Article ID 0071 Published: 16 July 2019 RESEARCH ARTICLE
Myotonia congenita (MC) is a Mendelian inherited genetic disease caused by the mutations in the CLCN1 gene, encoding the main skeletal muscle ion chloride channel (ClC-1). The clinical diagnosis of MC should be suspected in patients presenting myotonia, warm-up phenomenon, a characteristic electromyographic pattern, and/or family history. Here, we describe the largest cohort of MC Spanish patients including their relatives (up to 102 individuals). Genetic testing was performed by CLCN1 sequencing and multiplex ligation-dependent probe amplification (MLPA). Analysis of selected exons of the SCN4A gene, causing paramyotonia congenita, was also performed. Mutation spectrum and analysis of a likely founder effect of c.180+3A>T was achieved by haplotype analysis and association tests. Twenty-eight different pathogenic variants were found in the CLCN1 gene, of which 21 were known mutations and seven not described. Gross deletions/duplications were not detected. Four probands had a pathogenic variant in SCN4A. Two main haplotypes were detected in c.180+3A>T carriers and no statistically significant differences were detected between case and control groups regarding the type of haplotype and its frequencies. A diagnostic yield of 51% was achieved; of which 88% had pathogenic variants in CLCN1 and 12% in SCN4A. The existence of a c.180+3A>T founder effect remains unsolved.
Article ID 0070 Published: 16 July 2019 RESEARCH ARTICLE
Somatic embryos (SE) of habanero pepper (Capsicum chinense Jacq.) represent persistent deformations in the shoot apical meristem (SAM), which inhibits their capacity to form organs and subsequently plants. In dicotyledonous plants, SAM is formed in the apex, between cotyledons and it plays a central role in postembryonic shoot organ formation. Based on the previous knowledge on the role of some families of gene in the formation, organization and maintenance of the SAM, the expression patterns of WUS, WOX2, NAM, STM, PIN1 and PIN7 genes were analysed, which would allow us to elucidate the possible implication of these genes in SAM deformations in the SE of C. chinense. The results show that the expression patterns of STM and PIN1 in the SE were completely opposite to the respective expression pattern obtained in zygotic embryos (ZE). Moreover, NAM and PIN7 showed an over accumulation of transcripts in SE, compared with ZE. This is the first time in the genus Capsicum that alterations in the expression pattern of key genes of the SE development are reported, as well as its possible implication in the persistent deformations of the SAM.
Article ID 0068 Published: 10 July 2019 RESEARCH ARTICLE
The hard clam (Meretrix petechialis) is a commercially important shellfish in China. To provide valuable insights into management and conservation of M. petechialis, we investigated the genetic variation and population structure of M. petechialis by analysing samples from nine geographical populations. In this study, the genetic diversity and differentiation of nine populations of M. petechialis were assessed using the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. A total of 90 COI sequences were obtained and each COI sequence was 699 bp in length. Fifty-one haplotypes were identified with 10 haplotypes sharedamong populations. The haplotype diversity was highest in Fujian, Panjin and Jiangsu (0.9778 ± 0.0540) and lowest in Dalian (0.7778 ± 0.1374). The nucleotide diversity was highest in Panjin (0.453401 ± 0.240463) and lowest in Jiangsu (0.006213 ± 0.004141). Neutral test (Fu’s Fs) and mismatch distribution analysis revealed that the hard clam experienced a population expansion event. Analysis of molecular variance (AMOVA) indicated that 91.7% of the genetic variance was within populations and 0.52% of the variance was among populations, demonstrating significant genetic differentiation among populations (P < 0.05). The neighbour-joining tree showed that the haplotypes were not clustered according to the geographical location, but some haplotypes from the same or neighbouring locations grouped together. The results obtained in this study provide useful information on the genetic diversity and population structure of M. petechialis and shed light on the management and protection of resources of M. petechialis in the northwestern Pacific.
Article ID 0067 Published: 10 July 2019 RESEARCH ARTICLE
This study aims to analyse the potential relationship between single-nucleotide polymorphism (SNPs) in trace element related metabolic genes GSTM3, GSTP1, GPX1 and NKG2D and the risk of gastric cancer. A case–control study was conducted in the hospital of Xianyou, Fujian, China. In this study, a total of 299 patients with histopathological diagnosis in gastric cancer and 295 healthy control subjects were involved. Association between the SNPs in trace element-related metabolic genes and gastric cancer risk was analysed using the unconditional logistic regression model. No relationship was found between the SNPs of GSTM3 and GPX1 genes and gastric cancer risk. However, the risk of gastric cancer is related to the SNPs of NKG2D gene (rs1049174). Patients who carry the rs1049174 GG genotype have a higher incidence of the gastric cancer and a multivariate odds ratio (OR) of 1.85 (95% confidence intervals (CI): 1.02–3.38). Through haplotype analysis, two haplotypes (i.e. A_rs1746123-T_rs10431294-G_rs1049174 and T_rs1746123-T_rs10431294-C_rs1049174), OR of 0.29 (95% CI: 0.15–0.56) and 0.33, (95% CI: 0.22–0.50), respectively, were found to have lower incidence of gastric cancer. Meanwhile, another two haplotypes (T_rs1746123-C_rs10431294-C_rs1049174 and T_rs1746123-T_rs10431294-G_rs1049174), OR of 1.81 (95% CI: 1.40–2.34) and 3.09 (95% CI: 2.30–4.16), respectively, were found to have a higher incidence of gastric cancer. Further, no influence of the haplotype on the risk of cardia gastric cancer was found. However, the haplotype T_rs1746123-T_rs10431294-C_rs1049174 had lower incidence of noncardia gastric cancer by 46%. Our data showed that polymorphisms of trace element-related metabolic genes are important in gastric cancer pathology.
Article ID 0069 Published: 10 July 2019 RESEARCH ARTICLE
Genetic information of polymerase chain reaction (PCR)-based markers, one of the main tools of genetics and genomics research in wheat, have been well documented in wheat. However, the physical position in relation to these markers has not yet been systematically characterized. Aim of this study was to characterize the physical information of thousands of widely usedmolecular markers.We first assigned 2705 molecular markers to wheat physical map, of which 86.1% and 84.7% were the best hits to chromosome survey sequencing (CSS) project (CSS-contigs) and International Wheat Genome Sequencing Consortium Reference Sequence v1.0 (IWGSC RefSeq v1.0), respectively. Physical position of 96.2% markers were predicated based on BLAST analysis, were in accordance with that of the previous nullisomic/aneuploidy/linkage analysis. A suggestive high-density physical map with 4643 loci was constructed, spanning 14.01 Gb (82.4%) of the wheat genome, with 3.02Mb between adjacent markers. Both forward and reverse primer sequences of 1166 markers had consistent best hits to IWGSC RefSeq v1.0 based on BLAST analysis, and the corresponding allele sizes were characterized. A detailed physical map with 1532 loci was released, spanning 13.93 Gb (81.9%) of the wheat genome, with 9.09Mb between adjacent markers. Characteristic of recombination rates in different chromosomal regions was discussed. In addition, markers with multiple sites were aligned to homoeologous sites with a consistent order, confirming that a collinearity existed among A, B and D subgenomes. This study facilitates the integration of physical and genetical information of molecular markers, which could be of value for use in genetics and genomics research such as gene/QTL map-based cloning and marker-assisted selection.
Article ID 0063 Published: 8 June 2019 PERSPECTIVES
Article ID 0062 Published: 7 June 2019 RESEARCH NOTE
The aetiology of developmental dyslexia (DD) is complex; although candidate genes have been suggested, the molecular mechanism and risk factors remain unknown. The KIAA0319 gene is functionally related to neuronal migration and axon growth, and several studies have examined associations between KIAA0319 polymorphisms with DD, but the results remain inconsistent. The sample size affects the results of meta-analysis. The aim of this meta-analysis was to clarify the effect of KIAA0319 polymorphisms on dyslexia susceptibility according to the available evidence. All eligible case–control and transmission/disequilibrium test (TDT) studies published until March 2018 were identified by searchingMedline, PubMed, Embase, Web of Science and Chinese Biomedical Database, limited to Chinese and English language papers. Pooled odds ratios and 95% confidence intervals were calculated using STATS package v12.0. A total of 11 related studies, including 3130 cases of dyslexia and 3460 healthy control subjects, as well as four TDT studies with 842 families were included in our meta-analysis. The results indicated that the polymorphisms rs4504469, rs2038137, rs2179515, rs3212236, rs6935076, rs9461045, rs2143340 and rs761100 have no association between the polymorphisms and dyslexia risk. Three subgroup meta-analyseswere performed according to the study design, country and population. The stratified analysis revealed that the KIAA0319 rs4504469 minor allele was a risk allele t in the TDT subgroup, rs3212236 minor allele was a risk allele t in the UK subgroup and rs6935076 minor allele was a risk allele t in the Canada subgroup. Further studies with larger sample sizes that assess gene–gene and gene–environment interactions are required. The sample size of our study is larger than that of the previous studies, and the results are different from those of the previous studies.We have synthesized all the current studies on KIAA0319 and obtained reliable results.
Article ID 0061 Published: 6 June 2019 RESEARCH ARTICLE
Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity
Being an economical and nutritional crop, Capsicum appeases people’s peppery taste and is found to bewidely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.
Article ID 0060 Published: 5 June 2019 RESEARCH ARTICLE
Schizophrenia (SZ) is a debilitating mental illness with a multigenic aetiology and significant heritability. Despite extensive genetic studies, the molecular aetiology has remained enigmatic. A recent systems biology study suggested a protein–protein interaction network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominant during adolescence, often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan Atlas data allowed us to re-examine the genes present in the SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and nonpsychiatric Exome Aggregation Consortium database allowed us to identify the variants of criticality. The expression of the SZ candidate genes responsible for cognition and disease onset was studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by theprevious interactome study to 10 proteins. These proteins belonging to 81 biological pathways are targeted by 34 known Food and Drug Administration-approved drugs that have distinct potential for the treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to celecoxib pharmacodynamics, Gα signalling and cGMP-PKG signalling pathwaysthat are not known to be specific to SZ aetiology.
