Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Rajeev K Varshney; Mahendar Thudi; Manish Roorkiwal; Weiming He; Hari D. Upadhyaya; Wei Yang; Prasad Bajaj; Philippe Cubry; Abhishek Rathore; Jianbo Jian; Dadakhalandar Doddamani; Aamir Khan; Vanika Garg; Annapurna Chitikineni; Dawen Xu; Pooran M. Gaur; Narendra Pratap Singh; Sushil K. Chaturvedi; Gangarao V. P. R. Nadigatla; Lakshmanan Krishnamurthy; Girish Prasad Dixit; Asnake Fikre; Paul Kimurto; Sheshshayee M. Sreeman; Chellapilla Bharadwaj; Shailesh Tripathi; Jun Wang; Suk-Ha Lee; David Edwards; Kavi Kishor Bilhan Polavarapu; R. Varma Penmetsa; José Crossa; Henry T. Nguyen; Kadambot H. M. Siddique; Timothy D. Colmer; Tim Sutton; Eric von Wettberg; Yves Vigouroux; Xun Xu; Xin Liu

doi:10.1038/s41588-019-0401-3

Back

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Journal article

Peer reviewed

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Rajeev K Varshney, Mahendar Thudi, Manish Roorkiwal, Weiming He, Hari D. Upadhyaya, Wei Yang, Prasad Bajaj, Philippe Cubry, Abhishek Rathore, Jianbo Jian, …

Nature Genetics, Vol.51(5), pp.857-864

05/2019

DOI: https://doi.org/10.1038/s41588-019-0401-3

Abstract

Domestication

Genome-wide Association Studies

Genetic markers

Genetic variation

Phylogeny

Plant breeding

Hight-throughput sequencing

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

Files and links (1)

url

Find in HALView

Metrics

1 Record Views

See more details

Details

Title: Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits
Creators - without role: Rajeev K Varshney - International Crops Research Institute for the Semi-Arid Tropics
Mahendar Thudi - International Crops Research Institute for the Semi-Arid Tropics
Manish Roorkiwal - International Crops Research Institute for the Semi-Arid Tropics
Weiming He - BGI Group
Hari D. Upadhyaya - International Crops Research Institute for the Semi-Arid Tropics
Wei Yang - BGI Group
Prasad Bajaj - International Crops Research Institute for the Semi-Arid Tropics
Philippe Cubry - Université de Montpellier, Diversité, Adaptation et Développement des plantes - DIADE
Abhishek Rathore - International Crops Research Institute for the Semi-Arid Tropics
Jianbo Jian - BGI Group
Dadakhalandar Doddamani - International Crops Research Institute for the Semi-Arid Tropics
Aamir Khan - International Crops Research Institute for the Semi-Arid Tropics
Vanika Garg - International Crops Research Institute for the Semi-Arid Tropics
Annapurna Chitikineni - International Crops Research Institute for the Semi-Arid Tropics
Dawen Xu - BGI Group
Pooran M. Gaur - International Crops Research Institute for the Semi-Arid Tropics
Narendra Pratap Singh - Indian Institute of Pulses Research
Sushil K. Chaturvedi - Indian Institute of Pulses Research
Gangarao V. P. R. Nadigatla
Lakshmanan Krishnamurthy - International Crops Research Institute for the Semi-Arid Tropics
Girish Prasad Dixit - Indian Institute of Pulses Research
Asnake Fikre - Ethiopian Institute of Agricultural Research
Paul Kimurto - Egerton University
Sheshshayee M. Sreeman - University of Agricultural Sciences, Bangalore
Chellapilla Bharadwaj - Indian Agricultural Research Institute
Shailesh Tripathi - Indian Agricultural Research Institute
Jun Wang - BGI Group
Suk-Ha Lee - Seoul National University
David Edwards - University of Western Australia
Kavi Kishor Bilhan Polavarapu - Osmania University
R. Varma Penmetsa - University of California, Davis
José Crossa - Centro Internacional de Mejoramiento de Maíz Y Trigo
Henry T. Nguyen - University of Missouri
Kadambot H. M. Siddique - University of Western Australia
Timothy D. Colmer - University of Western Australia
Tim Sutton - South Australian Research and Development Institute
Eric von Wettberg - University of Vermont
Yves Vigouroux - Université de Montpellier, Diversité, Adaptation et Développement des plantes - DIADE
Xun Xu - China National GeneBank
Xin Liu - Agricultural Genomics Institute at Shenzhen
Publication Details: Nature Genetics, Vol.51(5), pp.857-864
Grant note: R.K.V. acknowledges the funding support from CGIAR Generation Challenge Programme, Department of Science and Technology Government of India under the Australia-India Strategic Research Fund, Ministry of Agriculture and Farmers Welfare, Government of India and Bill & Melinda Gates Foundation, USA. Shenzhen Municipal Government of China (grant no. JCYJ20150831201643396 and no. JCYJ20170817145512476 under the Basic Research Program) and the Guangdong Provincial Key Laboratory of Genome Read and Write (grant no. 2017B030301011) are acknowledged to provide support to X.X. and X.L. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals.
Identifiers: 9935247009311
Academic Unit: Diversité, Adaptation et Développement des plantes - DIADE
Language: English
Resource Type: Journal article
Local Fields: hal-03373029