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 W Khan; Vanika Garg; Annapurna Chitikineni; Dawen Xu; Pooran M Gaur; Narendra P Singh; Sushil K Chaturvedi; Gangarao V P R Nadigatla; Lakshmanan Krishnamurthy; G P Dixit; Asnake Fikre; Paul K 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

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

Nat Genet. 2019 May;51(5):857-864. doi: 10.1038/s41588-019-0401-3. Epub 2019 Apr 29.

Authors

Rajeev K Varshney¹, Mahendar Thudi², Manish Roorkiwal², Weiming He³, Hari D Upadhyaya², Wei Yang³, Prasad Bajaj², Philippe Cubry⁴, Abhishek Rathore², Jianbo Jian³, Dadakhalandar Doddamani², Aamir W Khan^{2

5}, Vanika Garg^{2

6}, Annapurna Chitikineni², Dawen Xu³, Pooran M Gaur², Narendra P Singh⁷, Sushil K Chaturvedi^{7

8}, Gangarao V P R Nadigatla⁹, Lakshmanan Krishnamurthy², G P Dixit⁷, Asnake Fikre^{10

11}, Paul K Kimurto¹², Sheshshayee M Sreeman¹³, Chellapilla Bharadwaj¹⁴, Shailesh Tripathi¹⁴, Jun Wang^{3

15}, Suk-Ha Lee¹⁶, David Edwards⁵, Kavi Kishor Bilhan Polavarapu⁶, R Varma Penmetsa¹⁷, José Crossa¹⁸, Henry T Nguyen¹⁹, Kadambot H M Siddique⁵, Timothy D Colmer⁵, Tim Sutton^{20

21}, Eric von Wettberg²², Yves Vigouroux⁴, Xun Xu^{23

24}, Xin Liu^{25

26}

Affiliations

¹ International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. r.k.varshney@cgiar.org.
² International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
³ BGI-Shenzhen, Shenzhen, China.
⁴ Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France.
⁵ The University of Western Australia (UWA), Crawley, Western Australia, Australia.
⁶ Osmania University, Hyderabad, India.
⁷ Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, India.
⁸ Rani Lakshmi Bai Central Agricultural University, Jhansi, India.
⁹ International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya.
¹⁰ Ethiopian Institute of Agricultural Research (EIAR), Debre Ziet, Ethiopia.
¹¹ International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Addis Ababa, Ethiopia.
¹² Egerton University, Njoro, Kenya.
¹³ University of Agricultural Sciences-Bangalore, Bangalore, India.
¹⁴ ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India.
¹⁵ iCarbonX, Shenzhen, China.
¹⁶ Seoul National University, Seoul, South Korea.
¹⁷ University of California-Davis, Davis, CA, USA.
¹⁸ International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico.
¹⁹ University of Missouri, National Center for Soybean Biotechnology, Columbia, SC, USA.
²⁰ South Australian Research and Development Institute, Adelaide, South Australia, Australia.
²¹ University of Adelaide, Glen Osmond, South Australia, Australia.
²² University of Vermont, Burlington, VT, USA.
²³ BGI-Shenzhen, Shenzhen, China. xuxun@genomics.cn.
²⁴ China National Gene Bank (CNGB), Shenzhen, China. xuxun@genomics.cn.
²⁵ BGI-Shenzhen, Shenzhen, China. liuxin@genomics.cn.
²⁶ State Key Laboratory of Agricultural Genomics, Shenzhen, China. liuxin@genomics.cn.

PMID: 31036963
DOI: 10.1038/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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cicer / classification
Cicer / genetics*
DNA, Plant / genetics
Domestication
Genetic Markers
Genetic Variation
Genome, Plant
Genome-Wide Association Study
High-Throughput Nucleotide Sequencing
Linkage Disequilibrium
Phylogeny
Plant Breeding
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Sequence Analysis, DNA

Substances

DNA, Plant
Genetic Markers