Article ID 0059 Published: 4 June 2019 RESEARCH ARTICLE
Several studies including genomewide association studies (GWASs) in diverse ethnic populations have reported a significant association of genetic variant rs10937405 of TP63 with nonsmall cell lung cancer (NSCLC). However, no data are available from any Indian population on the association of this variant with NSCLC. Using TaqMan genotyping chemistry, we conducted a case–control study involving 190 NSCLC cases and 400 ethnic, age-matched controls to explore the association of rs10937405 genetic variant with NSCLC in patients from north India. Our data support that the rs10937405 variant is also significantly associated with the NSCLC and is a risk factor in the north Indian populations to develop NSCLC. However, unlike most other studies, the wild-type allele T appears to be the risk allele, as its frequency was significantly higher in the cases than controls (0.439 in cases versus 0.383 in controls. OR=1.95 (1.23–3.09 at 95% CI); P value (adjusted)= 0.004). Genetic association was also observed by applying different genetic models. The present study provides important information of the genetic aetiology of NSCLC and strengthens GWAS findings, highlighting the role of TP63 in lung cancer risk.
Article ID 0058 Published: 3 June 2019 RESEARCH ARTICLE
Screening of trait-associated molecular markers can be used to enhance the efficiency of selective breeding. Previously, we produced the first high-density genetic linkage map for the mandarin fish (Siniperca chuatsi) and identified 11 quantitative-trait loci significantly associated with growth, of which one is located within the growth hormone (GH) gene. To investigate the GH gene polymorphisms and their correlation with growth, the complete sequence was cloned and 32 single-nucleotide polymorphisms (SNPs) and one simple-sequence repeat (SSR)were identified. Of which, eight SNPs (G1–G8) and the SSR (GH-AG)were selected for genotyping and correlation analysis with growth traits in a random population. The results showed that the four novel polymorphicloci (G1, G2, G3 and GH-AG) were significantly correlated with growth traits of mandarin fish (P < 0.05). Of these, G1, G3 and GH-AG showed highly significant correlations with multiple growth traits (P < 0.01) and the combined SNP analysis showed that G1–G3 formed four effective diplotypes (D1–D4), among which D1 was highly significantly greater than D4 (P < 0.01) for some important growth traits. In conclusion, our results show that the four polymorphic loci G1–G3 and GH-AG within the mandarin fish GH gene are significantly correlated with growth traits and could be used as candidate molecular markers for selective breedingof superior varieties of mandarin fish.
Article ID 0056 Published: 1 June 2019 RESEARCH NOTE
The 16p12.2 chromosome band contains three large segmental duplications: BP1, BP2 and BP3, providing a substrate for recombination and recurrent chromosomal rearrangements. The ‘16p12.2 microdeletion’ is a recurrent deletion comprised between BP2 and BP3, associated with variable clinical findings. We identified a heterozygous 16p12.2 microdeletion spanning between BP1 and BP2 in a child evaluated for short stature and mild dyslexia. Unexpectedly, the mother carried the same deletion in the homozygous state and suffered from severe hearing loss. Detailed family history revealed consanguinity of the maternal grandparents. The 16p12.2 microdeletion is a rare condition and contains only three genes: METTL9, IGSF6 and OTOA of which the OTOA is considered responsible for DFNB22 hearing loss (MIM: 607039) under its homozygous condition. A number of OTOA mutations have been described, whereas very few cases of a 16p12.2 microdeletion similar to that observed in our family have been reported. In conclusion, we describe a rare ‘distal 16p12.2microdeletion’ widening the phenotypic spectrum associated with the recurrent 16p12.2 microdeletion and support the causative role of OTOA microdeletion in hearing impairment.
Article ID 0057 Published: 1 June 2019 RESEARCH ARTICLE
Ceratitis capitata is one among the most destructive and economically important agricultural pests worldwide. Despite its economic significance, the population structures of this pest have remained relatively unexplored in the eastern Mediterranean basin. Using two mitochondrial markers, the present study aimed to examining the population genetic structure and diversity of C. capitata populations in Turkey, the region that covers a large part of the eastern Mediterranean area. Our results revealed that the Turkish Mediterranean fruit fly populations are characterized by low levels of genetic diversity and limited population differentiation. For comparison purposes, wemerged the sequences identified in the present study with the previously reported sequences from acrossthe world into the data matrix. The haplotype network showed that, unlike the African samples the Mediterranean samples and samples from the new world (America, Pacific region and Australia) did not show any clear pattern of geographical structuring, which indicates that the Mediterranean basin, particularly the eastern Mediterranean region populations, may have played a moreimportant role in the colonization of C. capitata populations to the new world. The results also revealed a close genetic relationship between the Turkish and Iranian populations, suggesting that the Iranian C. capitata populations probably originated from Turkey.
Article ID 0055 Published: 1 June 2019 RESEARCH NOTE
Restorer line F6 (Oryza sativa L. ssp. indica) has been widely used in hybrid rice breeding systems in southern China. However, line F6 is susceptible to drought stress, which restricts its utilization in many areas. Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) has strong drought stress resistance, but the molecular factors responsible for drought resistance in DXWR remain unknown. In this study, we used the combination of phenotypic selection and molecular marker-assisted selection (MAS) to improve the drought stress resistance of line F6 by introgression of qSDT12-2, a large effect drought stress-related quantitative trait locus identified in DXWR. Molecular MAS was carried out using linked marker RM1226, which is associated with qSDT12-2. Genomic background assessmentwas performed using 112 polymorphic markers. Finally, a stable drought stress-resistant backcross inbred line (BIL) was developed from a BC5F5 population, termed BIL627. Genetic constitution analysis revealed that the genome of BIL627 is almost identical (99.1%) to that of the restorer line F6. Further, BIL627 showed no yield penalty and no decrease in restorationability under normal conditions. Taken together, our findings reveal the intrinsic value of using genetic resources present in wild species of Oryza to improve undesirable traits found in cultivated rice.
Article ID 0054 Published: 30 May 2019 RESEARCH NOTE
Neuronal migration disorders (NMDs) are a heterogeneous group of conditions caused by the abnormal migration of neuroblasts in the developing brain and nervous system, resulting in severe developmental impairment, intractable epilepsy and intellectual disability (Spalice et al. 2009). To date, many genes have been identified as the leading cause of migration defects, i.e. agyria/pachygyria, polymicrogyria, heterotopias, agenesis of the corpus callosum and agenesis of the cranial nerves (Spalice et al. 2009). Here, we present a patient with early infantile epileptic encephalopathy (Ohtahara syndrome) with seizure onset on the first dayof life, severe developmental delay and an abnormal brain MRI with excessive folding of small, fused gyri and bilateral perisylvian polymicrogyria, suggestive of neuronal migration disorder. To clarify the unknown aetiology, we conducted whole-exome sequencing, which detected a de novo missense variant (c.5308A>T; p.(Met1770Leu)) in the SCN2A gene. This is a report of SCN2A gene variant identified in a patient with neuronal migration disorder which could further expand the phenotypic spectrum of these genetic disorders.
Article ID 0053 Published: 23 May 2019 RESEARCH ARTICLE
In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated thatthere is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had α-turns and β-turns, and α-amphipathic regions up to 129, 138–156 and 151–155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima’s D value was negative (−2.404165), indicative of negative selection pressure.
Article ID 0052 Published: 21 May 2019 RESEARCH ARTICLE
NAC transcription factors (TFs) are master regulators of environmental stresses exerting a crucial role in plant growth and development. However, the studies on NAC TFs from Bambusa emeiensis are scarce. In this investigation, a novel gene from B. emeiensis encoding NAC protein was cloned and characterized. The gene was isolated based on the amino acid sequence data of stress-responsive SNAC1 of rice, named ‘BeSNAC1 (accession no. MG763922)’. The full-length sequence of 1681 bp was found to contain an open-reading frame of 912 bp that encode a protein of 303 amino-acid residues. The multiple protein sequence alignments unveiled that BeSNAC1 contains a typical NAC domain. Additionally, the phylogenetic analysis showed that the corresponding protein belonged to the SNAC group, as it cladded with SNAC1, HvSNAC1, TaNAC2, SbSNAC1 and ZmSNAC1 proteins. Transactivation and subcellular localization assay disclosed that BeSNAC1 is a transcriptional activator localized in the cell nucleus.Moreover, the time-dependent expression pattern of BeSNAC1 was profiled under abscisic acid (ABA), polyethylene glycol 6000 (PEG-6000), NaCl, H2O2 and Na2SO4 treatments via a quantitative real-time polymerase chain reaction. The results revealed that the expression of BeSNAC1 was significantly upregulated in all treatments, a significant difference was observed under H2O2, NaCland ABA (P 0.001) and PEG and Na2SO4 (P < 0.01) treatments, respectively. Conclusively, our findings provide evidence that ‘BeSNAC1’ is a nuclear protein that might act as part of the transcription regulation complex and is involved in the ABA signalling pathway and abiotic stress tolerance mechanisms in B. emeiensis.
Article ID 0051 Published: 14 May 2019 RESEARCH NOTE
Mutations in several genes, including SERPRINF1 and COL1A1, have been associated with the development of osteogenesis imperfecta (OI). Here, we reported the co-occurrence of a rare heterozygous variant (c.167C>G p.Ala56Gly) in SERPRINF1 and a novel heterozygous mutation (c.1634G>A p.Gly545Asp) in COL1A1 in a foetus with a severe form of OI. Bioinformatics modelling revealed that the effect of the mutation on SPERINF1 is neutral. In contrast, the mutation in COL1A1 is deleterious. It is predicted to cause distortion of the α (1) chain of the type I collagen and results in structural instability of the protein. Therefore, a novel dominant variant of COL1A1 likely underlies the severe foetal pathology observed, although we do not exclude the possibility that the heterozygous mutations in SERPINF and COL1A1 may interact and co-ordinately cause pathogenesis. This novel COL1A1 mutation is recommended to be included in the diagnostic panels for OI.
