Institutional Publications

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Author: search.filters.author.Parida, Swarup K.Subject: search.filters.subject.seed size

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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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    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.