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 & 20 others 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

Research output: Contribution to journalArticle

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 languageEnglish
Pages (from-to)857-+
Number of pages11
JournalNature Genetics
Volume51
Issue number5
DOIs
Publication statusPublished - May 2019

Cite this

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. ; Krishnamurthy, Lakshmanan ; Dixit, G. P. ; Fikre, Asnake ; Kimurto, Paul K. ; Sreeman, Sheshshayee M. ; Bharadwaj, Chellapilla ; Tripathi, Shailesh ; Wang, Jun ; Lee, Suk-Ha ; Edwards, David ; Polavarapu, Kavi Kishor Bilhan ; Penmetsa, R. Varma ; Crossa, Jose ; Nguyen, Henry T. ; Siddique, Kadambot H. M. ; Colmer, Timothy D. ; Sutton, Tim ; von Wettberg, Eric ; Vigouroux, Yves ; Xu, Xun ; Liu, Xin. / Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. In: Nature Genetics. 2019 ; Vol. 51, No. 5. pp. 857-+.
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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.",
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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-+. https://doi.org/10.1038/s41588-019-0401-3

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. / 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.; Krishnamurthy, Lakshmanan; Dixit, G. P.; Fikre, Asnake; Kimurto, Paul K.; Sreeman, Sheshshayee M.; Bharadwaj, Chellapilla; Tripathi, Shailesh; Wang, Jun; Lee, Suk-Ha; Edwards, David; Polavarapu, Kavi Kishor Bilhan; Penmetsa, R. Varma; Crossa, Jose; Nguyen, Henry T.; Siddique, Kadambot H. M.; Colmer, Timothy D.; Sutton, Tim; von Wettberg, Eric; Vigouroux, Yves; Xu, Xun; Liu, Xin.

In: Nature Genetics, Vol. 51, No. 5, 05.2019, p. 857-+.

Research output: Contribution to journalArticle

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

Y1 - 2019/5

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

VL - 51

SP - 857-+

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 5

ER -