Article ID 0049 Published: 13 May 2019 RESEARCH NOTE
Northern snakehead, Ophiocephalus argus Cantor, is an endemic freshwater fish in China. However, wild stocks of O. argus are dwindling sharply. Further, water conservancy projects, environmental pollution and human activities have caused the decrease of wild stocks, which has attracted much attention. Here, we have investigated the genomic information of O. argus using IlluminaHiseq 4000 sequencing. The transcriptomes of O. argus were sequenced by Illumina technology. A total of 67,564 sequences from 79,500,964 paired-end reads were generated, 33,710 unigenes were annotated based on protein databases (NCBI nonredundant (NR) databases). In total, 7182 unigenes had the clusters of orthologous group (COG) classifications, 33,710 unigenes were assigned to 59 gene ontology (GO) terms. Further, a total of 21,464 simple sequence repeats (SSRs) from 67,564 unigenes and 113,518 single nucleotide polymorphism (SNP) sites among 335 Mclean reads were yielded for O. argus based on a transcriptome-wide search. The new transcriptome data which is presented in this study for O. argus will provide valuable information for gene discovery and downstream applications, such as phylogenetic analysis, gene-expression profiling and identification of genetic markers (SSRs andSNP).
Article ID 0050 Published: 13 May 2019 RESEARCH ARTICLE
Panicle traits are the most important agronomic characters which directly relate to yield in rice. Panicle length (PL) being one of the major components of rice panicle structure is controlled by quantitative trait loci (QTLs). In our research, conducted at Research Farm of SKUAST-J, crosses of parental lines K343 and DHMAS were made for generating F2 mapping population, which were then transplanted into the field using augmented design-I. The F2 population was used for phenotypic evaluation, development of linkage map and identification of QTLs on the chromosomes by using SSR markers. A total of 450 SSR markers were used for screening both the parents of which 53 highly polymorphic markers were selected and used for genotyping of 233 genotypes of F2population. Linkage map was generated using MAPMAKER/EXP3.0 software, seven linkage groups were found distributed on 11 chromosomes of rice. QTLs were detected using QTL Cartographer (v2.5) software. Based on 1000 permutation tests, a logarithm of odds (LOD) threshold value 2.0 and 3.0 was set. Composite interval mapping was used to map QTLs in populations derived from bi-parental crosses. The phenotypic data, genotypic data and the genetic linkage map generated identified total three QTLs of which one was identified for PL qPL2, located at 85.01 cM position with 2.1 LOD value and in between the marker intervals RM324–RM208, this QTL explained the phenotype variation by 4.36%. The other two QTLs were identified for spikelet density (SD) qSD3.1 and qSD3.2, located at 28.91 and 39.51 cM, respectively, both with a flanking marker RM6832 on chromosome 3. The LOD value and phenotypic variation explained for qSD3.1 and qSD3.2 was 3.00 and 3.25; 9.70 and 12.34% respectively. The reported QTLs identified in the study suggested a less diversity in the parents used and also the rejection of not so useful markers from the used set of markers for PL and SD.
Article ID 0048 Published: 9 May 2019 RESEARCH ARTICLE
Despite the ubiquitous occurrence of heat-shock protein 60 (Hsp60) and their role in maintenance of cell activity and integrity, this protein remains poorly characterized in many of the symbiotic soil mycorrhizal fungi such as Rhizophagus irregularis. Thus, in the current study, an attempt has been made to elucidate the evolutionary history, time of divergence followed by estimation of population genetic parameters of hsp60 using R. irregularis as a model organism. Sequence alignment reported here identified several close homologues for hsp60 (gene) and Hsp60 (protein) from diverse taxa, while the output from protein-based phylogenetic tree indicates that mitochondrial Hsp60 of R. irregularis shares close evolutionary relationship with classical α-proteobacteria. This is perhaps the first line of evidence elucidating the likelihood of hsp60 from fungal taxa sharing a close evolutionary relationship with classical α-proteobacteria as a common ancestor. Comprehensive analysis of mitochondrial hsp60 from selected fungal taxa from the evolutionary point of view explains the possibility of gene duplication and or horizontal gene transfer of this gene across various fungal species. Synteny relationships and population genetics credibly explain high genetic variability associated with fungal hsp60 presumably brought by random genetic recombination events. The results presented here also confirm a high level of genetic differentiation of hsp60 among all the three fungal populations analysed. In this context, the outcome of the current study, basedon computational approach, stands as a testimony for explaining the possibility of increased genetic differentiation experienced by hsp60 of R. irregularis.
Article ID 0046 Published: 9 May 2019 RESEARCH ARTICLE
Finger millet (Eleusine coracana (L.) Gaertn.), an important C4 species is known for its stress hardiness and nutritional significance. To identify novel drought responsive mechanisms, we generated transcriptome data from leaf tissue of finger millet, variety GPU-28, exposed to gravimetrically imposed drought stress so as to simulate field stress conditions. De novo assembly basedapproach yielded 80,777 and 90,830 transcripts from well-irrigated (control) and drought-stressed samples, respectively. A total of 1790 transcripts were differentially expressed between the control and drought-stress treatments. Functional annotation and pathway analysis indicated activation of diverse drought-stress signalling cascade genes such as serine threonine protein phosphatase 2A (PP2A), calcineurin B-like interacting protein kinase31 (CIPK31), farnesyl pyrophosphate synthase (FPS), signal recognition particle receptor α (SRPR α) etc. The basal regulatory genes such as TATA-binding protein (TBP)-associated factors (TAFs) werefound to be drought responsive, indicating that genes associated with housekeeping or basal regulatory processes are activated underdrought in finger millet. A significant portion of the expressed genes was uncharacterized, belonging to the category of proteins of unknown functions (PUFs). Among the differentially expressed PUFs, we attempted to assign putative function for a few, using anovel annotation tool, Proteins of Unknown Function Annotation Server. Analysis of PUFs led to the discovery of novel drought responsive genes such as pentatricopeptide repeat proteins and tetratricopeptide repeat proteins that serve as interaction modules in multiprotein interactions. The transcriptome data generated can be utilized for comparative analysis, and functional validation of the genes identified would be useful to understand the drought adaptive mechanisms operating under field conditions in finger millet, as has been already attempted for a few candidates such as CIPK31 and TAF6. Such an attempt is needed to enhance the productivity of finger millet under water-limited conditions, and/or to adopt the implicated mechanisms in other related crops.
Article ID 0047 Published: 9 May 2019 RESEARCH ARTICLE
Whole-genome resequencing provides the opportunity to explore the genomic variations and pave way for further functional assays to map the economical trait loci. In this study, we sequenced the genomes of mixed chicken samples from a full-sib family, with feathered and unfeathered legs at an average effective depth of 4.43×, using Illumina Hiseq 2000 instruments. Over 2.1 million nonredundant short indels (1–71 bp) were obtained. Among them, 16,375 common indels that were polymorphic between the comparison groups were revealed for further analysis. The majority of the common differential indels (76.52%) were novel. Follow-up validation assays confirmed that 80% randomly selected indels represented true variations. The indels were annotated based on the chicken genome sequence assembly. As a result, 16,375 indels were found to be located within 2756 annotated genes, with only 33 (0.202%) located in exons. By integrated analysis of the 2756 genes with gene function and known quantitative trait loci, we identified a total of 24 promising candidate genes potentially affecting feathered-leg trait, i.e. FGF1, FGF4, FGF10, FGFR1, FRZB, WNT1, WNT3A, WNT11, PCDH1, PCDH10, PCDH19, SOX3, BMP2, NOTCH2, TGF-β2, DLX5, REPS2, SCN3B, TCF20, FGF3, FSTL1, WNT7B, ELOVL2 and FGF8. Our findings provide a basis for further study and reveal key genes for feathered-leg trait in chickens.
Article ID 0044 Published: 8 May 2019 RESOURCES
Rapid molecular assays for species and sex identification of swamp deer and other coexisting cervids in human-dominated landscapes of the Terai region and upper Gangetic plains, northern India: implications in understanding species distribution and population parameters
Burgeoning pressures of habitat loss is a major cause of herbivore decline across India, forcing them to coexist with humans in non-protected areas. Their conservation in such landscapes is challenging due to paucity of ecological and demographic information. The northern subspecies of swamp deer, Rucervus duvaucelii duvaucelii, is one such herbivore that lives across human dominated landscapes in Terai region and upper Gangetic plains of north India. Here, we describe species-specific molecular markers and a cervid-specific molecular sexing assay for swamp deer and four other coexisting cervids sambar, chital, barking deer and hog deer. Our markers show species-specific band patterns and a high success rate of 88.21% in large number of field collected referencesamples for all species. Faecal pellets from pilot swamp deer survey samples from upper Ganges basin show 93.81% success rate, and only 5.5% misidentification based on morphological characteristics. Our cervid-specific molecular sexing multiplex assay accurately ascertained 81.15% samples to respective sexes. These molecular approaches provide an easy, quick and cheap option to generate critical information on herbivore population parameters and aid their conservation in this mosaic of protected and non-protected grassland habitats.
Article ID 0045 Published: 8 May 2019 RESEARCH ARTICLE
Hypoplastic right heart syndrome(HRHS) is characterized by hypoplastic right ventricle (RV); Numerous transcriptional cascades in the second heart field (SHF) regulateRVdevelopment. The relationship of SHF gene variants with humanHRHS remains unknown. The whole lengths of 17 SHF genes were sequenced in 16 HRHS, and the selected single-nucleotide variants (SNVs) were then genotyped in HRHS, other congenital heart disease (CHD) and healthy control. Luciferase assay was performed to verify the effect of FOXC2: rs34221221A>GandTBX20: rs59854940C>Gat the transcription level. There were 151 (12.86%) novel SNVs after sequence analysis, of which three were in exons (one was synonymous SNV and two were nonsynonymous SNVs), two in promoter, and most SNVs (89.95%) were in intronic regions. Genotype analyses revealed that the minor alleles of FOXC2: rs34221221 A>G and TBX20: rs59854940 C>G could increase HRHS risk (P<0.05), but not in other CHD or healthy control. Luciferase assay showed that the minor G allele in rs34221221 significantly increased FOXC2 transcription while in rs59854940 it decreased TBX20 transcription significantly. Novel variants of SHF gene associated with HRHS were identified. Minor alleles in two variants from FOXC2 and TBX20 could increase the risk of HRHS.
