A chickpea genetic variation map based on the sequencing of 3,366 genomes

R.K. Varshney; M. Roorkiwal; S. Sun; P. Bajaj; A. Chitikineni; M. Thudi; N.P. Singh; X. Du; H.D. Upadhyaya; A.W. Khan; Y. Wang; V. Garg; G. Fan; W.A. Cowling; J. Crossa; L. Gentzbittel; K.P. Voss-Fels; V.K. Valluri; P. Sinha; V.K. Singh; C. Ben; A. Rathore; R. Punna; M.K. Singh; B. Tar’an; C. Bharadwaj; M. Yasin; M.S. Pithia; S. Singh; K.R. Soren; H. Kudapa; D. Jarquin; P. Cubry; L.T. Hickey; G.P. Dixit; A-C Thuillet; A. Hamwieh; S. Kumar; A.A. Deokar; S.K. Chaturvedi; A. Francis; R. Howard; D. Chattopadhyay; D. Edwards; E. Lyons; Y. Vigouroux; B.J. Hayes; E. von Wettberg; S.K. Datta; H. Yang; H.T. Nguyen; J. Wang; K.H.M. Siddique; T. Mohapatra; J.L. Bennetzen; X. Xu; X. Liu

doi:10.1038/s41586-021-04066-1

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A chickpea genetic variation map based on the sequencing of 3,366 genomes

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A chickpea genetic variation map based on the sequencing of 3,366 genomes

R.K. Varshney, M. Roorkiwal, S. Sun, P. Bajaj, A. Chitikineni, M. Thudi, N.P. Singh, X. Du, H.D. Upadhyaya, A.W. Khan, …

Nature, Vol.599, pp.622-627

2021

DOI: https://doi.org/10.1038/s41586-021-04066-1

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Abstract

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Details

Title: A chickpea genetic variation map based on the sequencing of 3,366 genomes
Authors/Creators: R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Roorkiwal (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
S. Sun (Author/Creator) - Chinese Academy of Sciences
P. Bajaj (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Thudi (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
N.P. Singh (Author/Creator) - Indian Institute of Pulses Research
X. Du (Author/Creator)
H.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A.W. Khan (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Y. Wang (Author/Creator)
V. Garg (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
G. Fan (Author/Creator)
W.A. Cowling (Author/Creator) - The University of Western Australia
J. Crossa (Author/Creator) - Centro Internacional de Mejoramiento de Maíz Y Trigo
L. Gentzbittel (Author/Creator) - Skolkovo Institute of Science and Technology
K.P. Voss-Fels (Author/Creator)
V.K. Valluri (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P. Sinha (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
V.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
C. Ben (Author/Creator) - Université Fédérale de Toulouse Midi-Pyrénées
A. Rathore (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R. Punna (Author/Creator) - Cornell University
M.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
B. Tar’an (Author/Creator) - University of Saskatchewan
C. Bharadwaj (Author/Creator) - Indian Agricultural Research Institute
M. Yasin (Author/Creator)
M.S. Pithia (Author/Creator) - Junagadh Agricultural University
S. Singh (Author/Creator)
K.R. Soren (Author/Creator) - Indian Institute of Pulses Research
H. Kudapa (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
D. Jarquin (Author/Creator) - University of Nebraska–Lincoln
P. Cubry (Author/Creator) - Institut de Recherche pour le Développement
L.T. Hickey (Author/Creator) - The University of Queensland
G.P. Dixit (Author/Creator) - Indian Institute of Pulses Research
A-C Thuillet (Author/Creator) - Institut de Recherche pour le Développement
A. Hamwieh (Author/Creator) - International Center for Agricultural Research in the Dry Areas
S. Kumar (Author/Creator) - International Center for Agricultural Research in the Dry Areas
A.A. Deokar (Author/Creator) - University of Saskatchewan
S.K. Chaturvedi (Author/Creator) - Central Agricultural University
A. Francis (Author/Creator)
R. Howard (Author/Creator) - University of Nebraska–Lincoln
D. Chattopadhyay (Author/Creator)
D. Edwards (Author/Creator) - The University of Western Australia
E. Lyons (Author/Creator) - University of Arizona
Y. Vigouroux (Author/Creator) - Institut de Recherche pour le Développement
B.J. Hayes (Author/Creator) - The University of Queensland
E. von Wettberg (Author/Creator) - University of Vermont
S.K. Datta (Author/Creator) - University of Calcutta
H. Yang (Author/Creator)
H.T. Nguyen (Author/Creator) - University of Missouri
J. Wang (Author/Creator) - BGI Group (China)
K.H.M. Siddique (Author/Creator) - The University of Western Australia
T. Mohapatra (Author/Creator) - Indian Council of Agricultural Research
J.L. Bennetzen (Author/Creator) - University of Georgia
X. Xu (Author/Creator)
X. Liu (Author/Creator)
Publication Details: Nature, Vol.599, pp.622-627
Publisher: Springer Nature
Identifiers: 991005543867307891
Copyright: © 2021 The Author(s)
Murdoch Affiliation: Centre for Crop and Food Innovation; Food Futures Institute; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics