Publications of NIPGR Scientists

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    Analysis of genomic-transcriptomic dynamics delineates key molecular signatures modulating seed size and weight in lentil
    (John Wiley & Sons, 2026) Padhy, Asish Kumar; Singh, Sangeeta; Tripathi, Kuldeep; Parida, Swarup K.; Bhatia, Sabhyata
    Delineating key genetic determinants associated with seed size/weight is crucial for increasing productivity. In this study, the advantages of an integrated approach combining QTL mapping, GWAS and transcriptomics to identify robust candidates governing seed size and weight were demonstrated in lentil, an important grain legume. QTL mapping identified three stable QTLs harbouring 5113 genes. GWAS identified 42 MTAs (5 consistent) containing 192 underlying genes. Comparative transcriptome analysis identified 1202 differentially expressed transcripts. Integrated analysis of the results obtained from QTL mapping and GWAS revealed nine SNPs located in the three robust QTLs harbouring 32 candidate genes. Upon integration with transcriptome data, only one (LcWDL1) was identified as the most promising candidate. LcWDL1 (a member of TPX2 family involved in microtubule organisation and cell expansion) and its predicted interacting partners that is, LcGLIPs are known to function as regulators of seed size. Candidate gene-based association analysis identified a SNP on second exon of LcWDL1 to be significantly associated with seed size and weight of lentil. The genomic loci/candidate gene identified in the study will serve to expedite the molecular breeding and gene editing programs for enhancing seed size and seed weight in lentils.
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    Key determinants of seed size for enhancing genetic gain in legumes
    (John Wiley & Sons, 2026) Padhy, Asish Kumar; Singh, Ananya; Chaurasia, Shiksha; Parida, Swarup Kumar; Tripathi, Kuldeep; Bhatia, Sabhyata
    Legumes play a pivotal role in human nutrition due to their high nutritional value, especially protein content. Therefore, enhancing the productivity of grain legumes is desirable for ensuring food and nutritional security. Seed size and seed weight are key factors influencing productivity. This article consolidates the substantial amount of research conducted to uncover the molecular signatures associated with seed size into a structured format, providing a one-stop platform of available resources for enhancing genetic gains in legumes. The advent of NGS technologies enabled the decryption of genomes and transcriptomes of important grain legumes. Moreover, molecular signatures such as SSRs, SNPs, transcription factors, methylation patterns and so forth scanned from phenotypically and genotypically well-characterized natural and mapping populations helped identify the QTLs, MTAs and candidate genes associated with seed size. Many of these QTLs and candidate genes have been utilized in marker-assisted breeding for achieving larger seeds and enhanced yield in legumes. Besides, the characterization of legume orthologs of candidate genes from other crops using different omics approaches helped in understanding the regulatory pathways involved in seed size determination in legumes. This review provides a direction for the effective utilization of available resources to enhance legume productivity.
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    PROTEIN L-ISOASPARTYL METHYLTRANSFERASE protects enolase dysfunction by repairing isoaspartyl-induced damage and is positively implicated in agronomically important seed traits
    (John Wiley & Sons, 2024) Kamble, Nitin Uttam; Ghosh, Shraboni; Petla, Bhanu Prakash; Achary, Rakesh Kumar; Gautam, Shikha; Rao, Venkateswara; Salvi, Prafull; Hazra, Abhijit; Varshney, Vishal; Majee, Manoj
    The protein-repairing enzyme (PRE) PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT) influences seed vigor by repairing isoaspartyl-mediated protein damage in seeds. However, PIMTs function in other seed traits, and the mechanisms by which PIMT affects such seed traits are still poorly understood. Herein, through molecular, biochemical, and genetic studies using overexpression and RNAi lines in Oryza sativa and Arabidopsis thaliana, we demonstrate that PIMT not only affects seed vigor but also affects seed size and weight by modulating enolase (ENO) activity. We have identified ENO2, a glycolytic enzyme, as a PIMT interacting protein through Y2H cDNA library screening, and this interaction was further validated by BiFC and co-immunoprecipitation assay. We show that mutation or suppression of ENO2 expression results in reduced seed vigor, seed size, and weight. We also proved that ENO2 undergoes isoAsp modification that affects its activity in both in vivo and in vitro conditions. Further, using MS/MS analyses, amino acid residues that undergo isoAsp modification in ENO2 were identified. We also demonstrate that PIMT repairs such isoAsp modification in ENO2 protein, protecting its vital cellular functions during seed maturation and storage, and plays a vital role in regulating seed size, weight, and seed vigor. Taken together, our study identified ENO2 as a novel substrate of PIMT, and both ENO2 and PIMT in turn implicate in agronomically important seed traits.
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    CONSTANS, a key-player connecting day length to seed size
    (Elsevier B.V., 2023) Achary, Rakesh Kumar; Majee, Manoj
    Plants sense oscillation in the day length as a reliable seasonal cue to drive optimal vegetative and reproductive growth. A recent study by Yu et al. has revealed how day length regulates seed size through CONSTANS. The CONSTANS-APETALA2 module enables plants to optimize their reproductive growth based on their photoperiod response type.
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    Transcriptome analysis reveals key pathways and candidate genes controlling seed development and size in ricebean (Vigna umbellata)
    (Frontiers Media S.A., 2022) Verma, Sachin Kumar; Mittal, Shikha; Gayacharan; Wankhede, Dhammaprakash Pandhari; Parida, Swarup K.; Chattopadhyay, Debasis; Prasad, Geeta; Mishra, Dwijesh Chandra; Joshi, Dinesh Chandra; Singh, Mohar; Singh, Kuldeep; Singh, Amit Kumar
    Ricebean (Vigna umbellata) is a lesser known pulse with well-recognized potential. Recently, it has emerged as a legume with endowed nutritional potential because of high concentration of quality protein and other vital nutrients in its seeds. However, the genes and pathways involved in regulating seed development and size are not understood in this crop. In our study, we analyzed the transcriptome of two genotypes with contrasting grain size (IC426787: large seeded and IC552985: small seeded) at two different time points, namely, 5 and 10 days post-anthesis (DPA). The bold seeded genotype across the time points (B5_B10) revealed 6,928 differentially expressed genes (DEGs), whereas the small seeded genotype across the time point (S5_S10) contributed to 14,544 DEGs. We have also identified several candidate genes for seed development-related traits like seed size and 100-seed weight. On the basis of similarity search and domain analysis, some candidate genes (PHO1, cytokinin dehydrogenase, A-type cytokinin, and ARR response negative regulator) related to 100-seed weight and seed size showed downregulation in the small seeded genotype. The MapMan and KEGG analysis confirmed that auxin and cytokinin pathways varied in both the contrasting genotypes and can therefore be the regulators of the seed size and other seed development-related traits in ricebeans. A total of 51 genes encoding SCF TIR1/AFB , Aux/IAA, ARFs, E3 ubiquitin transferase enzyme, and 26S proteasome showing distinct expression dynamics in bold and small genotypes were also identified. We have also validated randomly selected SSR markers in eight accessions of the Vigna species (V. umbellata: 6; Vigna radiata: 1; and Vigna mungo: 1). Cross-species transferability pattern of ricebean-derived SSR markers was higher in V. radiata (73.08%) than V. mungo (50%). To the best of our knowledge, this is the first transcriptomic study conducted in this crop to understand the molecular basis of any trait. It would provide us a comprehensive understanding of the complex transcriptome dynamics during the seed development and gene regulatory mechanism of the seed size determination in ricebeans.