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<p>Chickpea (<i>Cicer arietinum</i> L.) is an important protein-rich legume crop; however, the molecular determinants underlying seed protein accumulation remain poorly understood. In this study, we integrated transcriptome (RNA-seq) and small RNA (miRNA) sequencing to uncover genetic, transcriptional, and post-transcriptional regulatory networks underlying seed protein variation between contrasting chickpea genotypes, ICC8397 (high protein) and FG212 (low protein). RNA-seq analysis of mature seeds identified 2810 significantly differentially expressed genes (DEGs), including several associated with seed storage proteins (SSP), sugar and fatty acid metabolism, transcription factors, hormone related regulatory pathways. To examine spatiotemporal expression patterns, selected genes and regulatory factors, were further analyzed using qRT-PCR across seed developmental stages (10, 20, 30, 40 DAA, and maturity). Genes <i>Ca_Albu7, Ca_VIC3.3, Ca_LEG4</i> and <i>Ca_GLUT6</i>, <i>Ca_LEG3.1</i> showed elevated expression during initial (10-20DAA) and later stages of seed development in ICC8397. While these patterns are consistent with coordinated regulation of seed development, they do not directly measure protein accumulation dynamics. Further, small RNA sequencing identified differentially expressed, 85 known and 46 novel miRNAs and integrated analysis revealed inverse relationship between several miRNAs (e.g., miR156, miR164, miR169, and miR319) and their predicted targets at different stages of seed development. Overall, such comprehensive multi-omics study provides a set of candidate genes and miRNAs associated with seed protein content in chickpea and establishes a framework for future functional, biochemical, and genetic studies to determine causal mechanism underlying protein accumulation.</p>

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Integrated Transcriptomic and Small RNA Profiling Reveals Regulatory Networks Associated With Seed Protein Accumulation in Chickpea (Cicer arietinum L.)

  • 期刊论文

  • 发表日期：

    2026年7月16日

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  • Gopal Kalwan,
  • Deshika Kohli,
  • Yashwant Kumar Yadava,
  • Sheel Yadav,
  • Suruchi Khanna,
  • Ila Joshi,
  • MS Nimmy,
  • S. V. Amitha Mithra,
  • Biswajit Mondal,
  • Shailesh Tripathi,
  • Satvir Kaur Grewal,
  • Kishor Gaikwad,
  • Pawan Kumar Agrawal,
  • Venkatraman Hegde,
  • Pradeep Kumar Jain

摘要

Chickpea (Cicer arietinum L.) is an important protein-rich legume crop; however, the molecular determinants underlying seed protein accumulation remain poorly understood. In this study, we integrated transcriptome (RNA-seq) and small RNA (miRNA) sequencing to uncover genetic, transcriptional, and post-transcriptional regulatory networks underlying seed protein variation between contrasting chickpea genotypes, ICC8397 (high protein) and FG212 (low protein). RNA-seq analysis of mature seeds identified 2810 significantly differentially expressed genes (DEGs), including several associated with seed storage proteins (SSP), sugar and fatty acid metabolism, transcription factors, hormone related regulatory pathways. To examine spatiotemporal expression patterns, selected genes and regulatory factors, were further analyzed using qRT-PCR across seed developmental stages (10, 20, 30, 40 DAA, and maturity). Genes Ca_Albu7, Ca_VIC3.3, Ca_LEG4 and Ca_GLUT6, Ca_LEG3.1 showed elevated expression during initial (10-20DAA) and later stages of seed development in ICC8397. While these patterns are consistent with coordinated regulation of seed development, they do not directly measure protein accumulation dynamics. Further, small RNA sequencing identified differentially expressed, 85 known and 46 novel miRNAs and integrated analysis revealed inverse relationship between several miRNAs (e.g., miR156, miR164, miR169, and miR319) and their predicted targets at different stages of seed development. Overall, such comprehensive multi-omics study provides a set of candidate genes and miRNAs associated with seed protein content in chickpea and establishes a framework for future functional, biochemical, and genetic studies to determine causal mechanism underlying protein accumulation.