Article ID 0041 Published: 4 May 2019 RESEARCH ARTICLE
Yak (Bos grunniens) is a unique bovine species and considered as lifeline of highlanders. The male subfertility in yak is a matter of concern that causes huge economic loses. The spermatogenesis and male reproduction machinery are critically governed by Y-linked genes which tend to acquire necessary information in the course of evolution. The Y-linked fertility genes are present in multiple copies with testis-limited expression. To understand this novel complexity, 12 male-specific region of Y chromosome (MSY) genes have been studied in the yak. Targeted genes are amplified in male and female genomic DNA and confirmed the male derived specificity. Moreover, testis and sperm-specific expressions of MSY genes are distinct among different tissues. The quantitative polymerase chain reaction results validate the expression pattern of these genes in various tissues with predominant expression intestis and sperm. The sequencing of resultant yak MSY genes gives significant result and shows similarity with cattle (Bos indicus), but few nucleotide mismatches define the proposition of infertile male in the F1 hybrid of cattle and yak. The identified MSY genes can be used to establish male-specific characteristics and to differentiate male and female yak genotypically. Further, these genes may act as valuable resources to understand the capacity of spermatogenesis, embryogenesis, cellular growth, azoospermia and malesubfertility in the yak.
Article ID 0043 Published: 4 May 2019 RESEARCH ARTICLE
The Hazaras are a distinct ethnic group from central Afghanistan and northwestern Pakistan of Mongoloid descent. Here, we sought to dissect the genetic admixture history of the Pakistani Hazaras and investigated their likely affiliation to ancient and extant West Eurasian populations. Our results indicated that the likely proportion of West Eurasian ancestry was low in the Hazaras and could be attributed putatively to a combination of Steppe populations from Early/Middle Bronze Age or Middle/Late Bronze Age and the Neolithic Iranians. Our results expand upon the current understanding and provide an improved resolution into the population history of the Pakistani Hazaras.
Article ID 0042 Published: 4 May 2019 RESEARCH ARTICLE
Diagnosis and treatment of velocardiofacial syndrome (VCFS) with variable genotypes and phenotypes are considered to be very complicated. Establishing an exact correlation between the phenotypes and genotypes of VCFS is still a challenging. In this paper, 88 Chinese VCFS patients were divided into five groups based on palatal anomalies and one or two of other four common phenotypes, and copy number variations (CNVs) were detected using multiplex ligation-dependent probe amplification (MLPA), array comparative genomic hybridization (aCGH) and quantitative polymerase chain reaction. The findings showed that palatal anomalies and characteristic malformation of face were important indicators for 22q11.2 microdeletion, and there was difference inthe phenotypic spectrum between the duplication and deletion of 22q11.2. MLPA was a highly cost-effective, sensitive and preferred method for patients with 22q11.2 deletion or duplication. Our results also firstly reported that all three patients who simultaneously exhibited palatal anomalies and cognitive disorder, without other phenotypes, have Top3b duplication, which strongly suggested thatTop3b may be a pathogenic gene for these patients. Further, the findings showed that patients with palatal anomalies and congenital heart disease or immune deficiency, with or without other uncommon phenotypes, exhibited heterogeneity in CNVs, including 4q34.1-qter, 6q25.3, 4q23, Xp11.4, 13q21.1, 17q23.2, 7p21.3, 2p11.2, 11q24.3 and 16q23.3, and some possible pathogenic genes, including BCOR, PRR20A, TBX2, SMYD1, KLKB1 and TULP4 have been suggested. For these patients, aCGH, whole genomic sequencing,combined with references and phenomics database to find pathogenic gene,may be choices of priority. Taking these findings together, we offered an alternative method for diagnosis of Chinese VCFS patients based on this phenotypic strategy.
Article ID 0040 Published: 27 April 2019 RESEARCH NOTE
The Hardy–Weinberg equilibrium (HWE) model states that allele and genotype frequencies in a population will remain constant for generations in the absence of evolutionary effects. A goodness-of-fit test can be used to test if a population is significantly different from the expectations of HWE. Pearson statistics are commonly used in goodness-of-fit tests for testing the HWE. In this paper, a simulation study is carried out to evaluate the performance of power divergence statistics under different sample sizes, effect sizes and minor allele frequencies. A real genotype dataset is also analysed to compare the results of several power divergence test statistics.
Article ID 0039 Published: 26 April 2019 REVIEW ARTICLE
The process of development of quantitative trait locus (QTL) involves interactions between many factors, both environmental and genetic, in which many genes interact often in no additive pathways together and with environment. Integration of the mathematical, statistical and biological aspects of these subjects has made important and interesting results. In this review, mathematical methods offered to study the QTL × environment interactions. The topic is circumscribed, going from basic selection equations to models of evolution of QTLs. Discrete and continuous time mathematical models and subsequently, QTL modelling were introduced with and without environmental interactions. The mathematical models derived here showed that the gradients of mean fitness which have revealed in studies by many researchers had a basic role in mathematical genetics, evolutionary aspects of biometrical genetics and QTL analysis. QTL × environment interactions were studied mathematically including fitness components too. It was revealed that QTL × environment interactions in fitness could generate a balancing selection. Also, QTL analysis could be used to calculate the geometry of the phenotype landscape. In this paper, models applied in biometrical genetics corresponds to QTL analysis and matched with results from other researchers. The originality of this synthesis is the evolutionary modelling of QTL × environment interactions which can be used to investigate the extinction or stability of a population. Also to emphasize that although some scientific subjects like Brownian motion, quantum mechanics, general relativity, differential geometry, and evolutionarybiometrical genetics were apparently different subjects, but the mathematical models were the backbone of these branches of science. This implies that such matters in nature have probably common and elegant basis. The perspective of the subject of this paper in future will be a new and interesting branch of interdisciplinary science.
Article ID 0037 Published: 16 April 2019 RESEARCH ARTICLE
Evaluation of sequence variations in the internal transcribed spacer (ITS) region of 19 accessions, comprising of 11 accessions of Chenopodium quinoa, eight accessions of Chenopodium album and 165 retrieved sequences of different species of Chenopodium belonging to subfamily Chenopodioideae revealed a higher intraspecific genetic diversity in Himalayan C. album than that in C. quinoa. ITS and amplified fragment-length profiles of the accessions suggest the existence of accessions of Himalayan C. album as heteromorphs of the same species rather than a heterogenous assemblage of taxa. While the evolutionary relationship reconstructed from variations in 184 sequences of ITS region from species belonging to Chenopodiaceae, Amaranthaceae, Polygonaceae and Nelumbonaceae established a paraphyletic evolution of family Chenopodiaceae, it also revealed a monophyletic evolution of Chenopodieae I. The reconstruction also established five independent lineages of the subfamily Chenopodioideae with C. album as a sister clade of C. quinoa within the tribe Chenopodieae I. The results also indicate a much younger age for Himalayan chenopods (C. album) than the reported crown age of Chenopodieae I.
Article ID 0038 Published: 16 April 2019 RESEARCH NOTE
Stanniocalcin-1 (STC1) is secreted by the variety of tissues having a major role in the regulation of calcium ions in the involuting mammary gland. The present work aims to sequence and structural characterization as well as expression profiling of STC1 gene in buffalo. Polymorphism identified in the 3-untranslated region (UTR) was analysed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) genotyping in riverine and swamp buffaloes. Expression profiling of STC1 was performed in different lactation stages of mammary gland and peripheral blood mononuclear cells to study the impact of 3'-UTR polymorphism on its expression. Different polymorphic sites were detected in the entire coding and noncoding regions of riverine and swamp buffaloes, including two INDELs. An identified polymorphic nucleotide locus A324G, having target sites for two miRNAs, namely bta-miR-2382 and bta-miR-1343, reported in cattle, was genotyped by PCR-RFLP to reveal variable allelic distribution among swamp and riverine buffaloes. Gene expression profiling across buffalo mammary tissues representing different lactation stages showed maximum expression of the STC1 gene in the involuting mammary gland. Ruminants’ specific genetic variation has been observed in STC1 and its implication in buffalo mammary gland involution as well as coregulation of gene expression throughmiRNA binding in the 3'-UTR is suggested.
Article ID 0036 Published: 11 April 2019 RESEARCH NOTE
The Chinese softshell turtle exhibits ZZ/ZW sex determination. To identify the sex of embryos, juvenile and adult individuals, we designed two pairs of polymerase chain reaction primers, SB1-196, which amplifies a fragment of 196 bp in the female and the other, CK1-482, which amplifies the 482-bp fragment in both the sexes. It is validated in 24 adult turtles of known sex, sampled from three different locations. This one-step sexing technique is rapid and easy to perform and is reported for the first time.
Article ID 0035 Published: 8 April 2019 RESEARCH NOTE
Noncoding somatic mutations have been demonstrated to play important role in tumourigenesis. Here we show that there exists an acute myeloid leukaemia associated noncoding somatic mutation at 3′ terminal of conserved HOXA cluster. The mutation was identified in the bone marrow blasts but not peripheral blood mononuclear cells or buccal cells of two M3 (acute promyelocytic leukaemia, APL) type patients from 45 acute myeloid leukaemia patients. The mutation also existed in a pair of twins one of them developed acute myeloid leukaemia M4 (acute myelomonocytic leukaemia) type. The mutation resides in about 2-kb downstream of HOXA1 gene where a functional retinoic acid response element is located and also bound by histone demethylase KDM3B. Reporter assay showed that the mutation results in the upregulation of transcriptional activity and unresponsiveness to retinoic acid receptor. To sum up, we identified a new acute myeloid leukaemia associated noncoding somatic mutation.
