplotype I2. The presence of I2 sub-haplotype in Trinket cattle may be due to the expansion of this I2 haplotype towards Southeast Asian countries. This is a novel input for the formulation of breeding strategy towards conservation of eco-friendly sustainable livestock in the isolated island ecosystem.
Article ID 0015 Published: 7 February 2020 RESEARCH ARTICLE
The risk of breast cancer (BC) in women is high and many factors including genetic factors increase the risk for the disease. It is revealed that the variations of low-penetrance susceptibility genes are important for carcinogenesis as they interact with the environmental and hereditary factors. Recently, the list of BC-associated common single nucleotide polymorphisms (SNPs) and chromosomal loci in low-penetrance susceptibility genes have been expanded in genomewide association studies. FGFR2, LSP1, MAP3K1, TGFB1, TOX3, 2q35 and 8q loci variations are some examples for these common SNPs. These SNPs and their association with BC risk was investigated in many different populations. Therefore in this study, we aimed to evaluate low-penetrance susceptibility SNPs; namely FGFR2 rs1219648, rs2981579, rs2981582; MAP3K1 rs889312; TOX3 rs3803662; LSP1 rs909116, rs3817198 and SLC4A7 rs4973768 together, for the firsttime in Turkish postmenopausal oestrogen receptor positive BC cases. Following the DNA isolation, multiplex PCR and matrix-assisted laser desorption/ionization mass spectrometry with time of flight measurement (MALDI-TOF) based SNP analysis were performed. MAP3K1 rs889312 SNP demonstrated the strongest association with BC risk among the other low penetrant SNPs, it was also associated with BC risk in a dominant model. Only in a ressesive model, TOX3 rs3803662 was associated with BC risk. In addition, rs4973768 CC and rs909116 CC genotypes are correlated with higher tumour size which is not reported in the literature as yet; on the other hand there are no associations between any of the other SNP genotypes and clinopathological parameters. In our opinion, MAP3K1 rs889312 may be a good BC susceptibility biomarker candidate for Turkish population.
Article ID 0014 Published: 7 February 2020 RESEARCH ARTICLE
The aim of this study was to identify the single-nucleotide polymorphisms (SNPs) in bovine candidate genes CLEC7A, CD209 and TLR4, and explore the association between these SNPs with the occurrence of bovine paratuberculosis (PTB) disease. For this purpose, 549 animals were screened by a panel of four diagnostic tests, namely Johnin PPD test, ELISA test, faecal microscopy and IS900 blood PCR against Mycobacterium avium ssp. paratuberculosis (MAP) to develop case–control populations. SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism method. Genotypic–phenotypic associations were assessed by the PROCLOGISTIC procedure of SAS 9.3. Of the seven SNPs; rs110353594 in CLEC7A gene and rs8193046 in TLR4 gene were found to be associated with PTB. For SNP rs110353594, odds of CC and CT genotypes vs TT genotype was 1.543 (0.420–5.667; 95% CI) and 0.284 (0.104–0.774; 95% CI), respectively which means that CT genotype was more resistant than TT and CC genotypes against bovine PTB. For SNP rs8193046, odds of AA and AG genotypes versus GG genotype was 0.947 (0.296–3.034; 95% CI) and 3.947 (1.555–10.022; 95% CI), respectively, i.e. probability for getting an infection in animals with AG genotype was 3.94 times more as compared to GG genotype. Hence, a selection programme favouring CT genotype for rs110353594 and against AG genotype for rs8193046 may be beneficial for conferring resistance against bovine PTB.
Article ID 0013 Published: 30 January 2020 RESEARCH ARTICLE
Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semidesert areas of northern China, and has high medicinal value and ecological function. Previous studies have reported the chemical composition and ecological functions of S. alopecuroides. However, only a few reports are available on the genomic information of S. alopecuroides, especially the chloroplast genome, which greatly limits the study of the evolutionary relationship between other species of Papilionoideae. Here, we report the complete chloroplast genome of S. alopecuroides. The size of the chloroplast genome is 155,207 bp, and the GC content is 36.44%. The S. alopecuroides chloroplast genome consists of 132 genes, including 83 protein-coding genes, 41 transfer RNA (tRNA) genes,and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed the taxonomic position of S. alopecuroides in Papilionoideae, and the genus Sophora and the genus Ammopiptanthus were highly related. Comparative genomics analysis revealed the gene rearrangement in the evolution of S. alopecuroides. The comparison between S. alopecuroides and the species of the Papilionoideae identified a novel 23 kb inversion between the trnC-GCA and trnF-GAA which occurred before the divergence of Sophora and Ammopiptanthus of Thermopsideae. This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides.
