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

An Author Correction to this article was published on 29 May 2024

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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.

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Fig. 1: Genomic features of Cicer species.
Fig. 2: Evolution of Cicer genus.
Fig. 3: Landscape of the Cicer super-pangenome.
Fig. 4: Trait-linked SVs and new alleles identified in Cicer wild species.

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Data availability

The raw sequencing data generated in the study are available in the NCBI BioProject under accession number PRJNA729451. The genome assemblies are available in NCBI with BioProject number PRJNA1043734(GenBank IDs: JBBPBO000000000, JBBPBP000000000, JBBPBQ000000000, JBBPBR000000000, JBBPBS000000000, JBBPBT000000000, JBBPBU000000000 and JBBPBV000000000). The genome assemblies, annotation and graph-based super-pangenome are available on figshare at https://doi.org/10.6084/m9.figshare.23599143 (ref. 89).

Code availability

All data were analyzed with standard programs and open source packages/tools, as detailed in Methods.

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Acknowledgements

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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Contributions

R.K.V. conceived and designed the experiments. R.K.V., D.E. and X.L. coordinated the genome data analysis. R.K.V., A.W.K., A.C., O.D. and E.L.A. coordinated the genome sequencing. A.W.K., A.C. and O.D. performed the laboratory and field experiments. A.W.K., V.G., S.S., S.G., M.R., P.E.B., C.S., A.B., C.B., R.R.M., K.B., B.Y., K.C.B., H.T.N., G.R., E.V., K.H.M.S. and X.L. analyzed the data. A.W.K., V.G., S.S., S.G. and X.L. performed statistical analysis. R.K.V., A.C., O.D., E.L.A., C.J.C., H.D.U. and X.L. contributed to the reagents, materials and analysis tools. A.W.K., V.G., K.H.M.S., X.L., D.E. and R.K.V. wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to Xin Liu, David Edwards or Rajeev K. Varshney.

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Khan, A.W., Garg, V., Sun, S. et al. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 56, 1225–1234 (2024). https://doi.org/10.1038/s41588-024-01760-4

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