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

Nature Genetics volume 51, pages 857–864 (2019)Cite this article

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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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Fig. 1: A circos diagram illustrating the genome-wide variations among 429 chickpea lines.
Fig. 2: Genome-wide variations, population structure and genetic diversity in 429 chickpea genotypes.
Fig. 3: Population diversity in 429 chickpea genotypes. Phylogenetic tree constructed using SNPs identified.
Fig. 4: Selection sweeps and reduction of diversity

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Data availability

The data that support the findings of this study have been deposited in the NCBI under accession code SRA: SRP096939; BioProject: PRJNA362278, and these data are also available in the CNSA (https://db.cngb.org/cnsa/) of CNGBdb with accession code CNP0000370.

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Acknowledgements

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. ICRISAT is a member of the CGIAR Consortium.

Author information

Author notes

  1. Sushil K. Chaturvedi

    Present address: Rani Lakshmi Bai Central Agricultural University, Jhansi, India

  2. Asnake Fikre

    Present address: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Addis Ababa, Ethiopia

Authors and Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Rajeev K. Varshney, Mahendar Thudi, Manish Roorkiwal, Hari D. Upadhyaya, Prasad Bajaj, Abhishek Rathore, Dadakhalandar Doddamani, Aamir W. Khan, Vanika Garg, Annapurna Chitikineni, Pooran M. Gaur & Lakshmanan Krishnamurthy

  2. BGI-Shenzhen, Shenzhen, China

    Weiming He, Wei Yang, Jianbo Jian, Dawen Xu, Jun Wang, Xun Xu & Xin Liu

  3. Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France

    Philippe Cubry & Yves Vigouroux

  4. The University of Western Australia (UWA), Crawley, Western Australia, Australia

    Aamir W. Khan, David Edwards, Kadambot H. M. Siddique & Timothy D. Colmer

  5. Osmania University, Hyderabad, India

    Vanika Garg & Kavi Kishor Bilhan Polavarapu

  6. Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, India

    Narendra P. Singh, Sushil K. Chaturvedi & G. P. Dixit

  7. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya

    Gangarao V. P. R. Nadigatla

  8. Ethiopian Institute of Agricultural Research (EIAR), Debre Ziet, Ethiopia

    Asnake Fikre

  9. Egerton University, Njoro, Kenya

    Paul K. Kimurto

  10. University of Agricultural Sciences–Bangalore, Bangalore, India

    Sheshshayee M. Sreeman

  11. ICAR–Indian Agricultural Research Institute (IARI), New Delhi, India

    Chellapilla Bharadwaj & Shailesh Tripathi

  12. iCarbonX, Shenzhen, China

    Jun Wang

  13. Seoul National University, Seoul, South Korea

    Suk-Ha Lee

  14. University of California–Davis, Davis, CA, USA

    R. Varma Penmetsa

  15. International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico

    José Crossa

  16. University of Missouri, National Center for Soybean Biotechnology, Columbia, SC, USA

    Henry T. Nguyen

  17. South Australian Research and Development Institute, Adelaide, South Australia, Australia

    Tim Sutton

  18. University of Adelaide, Glen Osmond, South Australia, Australia

    Tim Sutton

  19. University of Vermont, Burlington, VT, USA

    Eric von Wettberg

  20. China National Gene Bank (CNGB), Shenzhen, China

    Xun Xu

  21. State Key Laboratory of Agricultural Genomics, Shenzhen, China

    Xin Liu

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  1. Rajeev K. Varshney
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  40. Xin Liu
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Contributions

R.K.V. conceived and designed the experiments. R.K.V., X.X. and X.L. coordinated sequencing and genome analysis. W.H., W.Y., J.J., H.D.U., N.P.S., S.K.C., G.V.P.R.N., L.K., A.F., K.K.B.P., P.M.G. and S.M.S. performed the experiments. W.H., P.B., A.R., D.D., V.G., A.W.K., H.D.U., J.C. and Y.V. performed statistical analysis. R.K.V., M.T., M.R., A.C., P.C., C.B., S.T., J.W., S.-H.L., D.E., K.K.B.P., R.V.P., J.C., H.T.N., K.H.M.S., T.D.C., T.S., E.v.W., Y.V., X.X. and X.L. analyzed the data. R.K.V., H.D.U., A.C., P.M.G., N.P.S., S.K.C., G.P.D., D.X., J.W., X.X. and X.L. contributed to the reagents, materials and analysis tools. R.K.V., M.T., M.R., W.H. and X.L. wrote the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Rajeev K. Varshney, Xun Xu or Xin Liu.

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Varshney, R.K., Thudi, M., Roorkiwal, M. et al. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nat Genet 51, 857–864 (2019). https://doi.org/10.1038/s41588-019-0401-3

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