Article ID 0034 Published: 8 April 2019 RESEARCH ARTICLE
AZUBEL RAMíREZ-VELAZCO THANIA ALEJANDRA AGUAYO-OROZCO LUIS FIGUERA HORACIO RIVERA LUIS JAVE-SUÁREZ ADRIANA AGUILAR-LEMARROY LUIS A. TORRES-REYES CARLOS CÓRDOVA-FLETES PATRICIO BARROS-NÚÑEZ SATURNINO DELGADILLO-PÉREZ INGRID PATRICIA DÁVALOS-RODRíGUEZ JOSÉ ELÍAS GARCíA-ORTIZ MARÍA G. DOMÍNGUEZ
Williams–Beuren syndrome (WBS) has a prevalence of 1/7500–20000 live births and results principally from a de novo deletion in 7q11.23 with a length of 1.5 Mb or 1.8 Mb. This study aimed to determine the frequency of 7q11.23 deletion, size of the segment lost, and involved genes in 47 patients with a clinical diagnosis of WBS and analysed by fluorescence in situ hybridization (FISH); among them, 31 had the expected deletion. Micro-array comparative genomic hybridization (aCGH) confirmed the loss in all 18 positive-patients tested: 14 patients had a 1.5 Mb deletion with the same breakpoints at 7q11.23 (hg19: 72726578–74139390) and comprising 24 coding genes from TRIM50 to GTF2I. Four patients showed an atypical deletion: two had a 1.6Mb loss encompassing 27 coding genes, from NSUN5 to GTF2IRD2; another had a 1.7 Mb deletion involving 27 coding genes, from POM121 to GTF2I; the remaining patient presented a deletion of 1.2 Mb that included 21 coding genes from POM121 to LIMK1. aCGH confirmed the lack of deletion in 5/16 negative-patients by FISH. All 47 patients had the characteristic facial phenotype of WBS and 45 of 47 had the typical behavioural and developmental abnormalities. Our observations further confirm that patients with a classical deletion present a typical WBS phenotype, whereas those with a high (criteria of the American Association of Pediatrics, APP) clinical scorebut lacking the expected deletion may harbour an ELN point mutation. Overall, the concomitant CNVs appeared to be incidental findings.
Article ID 0033 Published: 23 March 2019 REVIEW ARTICLE
The Juglans plants are economically important as they provide nuts, wood and garden trees. They also play an important ecological role by supplying food for wild insects and animals. The decoding of genome sequences has fundamental values for understanding the evolution of Juglans plants and molecules, and is also a prerequisite for molecular breeding. During the last three years, the rapid development of sequencing technology has made walnut research into the genome era. Here, we reviewed the progress of genome sequencing of six Juglans species, the resequencing of four Juglans populations as well as the genome sequencing of the closely related species Pterocarya stenoptera. The analysis of the Juglans regia genome uncovers a whole genome duplication (WGD) event. Based on the molecular dating of the divergence time of six Juglans species, we proposed this WGD event was associated with Cretaceous–Palaeogene (K-Pg) boundary occurred ∼65 million years ago. Genomic sequences also provide clear details for understanding the evolution and development of GGT and PPO genes involved in fruit development. The decoding of these genomes has made it easier for us to understand and enhance the use of walnuts. We expect that the functional genomics research of walnut will also develop rapidly in the near future.
Article ID 0032 Published: 13 March 2019 RESEARCH ARTICLE
Chronic periodontitis (CP) is the common form of inflammatory oral disease. Matrix metalloproteinases (MMPs) play a pivotal role in the progression of CP by degrading gingival tissue and its remodelling. Here, we conducted a case–control study to investigate a possible association of single-nucleotide polymorphism of MMP genes and their interaction with CP in the Indian population. A total of 357 DNA samples of venous blood was isolated, of which 157 were identified as CP patients and 200 were healthy individuals. Genotyping of six MMP genes (MMP1, MMP3, MMP7, MMP8, MMP12 and MMP13) was done using polymerase chain reaction following Sanger’s method of sequencing. Statistical analyses were performed by SPSS v16.0, R package (SNPassoc). Gene–gene interactions were evaluated by MDR 3.0.2. The frequency of 6A allele of MMP3 −11715A-6A gene polymorphisms (36%) and G allele of MMP8 +17G-C gene polymorphisms (34%) were higher in the CP population compared with the healthy population (19% and 24%, respectively). A significant association of T allele of MMP8 −799C-T gene promoter polymorphism was found with CP (OR = 2.95, 95%CI = 2.16 − 4.04, P < 0.0001). Genotypic frequency of MMP12 −82A-G polymorphism is associated with CP risk while its allelic distribution is not (OR = 1.32, 95%CI = 0.93 − 1.88, P = 0.129). Gene–gene interactions show the best cross validation consistency model, i.e. MMP1 −519A-G X MMP7 −181A-G X MMP8 −799C-T polymorphismswith a value of 9/10. This gene–gene interaction shows that the significant association of MMP8 −799C-T polymorphism with CP increased susceptibility. Allelic distribution of MMP8+17G-C and MMP3−11715A-6A polymorphisms revealed their protective role towards decreased risk of CP. MMP1 −519A-G and MMP7 −181A-G polymorphisms show combinatorial synergistic effect on CP risk.
Article ID 0031 Published: 9 March 2019 RESEARCH ARTICLE
Calmodulin-binding transcription activators (CAMTAs) are a family of transcription factors that play an important role in plants’ response to the various biotic and abiotic stresses. The common bean (Phaseolus vulgaris L.) is one of the most important crops in the world and plays a pivotal role in sustainable agriculture. To date, the composition of CAMTA genes in genomes of Phaseolus species and their role in resistance to drought stress are not known. In this study, five PhavuCAMTA genes were characterized in common bean genome through bioinformatics analysis, the morphological and biochemical response of 23 Ph.vulgaris genotypes to different levels of drought stress were evaluated and the expression patterns of PhCAMTA1 in the leaf tissues of sensitive and tolerant genotypes were analysed. Gene structure, protein domain organization and phylogenetic analyses showed that the CAMTAs of Phaseolus were structurally similar and clustered into three groups as other plant CAMTAs. Genotypes showeda differential response to drought stress. Thus, the plant height, number of nodes and flower, total chlorophyll and total protein content, and activity of antioxidant enzymes (ascorbate peroxidase and catalase) in plants significantly influenced by genotype and drought stress interaction. Moreover, the resistant and susceptible genotypes were identified according to three-dimensional plots and the expression patterns of PhavuCAMTA1 gene were studied using real-time quantitative polymerase chain reaction. The results of the present study serve as the basis for future functional studies on the Phaseolus CAMTA family.
Article ID 0028 Published: 9 March 2019 RESEARCH ARTICLE
To better understand the role of integrin subunit alpha 9 (ITGA9) gene polymorphism in epithelial ovarian cancer (EOC), we investigated the distribution of ITGA9 gene polymorphisms (rs2212020 and rs189897) and revealed whether these polymorphisms were associated with a curative effect in EOC. It was found that rs2212020 and rs189897 were correlated significantly with EOC incidence. The frequency of the C allele of rs2212020 was significantly higher in EOC patients than in the control group (P = 0.009, χ2 = 6.857). The population with the C allele of rs2212020 had a higher EOC risk than the population with the T allele (hazard ratio = 1.97, 95.0% CI = 1.178−3.299). Further, our results showed that the CC genotype was a risk factor for EOC. Regarding the association between ITGA9 and the sensitivity to platinum-based chemotherapy in EOC, there were no statistically significant differences in the frequencies of the rs189897 and rs2212020 polymorphisms between the chemosensitivegroup and the control group. In multivariate analysis, the patients with the TT genotype of rs189897 had longer progression free survival (PFS) than the patients without this genotype (P = 0.010, OR = 2.491). The AT genotype of rs189897 was a risk factor for PFS in EOC. These findings suggested that rs189897 and rs2212020 could play important roles in EOC diagnosis and prognosis.
Article ID 0029 Published: 9 March 2019 REVIEW ARTICLE
Nonalcoholic fatty liver disease (NAFLD) is characterized by the accumulation of fat in the liver without any history of chronic alcohol consumption. It encompasses a wide spectrum of diseases that range from simple steatosis to nonalcoholicsteatohepatitis. NAFLD is strongly associated with obesity, insulin resistance / type-2 diabetes mellitus and the metabolic syndrome. NAFLD is a complex disorder; environmental and genetic factors interact with NAFLD manifestation and determine its progression. In this review, an attempt was made to provide current information on the genetic variants of NAFLD in Asian populations. Literature search was performed by using PubMed, Medline and Google Scholar database. Candidate gene, validation and genomewide association studies (GWASs) were included in this review. A total of 41 studies fulfilled inclusion criteria of which 12 candidate gene studies exclusively focussed on the PNPLA3 gene and 17 other studies on other important candidate genes such as NCANCILP2, PPARG,AGTR1, FABP1, APOC3 etc. reported significant association with NAFLD. Eight validation studies identified associations of variants on PNPLA3, LYPLAL1, TM6SF2, ADIPOR2, STAT3, GCKR, SAMM50 etc. with NAFLD. Thus, so far, four GWASs have been conducted in Asian population that reported PNPLA3, SAMM50, PARVB and GATAD2A genes which were significantly associated with NAFLD. Findings indicate that PNPLA3, APOC3, PPARG, NCAN and GCKR genes emerge out to be the important biological markers associated with NAFLD.
Article ID 0027 Published: 9 March 2019 RESEARCH ARTICLE
Creation of genetic variability and development of varieties having higher yield potential depends on information about nature of gene action. The present investigation was undertaken to decipher the nature of gene action and allied genetic parameters involved in the inheritance of yield and yield-related component traits in opium poppy (Papaver somniferum L.). The biparental inbreeding progenies derived from four segregating base populations of crosses NB-1Kr40-3/3×NB-1Kr30+0.2-2/1, NB-5Kr40-7/2×58/1, NB-1Kr30+0.2-2/1×58/1 and NB-Kr40-3/3×NB-5Kr40-7/2 of opium poppy were analysed to study the gene actions involved in the inheritance of yield and component traits. Additive component of variance played a predominant role in North Carolina design (NCD)-I, while both additive and dominance genetic components were found important in NCD-III design. The presence of additive as well as nonadditive components of variance suggested that one or two generations of intermating in further generations followed by selection may lead to development of novel genotypes.
