Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

Aamir W. Khan, Vanika Garg, Shuai Sun, Saurabh Gupta, Olga Dudchenko, Manish Roorkiwal, Annapurna Chitikineni, Philipp E. Bayer, Chengcheng Shi, Hari D. Upadhyaya, Abhishek Bohra, Chellapilla Bharadwaj, Reyazul Rouf Mir, Kobi Baruch, Bicheng Yang, Clarice J. Coyne, Kailash C. Bansal, Henry T. Nguyen, Gil Ronen, Erez Lieberman AidenErik Veneklaas, Kadambot H.M. Siddique, Xin Liu, David Edwards, Rajeev K. Varshney

Research output: Contribution to journalArticlepeer-review

1 Citation (Web of Science)

Abstract

Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

Original languageEnglish
Pages (from-to)1225-1234
Number of pages20
JournalNature Genetics
Volume56
Issue number6
Early online date23 May 2024
DOIs
Publication statusPublished - Jun 2024

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