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      Volume 98, All articles

      Continuous Article Publishing mode

    • Editorial

      Ranganath H.A.

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    • Phaseolus vulgaris genome possesses CAMTA genes, and phavuCAMTA1 contributes to the drought tolerance

      KOBRA SAEIDI NASSER ZARE AMIN BAGHIZADEH RASOOL ASGHARI-ZAKARIA

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      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.

    • Development and characterization of 20 polymorphic microsatellite loci in the deep sea squat lobster, Munida isos Ahyong and Poore, 2004 and cross-amplification in two congeneric species

      RUO-JIN YAN KAREEN E. SCHNABEL XIANG-ZHAO GUO JONATHAN P. A. GARDNER

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      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.

    • A small supernumerary marker chromosome resulting in mosaic partial tetrasomy 4q26-q31.21 in a foetus with multiple congenital malformations

      ZHI-TAO ZHANG WEN-XU QI CAI-XIA LIU SHAO-WEI YIN YAN ZHAO JESSE LI-LING YUAN LV

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      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[52]/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.

    • Lateral transfer of organophosphate degradation (opdopd) genes among soil bacteria: mode of transfer and contributions to organismal fitness

      DAYANANDA SIDDAVATTAM HARSHITA YAKKALA DEVYANI SAMANTARRAI

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      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.

    • A novel heterozygous duplication of the SLC12A3 gene in two Gitelman syndrome pedigrees: indicating a founder effect

      PAVLOS FANIS ELISAVET EFSTATHIOU VASSOS NEOCLEOUS LEONIDAS A. PHYLACTOU ADAMOS HADJIPANAYIS

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      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.

    • Estimation of genetic architecture of biochemical traits in mid–late cauliflower (Brassica oleracea L. var. botrytis) under sub-temperate conditions of north western Himalayas

      ARTI VERMA YUDHVIR SINGH

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      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.

    • Clinical relationships between the rs2212020 and rs189897 polymorphisms of the ITGA9 gene and epithelial ovarian cancer

      JINYANG LIU TING LIU LIN LIANG MANYING ZHANG YANSHAN GE SHAN LIAO YANHONG ZHOU KEQIANG ZHANG

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      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.

    • Novel mutation of type-1 insulin-like growth factor receptor (IGF-1R) gene in a severe short stature pedigree identified by targeted next-generation sequencing

      YU YANG HUI HUANG KA CHEN LI YANG LI-LING XIE TING XIONG XIAN WU

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      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.

    • Genomewide association study of C-peptide surfaces key regulatory genes in Indians

      KHUSHDEEP BANDESH GAURI PRASAD ANIL KUMAR GIRI V. SAROJA VORUGANTI NANCY F. BUTTE SHELLEY A. COLE ANTHONY G. COMUZZIE INDICO CONSORTIUM NIKHIL TANDON DWAIPAYAN BHARADWAJ

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      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.

    • Transcriptome profiling of coriander: a dual purpose crop unravels stem gall resistance genes

      SHARDA CHOUDHARY MAHANTESHA B. N. NAIKA RADHESHYAM SHARMA R. D. MEENA GOPAL LAL

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      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.

    • Genomewide association study for C-reactive protein in Indians replicates known associations of common variants

      GAURI PRASAD ANIL K. GIRI INDICO CONSORTIUM ANALABHA BASU NIKHIL TANDON DWAIPAYAN BHARADWAJ

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      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.

    • Genetics of nonalcoholic fatty liver disease in Asian populations

      ARUN KUMAR SHALIMAR GAGANDEEP KAUR WALIA VIPIN GUPTA M. P. SACHDEVA

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      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.

    • Spectrum of X-linked intellectual disabilities and psychiatric symptoms in a family harbouring a Xp22.12 microduplication encompassing the RPS6KA3 gene

      VERA ULIANA FRANCESCO BONATTI VALENTINA ZANATTA PAOLA MOZZONI DAVIDE MARTORANA ANTONIO PERCESEPE

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      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.

    • Population structure and genetic diversity in yellow catfish (Pelteobagrus fulvidraco) assessed with microsatellites

      WENJIE GUO CHENGTAO GUO YUHONG WANG WEIHUA HU JIE MEI

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      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.

    • Genetic and expression changes in TNF-α as a risk factor for rheumatoid arthritis pathogenesis in northeast India

      SOMDATTA DAS CHITRALEKHA BARUAH ANJAN KUMAR SAIKIA DIPTIKA TIWARI SUJOY BOSE

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      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.

