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; Jose 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

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 KrishnamurthyG. 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, Jose Crossa, Henry T. Nguyen, Kadambot H. M. Siddique, Timothy D. Colmer, Tim Sutton, Eric von Wettberg, Yves Vigouroux, Xun Xu, Xin Liu

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

215 Citations (Scopus)

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.

Original language	English
Pages (from-to)	857-864
Number of pages	8
Journal	Nature Genetics
Volume	51
Issue number	5
DOIs	https://doi.org/10.1038/s41588-019-0401-3
Publication status	Published - 1 May 2019

Access to Document

10.1038/s41588-019-0401-3

http://oar.icrisat.org/11191/1/2019_NatureGenetics_chickpeas.pdf

Cite this

Varshney, R. K., Thudi, M., Roorkiwal, M., He, W., Upadhyaya, H. D., Yang, W., Bajaj, P., Cubry, P., Rathore, A., Jian, J., Doddamani, D., Khan, A. W., Garg, V., Chitikineni, A., Xu, D., Gaur, P. M., Singh, N. P., Chaturvedi, S. K., Nadigatla, G. V. P. R., ... Liu, X. (2019). Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics, 51(5), 857-864. https://doi.org/10.1038/s41588-019-0401-3

@article{9c1941d472264a34b40f3ea374e005cb,

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

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.",

keywords = "SITE-FREQUENCY-SPECTRUM, POPULATION-STRUCTURE, GENETIC DIVERSITY, ASSOCIATION, ADAPTATION, SEQUENCE, YIELD, WILD, FLOW",

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

year = "2019",

month = may,

day = "1",

doi = "10.1038/s41588-019-0401-3",

language = "English",

volume = "51",

pages = "857--864",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group - Macmillan Publishers",

number = "5",

}

Varshney, RK, Thudi, M, Roorkiwal, M, He, W, Upadhyaya, HD, Yang, W, Bajaj, P, Cubry, P, Rathore, A, Jian, J, Doddamani, D, Khan, AW, Garg, V, Chitikineni, A, Xu, D, Gaur, PM, Singh, NP, Chaturvedi, SK, Nadigatla, GVPR, Krishnamurthy, L, Dixit, GP, Fikre, A, Kimurto, PK, Sreeman, SM, Bharadwaj, C, Tripathi, S, Wang, J, Lee, S-H, Edwards, D, Polavarapu, KKB, Penmetsa, RV, Crossa, J, Nguyen, HT, Siddique, KHM , Colmer, TD, Sutton, T, von Wettberg, E, Vigouroux, Y, Xu, X & Liu, X 2019, 'Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits', Nature Genetics, vol. 51, no. 5, pp. 857-864. https://doi.org/10.1038/s41588-019-0401-3

TY - JOUR

T1 - Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

AU - Varshney, Rajeev K.

AU - Thudi, Mahendar

AU - Roorkiwal, Manish

AU - He, Weiming

AU - Upadhyaya, Hari D.

AU - Yang, Wei

AU - Bajaj, Prasad

AU - Cubry, Philippe

AU - Rathore, Abhishek

AU - Jian, Jianbo

AU - Doddamani, Dadakhalandar

AU - Khan, Aamir W.

AU - Garg, Vanika

AU - Chitikineni, Annapurna

AU - Xu, Dawen

AU - Gaur, Pooran M.

AU - Singh, Narendra P.

AU - Chaturvedi, Sushil K.

AU - Nadigatla, Gangarao V. P. R.

AU - Krishnamurthy, Lakshmanan

AU - Dixit, G. P.

AU - Fikre, Asnake

AU - Kimurto, Paul K.

AU - Sreeman, Sheshshayee M.

AU - Bharadwaj, Chellapilla

AU - Tripathi, Shailesh

AU - Wang, Jun

AU - Lee, Suk-Ha

AU - Edwards, David

AU - Polavarapu, Kavi Kishor Bilhan

AU - Penmetsa, R. Varma

AU - Crossa, Jose

AU - Nguyen, Henry T.

AU - Siddique, Kadambot H. M.

AU - Colmer, Timothy D.

AU - Sutton, Tim

AU - von Wettberg, Eric

AU - Vigouroux, Yves

AU - Xu, Xun

AU - Liu, Xin

PY - 2019/5/1

Y1 - 2019/5/1

N2 - 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.

AB - 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.

KW - SITE-FREQUENCY-SPECTRUM

KW - POPULATION-STRUCTURE

KW - GENETIC DIVERSITY

KW - ASSOCIATION

KW - ADAPTATION

KW - SEQUENCE

KW - YIELD

KW - WILD

KW - FLOW

U2 - 10.1038/s41588-019-0401-3

DO - 10.1038/s41588-019-0401-3

M3 - Article

C2 - 31036963

SN - 1061-4036

VL - 51

SP - 857

EP - 864

JO - Nature Genetics

JF - Nature Genetics

IS - 5

ER -

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

Abstract

Access to Document

Fingerprint

Cite this