Article ID 0012 Published: 24 January 2020 REVIEW ARTICLE
Mutation and recombination are primarily responsible for generating the genetic variability in natural populations of microorganisms, plant and animal species including humans. Upon such genetic variations, elemental forces of evolution such as natural selection, random genetic drift and migration operate to bring about micro-evolutionary changes. Recombination or crossing-over produces new combinations of genes due to interchange of corresponding segments between nonsister chromatids of homologous chromosomes, thus, it is an important evolutionary factor. Since the time of T. H. Morgan, Drosophila has been subjected to extensive investigations on crossing over while employing a number of markers, which were used for gene mapping. Interestingly, recombination occurs in females of D. melanogaster but not in males. Later on, male crossing over was investigated in various species and its occurrence was reported in D. melanogaster, D. ananassae, D. simulans, D. willistoni, D. littoralis and D. bipectinata. Recombination occurs at very low rate in all these species except for D. ananassae, which shows spontaneous male crossing over in appreciable frequency, which is meiotic in origin. This unusual phenomenon in D. ananassae is influenced by various genetic factors as well as it shows strain variation as far as frequency of male recombination is concerned. Further, the presence of chiasmata during meiosis in males at a frequency capable of accounting for the observed recombination frequency extends evidence for meiotic origin of recombination in males of D. ananassae.
Article ID 0011 Published: 20 January 2020 RESEARCH ARTICLE
The endangered medicinal plant Glehnia littoralis is one of the important natural source of furanocoumarin, which has been used as mucolytic, antitussive, antitumour and antibacterial. However, the genetic information of furanocoumarin biosynthesis in G. littoralis is scarce at present. The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathwayof furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. Further, the CYP450 genes were mined using phylogenetic analyses using MEGA 6.0 software. Atotal of 156,949 unigenes were generated, of which 9021 were differentially-expressed between leaves and roots. A total of 82 unigenes encoding eight enzymes in furanocoumarin biosynthetic pathway were first obtained. Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. Twenty-six candidate CYP450 unigenes expressed abundantly in roots and were chiefly concentrated in CYP71, CYP85 and CYP72 clans. Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. The transcriptome of G. littoralis was characterized which would help to elucidate the furanocoumarin biosynthetic pathway in G. littoralis and provide an invaluable resource for further study of furanocoumarin.
Article ID 0010 Published: 20 January 2020 RESEARCH ARTICLE
Class III peroxidase (CIII prx) is a plant-specific multigene family that regulates the physiological and stress responses. This research aimed to exhaustively annotate and analyse the CIII prx family in sweet orange and to explore the regulated expression profiles by Xanthomonas citri subsp. citri (Xcc) and plant hormones. We further assessed the relationship between CIII prxs and citrus bacterial canker. The phylogeny, gene structure, conserved motifs, gene duplications and microsynteny of the CIII prx family were analysed. Expression profiles of specific CsPrxs induced by Xanthomonas citri subsp. citri and plant hormones were detected by quantitative reverse transcription-polymerase chain reaction. Subcellular localization was analysed through transient expression assessments. A total of 72 CIII prx members were identified from the genomes of sweet orange. In all chromosomes of sweet orange, the CsPrxs could be detected except in chromosome 8. In addition, three segmental duplications, four tandem duplications and 11 whole-genome duplications occurred among the CsPrxs, contributing to the family size expansion. From the Ka/Ks ratios, 15 of 18 duplicated CsPrxs pairs have experienced purifying selection process. A total of 15 conserved motifs were detected in CsPrxs, four of which were detected in all complete CsPrxs. A total of 12 expressed genes were identified from the EST database. The expression trends of 12 CsPrxs were differently expressed at different stages of infection by Xcc, five of which were potential candidate genes involved in Xcc resistance. These genes could be induced by salicylic acidand methyl jasmonate, and were extracellular proteins. These results further support our understanding of CIII prxs in citrus, particularly incitrus bacterial canker studies.