Article ID 0030 Published: 9 March 2019 RESEARCH ARTICLE
Long noncoding RNAs (lncRNAs) are important regulators of biological processes, and regulate genomic imprinting in cis and/or trans to induce monoallelic expression with parent-origin-specific pattern. DLK1–DIO3 domain is one of the largest imprinted clusters in mammals, and maternally expressed noncoding RNAs of this region is related to the pluripotency of the embryonic stem cells. Previously, we sequenced the cDNA of two maternally expressed noncoding RNAs, MEG8 and MEG9, and mapped a lncRNA (LINC24061) between the two genes in the cattle DLK1–DIO3 domain on chromosome 21. In this study, we identified LINC24065, a novel long intergenic noncoding RNA (lincRNA), which was also located between MEG8 and MEG9. We identified four variants of LINC24065 (LINC24065-v1, LINC24065-v2, LINC24065-v3 and LINC24065-v4) that were a result of alternative splicing from 18 exons. LINC24065-v1 and LINC24065-v2 showed tissue-specific expression patterns in adultbovine tissues, and LINC24065-v3 and LINC24065-v4 were detected in all eight analysed tissues (heart, liver, spleen, lung, kidney, skeletal muscle, adipose and brain). Using single-nucleotide polymorphism (SNP)-based method, LINC24065 was identified to have monoallelic expression in adult tissues, suggesting that it is imprinted in cows. These results provide a foundation for further investigation about whether LINC24065 plays a role in regulating imprinting of the DLK1–DIO3 domain.
Article ID 0026 Published: 4 March 2019 RESEARCH NOTE
Yellow catfish (Pelteobagrus fulvidraco) is an important aquaculture species which is widely distributed, especially in the Yangtze River of China. To facilitate its conservation and stock improvement, 273 yellow catfish samples from the Yangtze River (seven populations) and Baiyangdian (BYD) Lake were genotyped using eight microsatellites in combination with capillary electrophoresis. A total of 250 alleles were detected at eight loci in eight populations showing high allelic (Na= 31.25 ± 7.38) and genetic diversity (He = 0.888–0.944). Both FST and clustering analyses revealed the presence of subtle population differences between the species of Yangtze River and the BYD lake. Mantel tests suggest that genetic distance is significantly correlated with geographical distance (R = 0.9294 and P < 0.05). The results of genetic diversity and population structure will help in conservation and improvement of yellow catfish.
Article ID 0025 Published: 4 March 2019 RESEARCH ARTICLE
The expression of four genes involved in milk regulation and production in bovine milk and tissue samples profiled using quantitative PCR to identify differential gene expression. Our goal focussed on the differential mRNA expression of milk genes (KCN, PRL, BLG and PIT-1) in milk samples and different tissues from four different breeds of ecologically adapted and geographically separated cattle species. The mRNA expression identified the four milk genes understudiedmost upregulated in mammary gland and milk samples as compared with other tissues. The expression of PIT-1 gene in the brain identified to have influenced the expression of PRL and K-CN in the mammary and milk samples. Among the four genes, PRL had the highest mRNA expression (144.19-fold change) in Holstein followed by K-CN with 100.89-fold change, while the smallest relative expression for most genes in this study are in the range from 0.79 to 7.35-fold difference. White Fulani cattle was identified to have a higher expression for K-CN, PRL and BLG compared with Angus and Ndama cattle, while Holstein cattle is on top of the list on the basis of the gene expression and gene regulation for all the four genes in this study. Also, White Fulani and Holstein are in the same cluster based on their mRNA expression for milk genes. Our data showed the first evidence of the molecular identification of indigenous White Fulani cattle ofhaving potential for higher milk production.
Article ID 0000 Published: March 2019 Editorial
Article ID 0022 Published: 28 February 2019 RESEARCH NOTE
A parental diagnosis was performed for an unborn foetus of a healthy couple, who was due for ultrasound detection of multiple malformations and abnormal amniotic fluid karyotypes. For an accurate diagnosis, routine G-banding analysis and nextgeneration sequencing (NGS)were carried out. Finally, conventional cytogenetic analysis suggested that the foetus had a karyotype of47,XX,+mar/46,XN,meanwhileNGSalso revealed a partial tetrasomy of 27.84Mbfrom4q26-q31.21 (117,385,735–145,225,759), and G-banding analysis excluded the couple to have carried the 4q26-q31.21 duplication. We have identified a de novo mosaic small supernumerary marker chromosomes (sSMC) derived from 4q26-q31.21 in a foetus with hemivertebra, polydactyly, abnormal ears, and heart and ventricular septal defect.
Article ID 0023 Published: 28 February 2019 REVIEW ARTICLE
Genes encoding structurally independent phosphotriesterases (PTEs) are identified in soil bacteria. These pte genes, often identified on mobilizable and self-transmissible plasmids are organized as mobile genetic elements. Their dissemination through lateral gene transfer is evident due to the detection of identical organophosphate degradation genes among soil bacteria with little orno taxonomic relationship. Convergent evolution of PTEs provided selective advantages to the bacterial strain as they convert toxic phosphotriesters (PTs) into a source of phosphate. The residues of organophosphate (OP) compounds that accumulate in a soil are proposed to contribute to the evolution of PTEs through substrate-assisted gain-of-function. This review provides comprehensiveinformation on lateral transfer of pte genes and critically examines proposed hypotheses on their evolution in the light of the short half-life of OPs in the environment. The review also proposes alternate factors that have possibly contributed to the evolution and lateral mobility of PTEs by taking into account their biology and analyses of pte genes in genomic and metagenomic databases.
Article ID 0024 Published: 28 February 2019 RESEARCH ARTICLE
Understanding the genetic basis of biochemical traits of different cauliflower genotypes is essential for planning the effective breeding strategies in genetic improvement. To determine the mode of inheritance of dry matter content and biochemical traits, we made crosses using four genotypes of cauliflower, and obtained F1, F2, BC1 and BC2 populations. The six generations obtained were replicated thrice and evaluated in a randomized block design. The generation mean analysis of data showed the presence of duplicate epistasis in dry matter content which suggested the adoption of reciprocal recurrent selection and biparental mating for the improvement of the trait. However, in case of vitamin C, complementary type of epistasis was reported in three crosses, which indicated the exploitation of heterosis breeding of enhancing vitamin C. It can be concluded that the role of gene action was in general more complex for the traits studied. The nature and magnitude of gene effects varies character-wise as well as cross-wise. Hence, for the improvement of dry matter content and biochemical traits in a particular cross, a specific breeding strategy has to be implemented.
Article ID 0021 Published: 28 February 2019 RESEARCH NOTE
This study evaluates a family with two siblings having severe growth retardation and facial dysmorphism, born to consanguineous normal healthy parents. Affymetrix CytoScan 750K microarray showed a 34-Mb pericentric homozygous region on chromosome 6 for both siblings. CUL7 was one of the 141 genes present in this region. Sanger sequencing of CUL7 gene detected a 2-bp novel deletion in the 15th exon (c.2943_2944delCT of the cDNA). This deletion leads to a frameshift and a premature termination signal much upstream of the wild-type termination signal, leading to a nonsense mediated decay of the mRNA. CUL7 protein plays an important role in formation of 3M complex, ubiquitination, microtubule dynamics and cell cycle regulation. Mutations in CUL7 gene is known to cause a rare 3M syndrome. Information about the novel mutation has been accepted in the ClinVar database with rs1064792895.
Article ID 0016 Published: 26 February 2019 RESEARCH NOTE
Insulin-like growth factor receptor (IGF-1R) deficiency is a rare form of short stature, and is difficult to clinically diagnose. Targeted next-generation sequencing (NGS) allows for the rapid and inexpensive assessment of short stature. We identified mutations in the pedigree of a Chinese boy with severe short stature using targeted NGS; we then assessed the clinical characteristicsand evaluated the efficacy of growth hormone therapy. NGS analysis revealed a novel heterozygous missense mutation in exon3 (c.926C>T, p.S309L) of the type-I IGF-1R gene in the proband, which was inherited from the mother. The proband, mother and grandfather suffered from severe growth failure. After recombinant human growth hormone therapy, the patient’s growth rate increased. The novel missensemutation in IGF-1R (c.926C > T, p.S309L) is associated with severe short stature in Chinese individuals. Targeted NGS may enable efficient diagnosis and genetic consultation of children with short stature.
Article ID 0019 Published: 26 February 2019 RESEARCH ARTICLE
Stem gall (Protomyces macrosporus Unger), a serious disease that affects leaves, petioles, stems and fruits of coriander (Coriandrum sativum L.) causing heavy loss in yield. Genetic improvement of coriander for stem gall disease is indispensable. Coriander cultivars of stem gall resistance (ACr-1) and susceptible (CS-6) leaf samples were utilized and transcriptome sequenced using Illumina NextSeq500 platform. After trimming low-quality reads and adapter sequences, a total of 49,163,108 and 43,746,120 high-quality reads were retained and further assembly resulted validated transcripts of 59,933 and 56,861. We have predicted 52,506 and 48,858 coding sequences (CDS) of which 50,506 and 46,945 were annotated using NCBInr database. Gene ontology analysis annotated 19,099 and 17,625 terms; pathway analysis obtained 24 different functional pathway categories; signal transduction, transport, catabolism, translation and carbohydrate metabolism pathways etc. were dominated. Differentially expressed genes analysis predicted 13,123 CDS commonly expressed of which 431 and 400 genes were significantly upregulated and downregulated, respectively, in which Rgenes, stress inducible transcription factors such as ERF, NAC, bZIP, MYB, DREB and WRKY and antifungal related genes were predicted. The real-time PCR analysis of HSP20 gene expression in resistance showed upregulation by 10-fold over susceptible sample and 18s used as a housekeeping gene for normalization. The present results provide an insights into various aspects underlying the development of resistance to stem gall in coriander.
