Publications of NIPGR Scientists

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    Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea
    (Oxford University Press, 2015) Bajaj, Deepak; Saxena, Maneesha S.; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.
    Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5′-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
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    CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea
    (Indian Academy of Sciences, 2015) Bajaj, Deepak; Das, Shouvik; Parida, Swarup K.
    The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
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    Development of EST- derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability
    (Blackwell Verlag GmbH, 2012) Mishra, Raghvendra K; Gangadhar, Banieka H; Nookaraju, Akula; Kumar, Sushil; Park, Se W
    Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are important resources for gene discovery and mapping. In this study, we developed EST-based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 800 unigenes were detected from 18 522 pea EST sequences (December 2009). Screening of 10 800 unigenes by MISA (MIcroSAtellite) revealed 2612 (14.1%) eSSRs in 2395 (12.9%) SSR-containing ESTs from which 577 (24.1%) primer pairs were designed. The most abundant repeat motif identified in eSSR was mononucleotide (85.2%), followed by trinucleotide (10.6%) and dinucleotide (2.8%). Among 108 randomly selected primer pairs, 40 were assessed for mapping and 68 to test cross-species transferability in six leguminous species. Out of 40 primer pairs, 85% produced amplicons, 60% showed polymorphism and 47.5% were mapped. Furthermore, 68 primer pairs revealed high rate of transferability (48–85%) in leguminous species. High levels of polymorphism, reproducibility, presence of alleles (3.8/locus) and transferability revealed the potential use of these eSSR markers in molecular mapping, quantitative trait loci (QTL) analysis and comparative mapping in pea and other legumes.
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    Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus
    (Oxford University Press, 2011) Shokeen, Bhumika; Choudhary, Shalu; Sethy, Niroj Kumar; Bhatia, Sabhyata
    BACKGROUND AND AIMS: Catharanthus roseus is a plant of great medicinal importance, yet inadequate knowledge of its genome structure and the unavailability of genomic resources have been major impediments in the development of improved varieties. The aims of this study were to develop co-dominant sequence-tagged microsatellite sites (STMS) and gene-targeted markers (GTMs) and utilize them for the construction of a framework intraspecific linkage map of C. roseus.
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    Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.)
    (Wiley-Blackwell, 2006) Choudhary, Shalu; Sethy, Niroj K.; Shokeen, Bhumika; Bhatia, Sabhyata
    Microsatellite loci were identified from chickpea (Cicer arietinum L.), the third most important grain legume crop in the world. A total of 13 sequence-tagged microsatellite markers were developed using two different approaches: (i) amplification using degenerate primers and (ii) cloning of intersimple sequence repeat (ISSR)-amplified fragments. Thirty-five chickpea accessions were analysed, which resulted in a total of 30 alleles at the 13 loci. The observed heterozygosity ranged from 0.1143 to 0.4571 with an average of 0.2284. The cross-species transferability of the sequence-tagged microsatellite site (STMS) markers was checked in Cicer reticulatum, the wild annual progenitor of chickpea. These microsatellite markers will be useful for assessing the genetic diversity patterns within chickpea as well as aid in construction of intra- and interspecific genetic linkage maps.
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    Development of STMS markers from the medicinal plant Madagascar periwinkle (Catharanthus roseus L.) G. Don
    (Wiley-Blackwell, 2005) Shokeen, Bhumika; Sethy, Niroj K.; Choudhary, Shalu; Bhatia, Sabhyata
    We report the isolation and characterization of the first set of sequence-tagged microsatellites sites (STMS) markers in Catharanthus roseus, a plant with a vast range of medicinal uses. The microsatellite loci were cloned from an enriched library constructed using degenerate primers. Based on the microsatellite motifs, seven STMS primer pairs were designed. They were used to amplify 32 accessions of C. roseus and one accession of Catharanthus trichophyllus. The primers amplified an average of 3.86 alleles per locus. The observed heterozygosity ranged from 0.2903 to 0.9688 with an average of 0.7511. The STMS markers of C. roseus also amplified corresponding loci in a related species (C. trichophyllus) suggesting conservation of the loci across the genus. These markers will prove useful for genetic diversity analysis and linkage map construction in C. roseus.
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    Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.)
    (Wiley-Blackwell, 2003) Sethy, Niroj K.; Shokeen, Bhumika; Bhatia, Sabhyata
    In this study we report the isolation of microsatellite sequences and their conversion to sequence-tagged microsatellite sites (STMS) markers in chickpea (Cicer arietinum L.). Thirteen putative recombinants isolated from a chickpea genomic library were sequenced, and used to design 10 STMS primer pairs. These were utilized to analyse the genetic polymorphism in 15 C. arietinum varieties and two wild varieties, C. echinospermum and C. reticulatum. All the primer pairs amplified polymorphic loci ranging from four to seven alleles per locus. The observed heterozygosity ranged from 0 to 0.6667. Most of the STMS markers also amplified corresponding loci in the wild relatives suggesting conservation of these markers in the genus. Hence, these polymorphic markers will be useful for the evaluation of genetic diversity and molecular mapping in chickpea.