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
Full text not available from this repository. (Request a copy)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.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Genome assembly algorithms, Sequence annotation |
| Subjects: | Mandate crops > Chickpea Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 27 May 2024 05:38 |
| Last Modified: | 27 May 2024 05:38 |
| URI: | http://oar.icrisat.org/id/eprint/12681 |
| Official URL: | https://www.nature.com/articles/s41588-024-01760-4 |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | R.K.V. is thankful to DivSeek International Network and its members, especially S. McCouch and G. King, for useful discussions. R.K.V. also acknowledges funding support in part from the Department of Agriculture and Farmers’ Welfare, Ministry of Agriculture and Farmers’ Welfare; Department of Biotechnology, Ministry of Science and Technology under the Indo- Australian Biotechnology Fund, Government of India, the Bill and Melinda Gates Foundation and Food Futures Institute of Murdoch University. X.L. acknowledges the National Key R&D Program of China (2019YFC1711000), the Shenzhen Municipal Government of China (JCYJ20170817145512476) and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011). A.W.K. acknowledges Faculty Scholarship for International Research Fees for funding support during his PhD tenure. C.J.C. acknowledges CRIS Project 2090-21000-037-000D for the United States Department of Agriculture portion of plant material preparation. |
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