Article ID 0020 Published: 26 February 2019 RESEARCH ARTICLE
Elevated C-reactive protein (CRP) serves as an independent biomarker for acute and chronic inflammation, and is also associated with metabolic diseases. Genomewide loci regulating CRP level in Indian population, a high-risk group for metabolic illness, is unexplored. Therefore, we aimed to discover common polymorphisms associated with plasma CRP level in 4493 Indians of Indo-European origin using genomewide association study. Genomewide strong associations of two known intronic variants in hepatocyte nuclear factor-1 α gene (HNF1A)were identified among Indian subjects. We also detected prior associations of several variants in/near metabolic and inflammatory process genes: APOC1, LEPR, CRP, HNF4A, IL6R and APOE with modest associations. This study confirms that Indians from Indo-European origin display similar core universal genetic factors for CRP levels.
Article ID 0015 Published: 26 February 2019 RESEARCH ARTICLE
Antheraea assamensis Helfer, popularly known as Muga silkworm, the golden silk producer of northeast India is economically important and unique among the Saturniid silkworms. In this study, the genetic diversity and phylogeny of semidomesticated and wild morphs of Muga silkwormcollected from different geographical locations of northeast India were investigated based on the sequences of five mitochondrial loci, i.e. 12S rRNA, 16S rRNA, CoxI, Cytb and CR. All the five mitochondrial loci showed a strong bias towards higher ‘A’ and ‘T’ contents. Transitional substitutions were found to be more than the transversional substitutions. The rate of nucleotide substitution and average genetic divergence were found to be highest in CR sequences and lowest in 12S rRNA gene sequences among the morphs of Muga silkworm. The morphs collected from same geographical area had identical 12S rRNA, 16S rRNA, CoxI and Cytb gene sequences. Moreover, the 12S rRNA and 16S rRNA gene sequences of somesemi-domesticated and wild morphs collected from different geographical locations were also found to be similar. In the phylogenetic trees generated based on themitochondrial loci, mixing of semi-domesticated and wild morphs was observed as they shared the same group. The information generated in this study will help in formulating strategies to conserve the natural biodiversity present among these unique silkworms in northeast India. In addition, this will be useful in identifying diverse morphs of Muga silkworm, which will help in effective breeding programmes to improve its productivity.
Article ID 0017 Published: 26 February 2019 RESEARCH NOTE
The medically important Indian red scorpion, Hottentotta tamulus, is one of the most poisonous scorpions of Indian subcontinent. We studied the haplotype diversity in eight populations of H. tamulus based on mitochondrial cytochrome oxidase subunit I (COI) partial gene sequence. Analyses revealed 22 haplotypes with a haplotype diversity of 0.941 and nucleotide diversity of 0.023. For the first two codon positions both transition and transversion types of substitutions were equally likely and the test for neutrality was not rejected. However, codon substitution pattern indicated that the gene has experienced purifying selection. Model-based clustering method indicated that the eight populations form three groups that correspond to high, moderate and low rainfall areas, indicating that there is biogeographical separation of haplotypes. Populations from three groups formed distinct clades in maximum likelihood analysis and median joining genetic network and were statistically supported by low within group and high among group variation in analyses of molecular variance. We provide the first account of haplotype diversity in Indian red scorpions and their biogeographical separation.
Article ID 0018 Published: 26 February 2019 RESEARCH ARTICLE
In this study, we show that NAC-like transcription factor (TF) has 90% sequence similarity with cDNA of the OsNac5 gene present in the NCBI database. Phylogenetic analysis of the NAC gene family was performed with inclusion of the highly diverse C-terminal sequences. We report that this gene is also found to be orthologous to Glycine max NAC8, NAC2, Triticum aestivum NAC6 and paralogous to OsNAC6. mRNA was purified from five recombinant inbred lines (RILs) and parents of rice at three different stages of grain filling under aerobic conditions, with grain protein content (GPC) spanning from 4 to 14%. TheNAC-like TF encoding a protein was found to be upregulated at the S2 stage in the leaf (3.9-fold) and panicle (1.84-fold) of parent HPR14 and in five RILs (1.9 to 4.51-fold in leaves and 0.47 to 3.2-fold in panicles). Expression analysis of the NAC-like TF encoding a protein for the rice gene was found to be upregulated at the S2 stage in the leaf and panicle of parental line HPR14 and RILs with high protein content.
Article ID 0011 Published: 21 February 2019 RESEARCH NOTE
Munida isos is a deep sea squat lobster species that is widely distributed across the New Zealand and east Australian region, and is often associated with deep sea vulnerable marine ecosystems. To investigate its population genetic structure and patterns of regional connectivity, microsatellite loci were developed for M. isos from two genomic libraries using the Illumina HiSeq 2500 sequencing platform. Twenty-six loci amplified consistently in M. isos from the Tasman Sea, among which 20 were polymorphic and selectively neutral. Evidence of null alleles was observed at eight loci. Most loci exhibited moderate to high levels of polymorphism, with an average polymorphic information content value of 0.482. The mean number of alleles per locus was 7.45, with a mean expectedheterozygosity of 0.520. Thirteen loci exhibited significant deviation from Hardy–Weinberg equilibrium, while only one locus pair was in linkage disequilibrium after false discovery rate correction for multiple testing (P < 0.05). Cross-species amplification tests revealed that the transferability of 14 loci (70%) was positive for the two congeners M. endeavourae and M. gracilis. The accessibility to new polymorphic microsatellite loci will facilitate population genetic studies and aid in developing conservation and management strategies for vulnerable marine ecosystems.
Article ID 0010 Published: 21 February 2019 RESEARCH NOTE
Microduplications of the X chromosome are a rare cause of X-linked intellectual disability (XLID), a clinically and genetically heterogeneous spectrum of disorders. In the present study, a 950-kb Xp22.12 microduplication including the RPS6KA3 gene was detected in affected members of a family, including the proband (male), his mother and one maternal uncle. Four female carriers had major depression and one of them also had mild intellectual disability. The present and previous cases with overlapping microduplications suggest that Xp22.12 microduplications can be included in the neuropsychiatric copy number variations.
Article ID 0013 Published: 21 February 2019 RESEARCH ARTICLE
Homeobox proteins (HOXs) comprise a large family in eukaryotes and share a highly conserved DNA-binding motif, the homeodomain (HD). HOXs play an important role in the regulation of plant growth, development and stress response. However, systematic analysis and expression profiling of these genes have not been reported in Malus domestica. In this study, a total of 207 HOXs of M. domestica (MdHOXs) were identified and classified into 11 distinct subfamilies, and an unclassified group according to their functional domains. The MdHOXs were localized in all 17 chromosomes with various densities and a majority of them tended to form gene clusters. Analysis of the Ka/Ks ratios suggested that the duplicated genes of MdHOXs mainly underwent purifying selection with restrictive functional divergence after the duplication events. The expression of MdHOXs has organ specific characteristics and were divided into seven different groups. Stress-related cis-acting elements were prevalent in the upstream sequence of MdHOXs by systematic analysis. To explore the response to abiotic stress, eight MdHOXs were randomly selected to investigate their expression using quantitative real-time polymerase chain reaction. Transcription levels of MdHOXs were upregulated in the leaves and roots under cold, osmotic, high salinity or exogenous ABA treatments, which suggested that they may take part in the plant response to abiotic stress. These results provided basic information of HOXs in apple and will further contribute to the functional research of MdHOXs, especially the response to abiotic stress.
Article ID 0012 Published: 21 February 2019 RESEARCH ARTICLE
The deep water penaeoid shrimp is an important commercial crustacean resource along the Indian coast. The molecular and morphological information of this group from the Indian coast is scarcely known. In this study, we investigated the identification and phylogenetic relationships of the deep water penaeoid shrimps using three mitochondrial (cytochrome oxidase subunit I (COI), cytochrome b, 16S rRNA) genes, which were compared with 54 morphological characters and further used to evaluate character evolution. Our study revealed remarkable molecular divergence (3.3–33.0%) in nine species from three genera of Solenoceridae, four species from three genera of Penaeidae and one species from Aristeidae using COI. Phylogenetic analysis using maximum likelihood and Bayesian approaches revealed that all species from these families are monophyletic. The present analysis revealed the existence of subgroups in the genus Solenocera suggesting the slow reduction of postrostral carina which corresponds to the increase in distributional depth during the evolutionary process which further indicates the origin of the genus in the continental shelf and extending up to the continental slope. In addition, we generated the DNA barcode database involving these species which can help further to investigate the detailed evolution and biogeography of these valuable crustacean resources.
Article ID 0009 Published: 21 February 2019 RESOURCES
Ionizing radiations (IRs) are widespread damaging stresses to plant growth and development. However, the regulatory networks underlying the mechanisms of responses to IRs remains poorly understood. Here, a set of publicly available transcriptomic data (conducted by Van Hoeck et al. 2015a), in which Lemna minor plants were exposed to a series of doses of gamma, beta and uranium treatments was used to perform gene coexpression network analysis. Overall, the genes involved in DNA synthesis and chromatin structure, light signalling, photosynthesis, and carbohydrate metabolism were commonly responsive to gamma, beta and uranium treatments. Genes related to anthocyanin accumulation and trichome differentiation were specifically downregulated, andgenes related to nitrogen and phosphate nutrition, cell vesicle transport, mitochondrial electron transport and ATP synthesis were specifically upregulated in response to uranium treatment. While genes involved in DNA damage and repair, RNA processing and RNA binding were specifically downregulated and genes involved in calcium signalling, redox and degradation of carbohydrate metabolism were specifically upregulated responding to gamma radiation. These findings revealed both dose-dependent and typespecific networks responding to different IRs in L. minor, and can be served as a useful resource to better understand the mechanisms of responses to different IRs in other plants.