    • Identification of microsatellite markers and their application in yellow catfish (Pseudobagrus fulvidraco Richardson, 1846) population genetics of Korea

      JEONG-NAM YU SANG-KI KIM JIN SAGONG SHI HYUN RYU BYUNGSOO CHAE

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      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.

    • Establishing gene Amelogenin as sex-specific marker in yak by genomic approach

      P. P. DAS G. KRISHNAN J. DOLEY D. BHATTACHARYA S. M. DEB P. CHAKRAVARTY P. J. DAS

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      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.

    • Genetic diversity and phylogeny analysis of Antheraea assamensis Helfer (Lepidoptera: Saturniidae) based on mitochondrial DNA sequences

      MOUSUMI SAIKIA RAMESH NATH DIPALI DEVI

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      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.

    • The complete chloroplast genome of the threatened Dipentodon sinicus (Dipentodontaceae)

      MING-TAI AN XING-YONG CUI JIA-XIN YANG GUO-XIONG HU

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      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).

    • Assessment of various genetic components through NCD-I and NCD-III designs of biparental mating in opium poppy

      KRISHNA NAND MAURYA PAWAN KUMAR PAL GEETA ASTHANA ALKA SRIVASTAVA SUDHIR SHUKLA

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      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.

    • Novel mutation in Cul7 gene in a family diagnosed with 3M syndrome

      SHAGUFTA SHAIKH SURESH K. G. SHETTIGAR SANTOSH KUMAR SURITA KANTHARIA JAGANNATH KURVA SUSAN CHERIAN

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      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.

    • Genomewide analysis of homeobox gene family in apple (Malus domestica Borkh.) and their response to abiotic stress

      RONG LI HONGJUAN GE YAQING DAI YUAN LI XIN LIU QINGHUA SUN XIAOYUN WANG

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      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.

    • Matrix metalloproteinase gene polymorphisms in chronic periodontitis: a case–control study in the Indian population

      POULAMI MAJUMDER SUJAY GHOSH SUBRATA KUMAR DEY

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      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.

    • LINC24065 is a monoallelically expressed long intergenic noncoding RNA located in the cattle DLK1–DIO3 cluster

      CUI ZHANG DA XU WEINA CHEN JUNLIANG LI QINGHUA GAO SHIJIE LI

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      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.

    • Cytogenetic microarray in structurally normal and abnormal foetuses: a five year experience elucidating in creasing acceptance and clinical utility

      MEENAKSHI LALLAR PRIYANKA SRIVASTAVA ARCHANA RAI DEEPTI SAXENA KAUSIK MANDAL SHUBHA R. PHADKE

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      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.

    • Integrative taxonomy of commercially important deep water penaeoid shrimps from India

      P. PURUSHOTHAMAN REKHA DEVI CHAKRABORTY G. KUBERAN G. MAHESWARUDU

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      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.

    • Association of polymorphisms of CYP11B2 gene –344C/T and ACE gene I/D with antihypertensive response to angiotensin receptor blockers in Chinese with hypertension

      HONGTAO GONG LIYING MU TONG ZHANG XIUYING XU FENGHE DU

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      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.

    • Gene coexpression analysis reveals dose-dependent and type-specific networks responding to ionizing radiation in the aquatic model plant Lemna minor using public data

      LILI FU ZEHONG DING ANUWAT KUMPEANGKEAW XUEPIAO SUN JIAMING ZHANG

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      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.

    • Transcriptome profiling of four candidate milk genes in milk and tissue samples of temperate and tropical cattle

      OLANREWAJU B. MORENIKEJI MABEL O. AKINYEMI MATHEW WHETO OLAWALE J. OGUNSHOLA ADEBANJO A. BADEJO CLIFFORD A. CHINEKE

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      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.

    • Haplotype diversity in medically important red scorpion (Scorpiones: Buthidae: Hottentotta tamulus) from India

      VIVEK SURANSE NITIN S. SAWANT D. B. BASTAWADE NEELESH DAHANUKAR

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      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.

    • OsNAC-like transcription factor involved in regulating seed-storage protein content at different stages of grain filling in rice under aerobic conditions

      GAURAV SHARMA ATUL KUMAR UPADYAY HANAMAREDDY BIRADAR SONIA SHAILAJA HITTALMANI

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      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.

    • Genetic diversity and population structure of two endemic Cupressus (Cupressaceae) species on the Qinghai-Tibetan plateau

      YARU FU SHAOKE LI QIQIANG GUO WEILIE ZHENG RUI YANG HUIE LI

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      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.

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