Article ID 0009 Published: 20 January 2020 RESEARCH ARTICLE
The sum of squared score (SSU) and sequence kernel association test (SKAT) are the two good alternative tests for genetic association studies in case–control data. Both SSU and SKAT are derived through assuming a dose-response model between the risk of disease and genotypes. However, in practice, the real genetic mode of inheritance is impossible to know. Thus, these two tests might losepower substantially as shown in simulation results when the genetic model is misspecified. Here, to make both the tests suitable in broad situations, we propose two-phase SSU (tpSSU) and two-phase SKAT (tpSKAT), where the Hardy–Weinberg equilibrium test is adopted to choose the genetic model in the first phase and the SSU and SKAT are constructed corresponding to the selected genetic model in the second phase. We found that both tpSSU and tpSKAT outperformed the original SSU and SKAT in most of our simulation scenarios. Byapplying tpSSU and tpSKAT to the study of type 2 diabetes data, we successfully identified some genes that have direct effects on obesity. Besides, we also detected the significant chromosomal region 10q21.22 in GAW16 rheumatoid arthritis dataset, with P<10-6. These findings suggest that tpSSU and tpSKAT can be effective in identifying genetic variants for complex diseases in case–control association studies.
Article ID 0008 Published: 20 January 2020 RESEARCH ARTICLE
The base composition of the chloroplast genes is of great interest because they play a highly significant role in the evolutionary development of the plants. Evaluation of the 48 chloroplast protein-coding genes of Hemiptelea davidii showed that the average GC content was about 37.32%, while at the third codon base position alone the average GC content was only 27.80%. The 48 genes were classified into five groups based on the gene function and each group displayed specific codon characteristics. Based on the relative synonymous codon usage analysis, a total of 30 high-frequency codons and 11 optimal codons were identified, most of them ended with A or T. Neutrality plot, ENC-plot and PR2-plot analyses showed that the codon usage bias of the chloroplast genes of H. davidii was greatly influenced by natural selection pressures. Meanwhile, the frequency of codon usage of chloroplast genes among different plant species displayed similarities, with some synonymous codons were preferred to be used in H. davidii. In this study, the codon usage pattern of the chloroplast protein coding genes of H. davidii provides us with a better understanding of the expression of chloroplast genes, and may advice the future molecular breeding programmes.
Article ID 0007 Published: 10 January 2020 RESEARCH ARTICLE
MARÍA ELENA RODRÍGUEZ-GARCÍA FRANCISCO JAVIER COTRINA-VINAGRE ELENA ARRANZ-CANALES ANA MARTÍNEZ DE ARAGÓN LAURA HERNÁNDEZ-SÁNCHEZ FÁTIMA RODRÍGUEZ-FORNÉS PATRICIA CARNICERO-RODRÍGUEZ MONTSERRAT MORALES-CONEJO ELENA MARTÍN-HERNÁNDEZ FRANCISCO MARTÍNEZ-AZORÍN
We report the case of a Caucasian Spanish boy, who showed profound neonatal hypotonia, feeding difficulties, apnea, severe developmental delay, epilepsy, bilateral convergent strabismus, poor verbal language development and a large brainstem. Whole-exome sequence uncovered a novel de novo mutation in the purine-rich element binding protein A gene (PURA; NM_005859.4:c.72del:p.(-Gly25AlafsTer53)) that encodes the transcriptional activator protein Pur-alpha (PURA). Mutations in this gene have been identified in patients with PURA syndrome, a rare disorder characterized by an early hypotonia, developmental delay, severe intellectual disability with or without epilepsy, and disability in expressive language development. Although, up to 75 cases have been identified worldwide, to the best of our knowledge, this is the first patient described with a brainstem larger than normal. In conclusion, our data expand both geneticand phenotypic spectrum associated with PURA gene mutations.
Article ID 0006 Published: 10 January 2020 RESEARCH ARTICLE
The CGG repeats in the FMR1 gene expand in patients with fragile X syndrome, fragile X-associated tremour/ataxia syndrome and fragile X-associated primary ovarian failure. In this study, the CGG repeats in the FMR1 gene were studied in 449 males and 207 females using traditional polymerase chain reaction and triplet repeat primed PCR methods, also 18 CVS samples (six males and 12 females) were tested for prenatal diagnosis. Further, methylation sensitive multiplexed ligation dependent probe amplification was performed on some samples to confirm the results. Regarding the male patients, 1.1% and 9.7% had premutation (PM) and full mutation (FM) alleles, respectively. Also three (0.66%) male patients were mosaic for PM and FM alleles. Among females, 1.9% were GZ carriers and 5.8% were PM carriers. Prenatal diagnosis resulted in detection of two PM and one FM males as well as one FM carrier female. Our results were in concordance with the previously published results.
