• Vinod

      Articles written in Journal of Genetics

    • Cytotaxonomical analysis of Momordica L. (Cucurbitaceae) species of Indian occurrence

      L. K. Bharathi A. D. Munshi Vinod Shanti Chandrashekaran T. K. Behera A. B. Das K. Joseph John Vishalnath

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      Somatic chromosome number and detailed karyotype analysis were carried out in six Indian Momordica species viz. M. balsamina, M. charantia, M. cochinchinensis, M. dioica, M. sahyadrica and M. cymbalaria (syn. Luffa cymbalaria; a taxon of controversial taxonomic identity). The somatic chromosome number $2n = 22$ was reconfirmed in monoecious species (M. balsamina and M. charantia). Out of four dioecious species, the chromosome number was reconfirmed in M. cochinchinensis $(2n = 28)$, M. dioica $(2n = 28)$ and M. subangulata subsp. renigera $(2n = 56)$, while in M. sahyadrica $(2n = 28)$ somatic chromosome number was reported for the first time. A new chromosome number of $2n = 18$ was reported in M. cymbalaria against its previous reports of $2n = 16$, 22. The karyotype analysis of all the species revealed significant numerical and structural variations of chromosomes. It was possible to distinguish chromosomes of M. cymbalaria from other Momordica species and also between monoecious and dioecious taxa of the genus. Morphology and crossability among the dioecious species was also studied. Evidence from morphology, crossability, pollen viability and chromosome synapsis suggests a segmental allopolyploid origin for M. subangulata subsp. renigera. The taxonomic status of the controversial taxon M. cymbalaria was also discussed using morphological, karyological and crossability data.

    • Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.)

      C. Vanniarajan K. K. Vinod Andy Pereira

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      In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker–trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genomewide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information.

    • Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers

      Sheel Yadav Ashutosh Singh M. R. Singh Nitika Goel K. K. Vinod T. Mohapatra A. K. Singh

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      Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-à-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer’s varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI’s Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.

    • Time for the zebrafish ENCODE

      Sridhar Sivasubbu Chetana Sachidanandan Vinod Scaria

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    • Personal genomes, participatory genomics and the anonymity-privacy conundrum

      Vinod Scaria

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    • Distinct patterns of epigenetic marks and transcription factor binding sites across promoters of sense-intronic long noncoding RNAs

      Saurav Ghosh Satish Sati Shantanu Sengupta Vinod Scaria

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      Long noncoding RNAs (lncRNAs) are a new class of noncoding RNAs that have been extensively studied in the recent past as a regulator of gene expression, including modulation of epigenetic regulation. The lncRNAs class encompasses a number of subclasses, classified based on their genomic loci and relation to protein-coding genes. Functional differences between subclasses have been increasingly studied in the recent years, though the regulation of expression and biogenesis of lncRNAs have been poorly studied. The availability of genome-scale datasets of epigenetic marks has motivated us to understand the patterns and processes of epigenetic regulation of lncRNAs. Here we analysed the occurrence of expressive and repressive histone marks at the transcription start site (TSS) of lncRNAs and their subclasses, and compared these profiles with that of the protein-coding regions. We observe distinct differences in the density of histone marks across the TSS of a few lncRNA subclasses. The sense-intronic lncRNA subclass showed a paucity for mapped histone marks across the TSS which were significantly different than all the lncRNAs and protein-coding genes in most cases. Similar pattern was also observed for the density of transcription factor binding sites (TFBS). These observations were generally consistent across cell and tissue types. The differences in density across the promoter were significantly associated with the expression level of the genes, but the differences between the densities across long noncoding and protein-coding gene promoters were consistent irrespective of the expression levels. Apart from suggesting general differences in epigenetic regulatory marks across long noncoding RNA promoters, our analysis suggests a possible alternative mechanism of regulation and/or biogenesis of sense-intronic lncRNAs.

    • Genetics and mapping of a new leaf rust resistance gene in Triticum aestivum L. × Triticum timopheevii Zhuk. derivative ‘Selection G12’

      AMIT KUMAR SINGH JAI BHAGWAN SHARMA VINOD PRADEEP KUMAR SINGH ANUPAM SINGH NIHARIKA MALLICK

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      A Triticum timopheevii-derived bread wheat line, Selection G12, was screened with 40 pathotypes of leaf rust pathogen, Puccinia triticina at seedling stage and with two most commonly prevalent pathotypes 77-5 and 104-2 at adult plant stage. Selection G12 showed resistance at both seedling and adult plant stages. Genetic analysis in F1, F2 and F2.3 families at the seedling stage revealed that leaf rust resistance in Selection G12 is conditioned by a single incompletely dominant gene. The leaf rust resistance gene was mapped to chromosome 3BL with SSR markers Xgwm114 and Xgwm547 flanking the gene at a distance of 28.3 cM and 6 cM, respectively. Based on the nature of resistance and chromosomal location, it is inferred that Selection G12 carries a new gene for leaf rust resistance, tentatively named as LrSelG12.

    • Marker-assisted pyramiding of Thinopyrum-derived leaf rust resistance genes Lr19 and Lr24 in bread wheat variety HD2733

      MONA SINGH N. MALLICK S. CHAND P. KUMARI J. B. SHARMA M. SIVASAMY P. JAYAPRAKASH K. V. PRABHU S. K. JHA VINOD

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      This study was undertaken to pyramid two effective leaf rust resistance genes (Lr19 and Lr24) derived from Thinopyrum (syn. Agropyron), in the susceptible, but agronomically superior wheat cultivar HD2733 using marker-assisted selection. In the year 2001, HD2733 was released for irrigated timely sown conditions of the north eastern plains zone (NEPZ) of India became susceptibleto leaf rust, a major disease of the region. Background selection helped in developing near-isogenic lines (NILs) of HD2733 with Lr19 and Lr24 with 97.27 and 98.94%, respectively, of genomic similarity with the parent cultivar, after two backcrossing and one generation of selfing.NILs were intercrossed to combine the genes Lr19 and Lr24. The combination of these two genes in the cultivarHD2733 is expected to provide durable leaf rust resistance in farmers’ fields.

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