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 Aiden; Erik Veneklaas; Kadambot H.M. Siddique; Xin Liu; David Edwards; Rajeev K. Varshney

doi:10.1038/s41588-024-01760-4

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 Aiden

Erik Veneklaas, Kadambot H.M. Siddique, Xin Liu, David Edwards, Rajeev K. Varshney

United Arab Emirates University

International Crops Research Institute for the Semi-Arid Tropics
University of Western Australia
University of Missouri
Murdoch University
BGI Research
Curtin University
Baylor College of Medicine
University of Georgia
ICAR - Indian Agricultural Research Institute
Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu
Park HaMada
BGI-Australia
Washington State University Pullman
NASC Complex
BGI Research

Research output: Contribution to journal › Article › peer-review

61 Scopus citations

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 language	English
Pages (from-to)	1225-1234
Number of pages	10
Journal	Nature Genetics
Volume	56
Issue number	6
DOIs	https://doi.org/10.1038/s41588-024-01760-4
State	Published - Jun 2024

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Khan, A. W., Garg, V., Sun, S., Gupta, S., 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., ... Varshney, R. K. (2024). Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nature Genetics, 56(6), 1225-1234. https://doi.org/10.1038/s41588-024-01760-4

@article{8a4235a96d454f82a0d0c7ecb55a1682,

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

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.",

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

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature America, Inc. 2024. corrected publication 2024.",

year = "2024",

month = jun,

doi = "10.1038/s41588-024-01760-4",

language = "English",

volume = "56",

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journal = "Nature Genetics",

issn = "1061-4036",

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Khan, AW, Garg, V, Sun, S, Gupta, S, Dudchenko, O, Roorkiwal, M, Chitikineni, A, Bayer, PE, Shi, C, Upadhyaya, HD, Bohra, A, Bharadwaj, C, Mir, RR, Baruch, K, Yang, B, Coyne, CJ, Bansal, KC, Nguyen, HT, Ronen, G, Aiden, EL, Veneklaas, E, Siddique, KHM, Liu, X, Edwards, D & Varshney, RK 2024, 'Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea', Nature Genetics, vol. 56, no. 6, pp. 1225-1234. https://doi.org/10.1038/s41588-024-01760-4

TY - JOUR

T1 - Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

AU - Khan, Aamir W.

AU - Garg, Vanika

AU - Sun, Shuai

AU - Gupta, Saurabh

AU - Dudchenko, Olga

AU - Roorkiwal, Manish

AU - Chitikineni, Annapurna

AU - Bayer, Philipp E.

AU - Shi, Chengcheng

AU - Upadhyaya, Hari D.

AU - Bohra, Abhishek

AU - Bharadwaj, Chellapilla

AU - Mir, Reyazul Rouf

AU - Baruch, Kobi

AU - Yang, Bicheng

AU - Coyne, Clarice J.

AU - Bansal, Kailash C.

AU - Nguyen, Henry T.

AU - Ronen, Gil

AU - Aiden, Erez Lieberman

AU - Veneklaas, Erik

AU - Siddique, Kadambot H.M.

AU - Liu, Xin

AU - Edwards, David

AU - Varshney, Rajeev K.

N1 - Publisher Copyright: © The Author(s), under exclusive licence to Springer Nature America, Inc. 2024. corrected publication 2024.

PY - 2024/6

Y1 - 2024/6

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85194047045

U2 - 10.1038/s41588-024-01760-4

DO - 10.1038/s41588-024-01760-4

M3 - Article

C2 - 38783120

AN - SCOPUS:85194047045

SN - 1061-4036

VL - 56

SP - 1225

EP - 1234

JO - Nature Genetics

JF - Nature Genetics

IS - 6

ER -

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

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