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

Article

Varshney, Rajeev K., Thudi, Mahendar, Roorkiwal, Manish, He, Weiming, Upadhyaya, Hari D., Yang, Wei, Bajaj, Prasad, Cubry, Philippe, Rathore, Abhishek, Jian, Jianbo, Doddamani, Dadakhalandar, Khan, Aamir W., Garg, Vanika, Chitikineni, Annapurna, Xu, Dawen, Gaur, Pooran M., Singh, Narendra P., Chaturvedi, Sushil K., Nadigatla, Gangarao V. P. R., ..., Liu, Xin. 2019. "Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits." Nature Genetics. 51, pp. 857-864. https://doi.org/10.1038/s41588-019-0401-3
Article Title

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

ERA Journal ID16629
Article CategoryArticle
AuthorsVarshney, Rajeev K. (Author), Thudi, Mahendar (Author), Roorkiwal, Manish (Author), He, Weiming (Author), Upadhyaya, Hari D. (Author), Yang, Wei (Author), Bajaj, Prasad (Author), Cubry, Philippe (Author), Rathore, Abhishek (Author), Jian, Jianbo (Author), Doddamani, Dadakhalandar (Author), Khan, Aamir W. (Author), Garg, Vanika (Author), Chitikineni, Annapurna (Author), Xu, Dawen (Author), Gaur, Pooran M. (Author), Singh, Narendra P. (Author), Chaturvedi, Sushil K. (Author), Nadigatla, Gangarao V. P. R. (Author), Krishnamurthy, Lakshmanan (Author), Dixit, G. P. (Author), Fikre, Asnake (Author), Kimurto, Paul K. (Author), Sreeman, Sheshshayee M. (Author), Bharadwaj, Chellapilla (Author), Tripathi, Shailesh (Author), Wang, Jun (Author), Lee, Suk-Ha (Author), Edwards, David (Author), Polavarapu, Kavi Kishor Bilhan (Author), Penmetsa, R. Varma (Author), Crossa, Jose (Author), Nguyen, Henry T. (Author), Siddique, Kadambot H. M. (Author), Colmer, Timothy D. (Author), Sutton, Tim (Author), von Wettberg, Eric (Author), Vigouroux, Yves (Author), Xu, Xun (Author) and Liu, Xin (Author)
Journal TitleNature Genetics
Journal Citation51, pp. 857-864
Number of Pages8
Year2019
Place of PublicationUnited States
ISSN1061-4036
1546-1718
Digital Object Identifier (DOI)https://doi.org/10.1038/s41588-019-0401-3
Web Address (URL)https://www.nature.com/articles/s41588-019-0401-3
Abstract

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.

Keywordschickpea, Genome-wide association studies, whole-genome resequencing
Contains Sensitive ContentDoes not contain sensitive content
ANZSRC Field of Research 2020300406. Crop and pasture improvement (incl. selection and breeding)
Public Notes

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Institution of OriginUniversity of Southern Queensland
Byline AffiliationsInternational Crops Research Institute for the Semi-Arid Tropics, India
Centre for Crop Health (Operations)
BGI Group, China
University of Montpellier, France
Indian Council of Agricultural Research, India
Rani Lakshmi Bai Central Agricultural University, India
International Crops Research Institute for the Semi-Arid Tropics, Kenya
International Crops Research Institute for the Semi-Arid Tropics, Ethiopia
Egerton University, Kenya
University of Agricultural Sciences Bangalore, India
iCarbonX, China
Seoul National University, Korea
University of Western Australia
Osmania University, India
University of California, United States
International Maize and Wheat Improvement Center, Mexico
University of Missouri, United States
Department of Primary Industries and Regions, South Australia
University of Vermont, United States
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