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<p>Chickpea (<i>Cicer arietinum</i> L.) is one of the important legumes providing a rich source of dietary intake. Although numerous genomics studies have been performed in chickpea, a comprehensive pan-transcriptome analysis across diverse chickpea accessions has not been conducted. In this study, we analyzed the transcriptomes of 32 chickpea accessions, comprising 21 desi-type, 9 kabuli-type, and 2 wild accessions, employing reference-based RNA-seq approach. We identified genes expressed in an accession-specific manner as well as the genes preferentially expressed in desi, kabuli, and wild chickpeas. The analysis of single-nucleotide polymorphisms (SNPs) across 32 accessions revealed phylogenetic relationships distinguishing the three chickpea types. The SNPs located within the coding regions linked to seed size/weight and drought stress response traits were identified. Further, we highlighted candidate genes for these traits based on their colocalization with quantitative trait loci and presence of non-synonymous SNPs with potential impact on the stability of the encoded proteins. Overall, this study provides a valuable resource for the pan-transcriptome, gene expression atlas, and transcriptome-wide SNP map to facilitate large-scale functional characterization and genotyping applications in chickpea.</p>

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Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits

  • 期刊论文

  • 发表日期：

    2026年3月28日

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  • Mohan Singh Rajkumar,
  • Ayushman Kumar Banerjee,
  • Juhi Bansal,
  • Mukesh Jain,
  • Rohini Garg

摘要

Chickpea (Cicer arietinum L.) is one of the important legumes providing a rich source of dietary intake. Although numerous genomics studies have been performed in chickpea, a comprehensive pan-transcriptome analysis across diverse chickpea accessions has not been conducted. In this study, we analyzed the transcriptomes of 32 chickpea accessions, comprising 21 desi-type, 9 kabuli-type, and 2 wild accessions, employing reference-based RNA-seq approach. We identified genes expressed in an accession-specific manner as well as the genes preferentially expressed in desi, kabuli, and wild chickpeas. The analysis of single-nucleotide polymorphisms (SNPs) across 32 accessions revealed phylogenetic relationships distinguishing the three chickpea types. The SNPs located within the coding regions linked to seed size/weight and drought stress response traits were identified. Further, we highlighted candidate genes for these traits based on their colocalization with quantitative trait loci and presence of non-synonymous SNPs with potential impact on the stability of the encoded proteins. Overall, this study provides a valuable resource for the pan-transcriptome, gene expression atlas, and transcriptome-wide SNP map to facilitate large-scale functional characterization and genotyping applications in chickpea.