Article ID 0005 Published: 9 January 2020 RESEARCH ARTICLE
A set of 24 genotypes were studied for 17 grain quality characters and validated with the reported associated rice microsatellite markers with grain quality characters. Using 23 polymorphic markers distributed across 11 chromosomes marker-trait associations were studied. The percentage of polymorphism information content (PIC) of the markers ranged between 54.0 and 86.7. Eight markers with >80% and seven markers with >70% of PIC were found to be efficient in differentiating the studied grain quality characters. A total of 37 significant marker-trait associations (P ≤ 0.09) were found with R2 ranging from 4.70% to 43.80%. Eight markers a (RM246, RM11, RM241, RM16427, RM421, RM3, RM234 and RM257) showed association with more than one character suggesting their utility for the selection for grain quality characters which can be deployed in the rice crop improvement programmes.
Article ID 0004 Published: 3 January 2020 RESEARCH ARTICLE
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous hereditary disease caused by the structural abnormalities and dysfunction of motile cilia. The DNAH5 is the most frequently mutated gene in PCD patients and hot spot exons were reported in this gene. Here, we aim to screen mutations in a set of five hot spot exons of DNAH5 gene in a cohort of 10 clinically diagnosed Tunisian PCD patients using an optimized polymerase chain reaction-single-strand conformational polymorphism screening technique. Only one patient harboured a novel heterozygous variant in exon 63 (c.10767A[G), which was inherited from his father. This variant activates a cryptic splicing site. No deleterious mutation has been identified while screening the exons of the remaining patients. Our results show that the reported hot spot exons of DNAH5 gene are not mutated in Tunisian PCD patients. This is probably due to the differences of ethnical background of the previously reported patients. Further investigations should be performed to identify the mutations underlying PCD in this group of patients.
Article ID 0003 Published: 9 January 2020 RESEARCH ARTICLE
Shi-related sequence (SRS) proteins are plant-specific transcription factors that play important roles in developmental processes, including regulating hormone biosynthesis, response or signal transduction. However, systematical analysis of the SRS gene family in maize has not yet been conducted. In this study, 11 SRS genes with 13 transcripts were identified and characterized. The characteristics of the gene family were analysed in terms of phylogenetic relationships, chromosome distribution and gene structure. RNA-sequencing data analysis showed that the expression patterns of SRS genes were quite different from each other in maize, indicating their divergence in function. Interestingly, the GRMZM2G077752 gene is highly expressed in senescent leaves. Using further coexpression network analysis, we determined that the module containing GRMZM2G077752 were over-represented by genes related to abscisic acid (ABA) stimulus and carbohydrate metabolic process. This result indicated that GRMZM2G077752 might perceive ABA signal and cause the activation of carbohydrate remobilization during leaf ageing. This study provides valuable information for understanding the functions of the SRS genes in maize.
Article ID 0002 Published: 1 January 2020 RESEARCH ARTICLE
Novel approaches to preterm births are underway building upon our prior discoveries and probing into unknown discovery pathways. The recent findings showed a high affinity of MMP-9 in serum and its polymorphisms for preterm birth. This study, which is a hospital-based case–control study, aims to investigate the association of MMP-1, MMP-8 and MMP-9 polymorphisms, and levels of MMP-9 in preterm birth. Increased level of MMP-9 was reported in cases as compared to control. The significant association of MMP-9 (-1562) CT (P = 0.001; OR = 1.44(CI = 0.97–2.14)) and TTgenotype (P = 0.05;OR = 2.6 (CI = 1.46–4.69)) were reported in preterm birth. Our findings suggest that the MMP-9 plays an important role in contributing preterm labour and this can be used as a diagnostic tool during pregnancy.
Article ID 0001 Published: 1 January 2020 RESEARCH NOTE
The hepatic lipase plays a central role in the lipid metabolism, catalyzing the hydrolysis of phospholipids, monoglycerides, diglycerides, and triglycerides, and acyl-CoA. It is also implied in the conversion of very low-density lipoprotein and intermediate density lipoprotein to low density lipoproteins. As a consequence, the gene encoding the hepatic lipase (LIPC) is associated with several diseases derived from the imbalance of lipids that are in general derived from the interaction between life styles and genetic architecture. Therefore, it is interesting to understand more about the characteristics of the microevolutionary processes affecting genes that, like LIPC, have a role in nutrition and lipid metabolism in human populations. We explored the selection signatures on LIPC in 26 populations, detecting three regions under recent positive selection.
Volume 99, 2020
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