Article ID 0014 Published: 21 February 2019 RESEARCH ARTICLE
Cupressus gigantea and C. torulosa are ecologically and economically important endemic species of the conifer family Cupressaceae on the Qinghai-Tibetan plateau. C. gigantea was previously classified as a subspecies of C. torulosa because of their similar morphological characteristics and close distribution. In this study, 401 individuals were sampled from 16 populations of the two Cupressus species. The specimens were genotyped using 10 polymorphic microsatellite loci through fluorescence polymerase chain reaction (PCR). The genetic diversity of C. gigantea and C. torulosa populations was generally low, with the highest genetic diversity detected in the population LLS of C. gigantea. Distance-based phylogenetic and principal co-ordinates analyses indicated a clear genetic structures for the 16 populations of the two Cupressus species. Moreover, Mantel test results showed indistinctive correlations between population-pairwise Fst values and geographic distances, as well as between genetic distances and geographic distances in C. gigantea and C. torulosa, respectively. AMOVA suggested that genetic variation mostly resided within populations. Sixteen naturalpopulations were evidently clustered into two major groups in the constructed neighbour-joining tree. The results demonstrated that C. gigantea and C. torulosa are different Cupressus species. The genetic information provided important theoretical references for conservation and management of the two endangered Cupressus species.
Article ID 0008 Published: 13 February 2019 RESEARCH ARTICLE
Insulin is a commonly used measure of pancreatic β-cell function but exhibits a short half-life in the human body. During biosynthesis, insulin release is accompanied by C-peptide at an equimolar concentration which has a much higher plasma half-life and is therefore projected as a precise measure of β-cell activity than insulin. Despite this, genetic studies of metabolic traits haveneglected the regulatory potential of C-peptide for therapeutic intervention of type-2 diabetes. The present study is aimed to search genomewide variants governing C-peptide levels in genetically diverse and high risk population for metabolic diseases—Indians. We performed whole genome genotyping in 877 healthy Indians of Indo-European origin followed by replication of variants with P ≤ 1 × 10−3 in an independent sample-set of 1829 Indians. Lead-associated signals were also tested in-silico in 773 Hispanics. To secure biological rationale for observed association, we further carried out DNA methylation quantitative trait loci analysis in 233 Indians and publicly available regulatory data was mined. We discovered novel lncRNA gene AC073333.8 with the strongest association with C-peptide levels in Indians that however missed genomewide significance. Also, noncoding genes, RP1-209A6.1 and RPS3AP5; protein gene regulators, ZNF831 and ETS2; and solute carrier protein gene SLC15A5 retained robust association with C-peptide after meta-analysis. Integration of methylation data revealed ETS2 and ZNF831 single-nucleotide polymorphisms as significant meth-QTLs in Indians. All genes showed reasonable expression in the human lung, signifying alternate important organs for C-peptide biology. Our findings mirror polygenic nature of C-peptide where multiple small-effect size variants in the regulatory genome principally govern the trait biology.
Article ID 0007 Published: 12 February 2019 RESEARCH NOTE
Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker. Thus, an attempt was made to use the gene as an advanced molecular marker of sexing of the yak to improve breeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. The test is further refined with qPCR validation by quantifying the DNA copy number of the Amelogenin gene in male and female. We observed a high level of sequence polymorphisms of AMELX and AMELY in yak considered as novel identification. These tests can be further extended into several other specialized fields includingforensics, meat production and processing, and quality control.
Article ID 0006 Published: 12 February 2019 RESEARCH ARTICLE
The aim of the present study was to evaluate the diagnostic yield of prenatal cytogeneticmicroarray (CMA) in structurally normal and abnormal foetuses and record the acceptance rate of CMA for prenatal diagnosis over a course of five year. In 128 structurally normal and abnormal foetuses, CMA was performed along with foetal karyotype, after exclusion of aneuploidy by quantitative fluorescence polymerase chain reaction. The microarray was able to detect the pathogenic variants in 5.5% cases; the diagnostic yield in structurally abnormal foetuses was 8.8% and 4.7% in foetuses with a high aneuploidy risk. Balanced and unbalanced translocations, and low level mosaicism were detected. Reanalysis of variants of uncertain significance identified pathogenic variant. The study shows higher diagnostic yield in structurally abnormal cases, the importance of foetal karyotype and reanalysis in microarray. The acceptance rate of prenatal CMA increased five-fold over a period of five year.
Article ID 0005 Published: 7 February 2019 RESEARCH NOTE
Gitelman syndrome is an autosomal recessive salt-wasting tubulopathy caused by mutations in the SLC12A3 gene. A female and a male sibling from two unrelated Greek-Cypriot families presenting with a severe salt-wasting tubulopathy dueto compound heterozygous mutations of a novel duplication and a previously reported missense mutation in the SLC12A gene are described. Sanger sequencing was used to identify possible mutations in the SLC12A3 gene. For the detection of duplications/conversions and deletions in the same gene, Multiplex ligation probe amplification (MLPA) analysis was performed. Direct sequencing and MLPA analysis of the SLC12A3 gene identified two compound heterozygous mutations in both unrelated probands. Both probands were identified to carry in compound heterozygosity the known p.Met581Lys and a novelheterozygous duplication of exons 9-14 (E9_E14dup). The diagnosis of Gitelman syndrome was made through clinical assessment, biochemical screening and genetic analysis. The identification of the novel SLC12A3 duplication seems to be characteristic of Greek-Cypriot patients and suggests a possible ancestral mutational event that has spread in Cyprus due to a possible founder effect. Testing for Gitelman syndrome probable variants can be performed before proceeding to a full gene sequencing dropping the diagnostic cost. In addition, this report adds to the mutational spectrum observed.
Article ID 0004 Published: 7 February 2019 RESEARCH NOTE
Dipentodon is a monotypic genus of Dipentodontaceae and the only species, Dipentodon sinicus, is scattered in southwest China as well as adjacent Myanmar, northeast India and northern Vietnam. This species was evaluated as vulnerable in ‘China Species Red List’. Here, we assembled and characterized the complete chloroplast (cp) genome of D. sinicus using Illumina sequencing data for the first time. The complete cp genome was 158,795 bp in length, consisting of a pair of inverted repeats of 26,587 bp, a large single-copy region of 87,233 bp and a small single-copy region of 18,388 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that D. sinicus is a member of Huerteales, consistent with its position in the latest classification of flowering plants (AGP IV).
Article ID 0003 Published: 31 January 2019 RESEARCH ARTICLE
Antitumour necrosis factor-alpha (TNF-α) therapy is used as a clinical intervention for rheumatoid arthritis (RA) but differences exist in response to the treatment which makes the candidature of the screening of TNF-α alteration(s) at genetic and expression levels an important agenda prior to treatment. This study aims to determine the associative role of TNF-α –308G/A polymorphism and differential expression of TNF-α in the pathogenesis of RA. A case–control study where a total of 126 RA patients were enrolled based on ACR-EULAR (2010) criteria, along with 160 community matched age and sex controls over a period of three years. The differential expression level of TNF-α mRNA and protein level was studied and TNF-α –308G/A polymorphism was screened by T-ARMS PCR assay. All statistical analysis was performed using SPSS software. mRNA expression level of TNF-α was upregulated in RA cases (avg. 15.85 ± 9.52 fold) compared to control. TNF-α protein level was found to be higher in RA cases (28.62±7.17 pg/mL) compared to control (23.14±6.91 pg/mL). TNF-α –308 variant GA genotype was higher in RA (46.03%) than in control (25%). The presence of TNF-α –308 variant A allele was associated with increased risk of RA susceptibility (odds ratio (OR) = 2.559 at 95% confidence interval (CI), P< 0.001) but not severity (OR = 1.617 at 95% CI, P = 0.571). The presence of –308 variant genotype was associated with a higher TNF-α mRNA and protein expression. The presence of TNF-α –308A allele is associated with increased risk of RA susceptibility and differential TNF-α expression, and has prognostic significance. Association of higher TNF-α pro-inflammatory cytokine levels with northeast Indian patients makes them suitable subjects for anti-TNF-α therapy.
Article ID 0002 Published: 31 January 2019 RESEARCH NOTE
Microsatellite markers from a fresh water yellow catfish, Pseudobagrus fulvidraco, were developed by whole-genome sequencing in the Ion S5 system. Of the 40 chosen sets of microsatellite markers, with tetra-repeat and penta-repeat motifs, from a total 19,743 sequence, only 13 markers were successfully applied in 78 individual fish sampled to detect genomic variability from four natural populations of Korea. On an average, the number of alleles per marker was 6.7. The observed heterozygosity varied from 0.048 to 0.810. Twelve microsatellite markers conformed to Hardy–Weinberg equilibrium and none exhibited significant linkage disequilibrium. In yellow catfish, genetic differentiation among four natural populations was further supported by FST (P < 0.05) and STRUCTURE analysis. The microsatellite markers identified could facilitate genetic diversity and population structure studies and thus aid in conservation of the yellow catfish.
Article ID 0001 Published: 30 January 2019 RESEARCH ARTICLE
The aim of this study was to determine whether the polymorphism of aldosterone synthase (CYP11B2) –344C/T and angiotensin-converting enzyme (ACE) insertion/deletion (I/D) were associated with the response of blood pressure (BP) to telmisartan treatment. After a two-week single-blind placebo run-in period, 148 patients with mild-to-moderate primary hypertension received monotherapy of telmisartan with 80 mg/day and then were followed up for eight weeks. Polymorphisms of CYP11B2 –344C/T and ACE I/D gene were determined through polymerase chain reaction-restriction fragment polymorphism analysis. The relationship between these polymorphisms and changes in BP was monitored and evaluated after eight weeks of treatment. With respect tothe polymorphism of CYP11B2 –344C/T, the reduction in diastolic BP was significantly greater in patients carrying the C allele (CC+CT) compared with those carrying the TT genotype. There was no significant differences between ACE I/D polymorphism and BP reduction after treatment. We concluded that the aldosterone synthase –344C/T polymorphism was related to the antihypertensive treatment with telmisartan in hypertensive patients.