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

OAR@ICRISAT

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Relation http://oar.icrisat.org/12681/
https://www.nature.com/articles/s41588-024-01760-4
https://doi.org/10.1038/s41588-024-01760-4
 
Title Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea
 
Creator Khan, A W
Garg, V
Sun, S
Gupta, Saurabh
Dudchenko, O
Roorkiwal, M
Chitikineni, A
Bayer, P E
Shi, C
Upadhyaya, H D
Bohra, A
Bharadwaj, C
Mir, R R
Baruch, K
Yang, B
Coyne, C J
Bansal, K C
Nguyen, H T
Ronen, G
Aiden, E L
Veneklaas, E
Siddique, K H M
Liu, X
Edwards, D
Varshney, R K
 
Subject Chickpea
Genetics and Genomics
 
Description 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.
 
Publisher Springer Nature
 
Date 2024-05-23
 
Type Article
PeerReviewed
 
Identifier Khan, A W and Garg, V and Sun, S and Gupta, Saurabh and Dudchenko, O and Roorkiwal, M and Chitikineni, A and Bayer, P E and Shi, C and Upadhyaya, H D and Bohra, A and Bharadwaj, C and Mir, R R and Baruch, K and Yang, B and Coyne, C J and Bansal, K C and Nguyen, H T and Ronen, G and Aiden, E L and Veneklaas, E and Siddique, K H M and Liu, X and Edwards, D and Varshney, R K (2024) Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nature Genetics (TSI). ISSN 1061-4036