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. 2022 Sep 12;256(4):79.
doi: 10.1007/s00425-022-03986-0.

Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea

Niraj Khemka  1 , Mohan Singh Rajkumar  1 , Rohini Garg  2 , Mukesh Jain  3
Affiliations

Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea

Niraj Khemka et al. Planta. .

Abstract

The integrated transcriptome data analyses suggested the plausible roles of lncRNAs during seed development in chickpea. The candidate lncRNAs associated with QTLs and those involved in miRNA-mediated seed size/weight determination in chickpea have been identified. Long non-coding RNAs (lncRNAs) are important regulators of various biological processes. Here, we identified lncRNAs at seven successive stages of seed development in small-seeded and large-seeded chickpea cultivars. In total, 4751 lncRNAs implicated in diverse biological processes were identified. Most of lncRNAs were conserved between the two cultivars, whereas only a few of them were conserved in other plants, suggesting their species-specificity. A large number of lncRNAs differentially expressed between the two chickpea cultivars associated with seed development-related processes were identified. The lncRNAs acting as precursors of miRNAs and those mimicking target protein-coding genes of miRNAs involved in seed size/weight determination, including HAIKU1, BIG SEEDS1, and SHB1, were also revealed. Further, lncRNAs located within seed size/weight associated quantitative trait loci were also detected. Overall, we present a comprehensive resource and identified candidate lncRNAs that may play important roles during seed development and seed size/weight determination in chickpea.

Keywords: Chickpea; Gene expression; LncRNAs; MicroRNAs; Quantitative trait loci; Seed development; Seed size/weight.

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