Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits


Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: An overview on diversity in 292 Cajanus accessions.
Figure 2: A Circos image representing variations identified across 292 Cajanus accessions.
Figure 3: Significant marker–trait associations for 100-seed weight, days to 50% flowering and plant height.

Accession codes

Primary accessions



  1. 1

    Van der Maesen, L.G.J. in The Pigeonpea (eds. Nene, Y.L., Hall, S.D. & Sheilla, V.K.) 15–46 (C.A.B. International, 1990).

  2. 2

    Saxena, R.K. et al. Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS One 9, e88568 (2014).

    Article  Google Scholar 

  3. 3

    Vavilov, N.I. The origin, variation, immunity, and breeding of cultivated plants. Chron. Bot. 13, 1–366 (1951).

    Google Scholar 

  4. 4

    Varshney, R.K. et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83–89 (2011).

    Article  Google Scholar 

  5. 5

    Varshney, R.K., Thudi, M., May, G.D. & Jackson, S.A. Legume genomics and breeding. Plant Breed. Rev. 33, 257–304 (2010).

    Google Scholar 

  6. 6

    Upadhyaya, H.D. et al. Phenotyping chickpeas and pigeonpeas for adaptation to drought. Front. Physiol. 3, 179 (2012).

    CAS  Article  Google Scholar 

  7. 7

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  Article  Google Scholar 

  8. 8

    Clark, R.M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsisthaliana. Science 317, 338–342 (2007).

    CAS  Article  Google Scholar 

  9. 9

    Lam, H.M. et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42, 1053–1059 (2010).

    CAS  Article  Google Scholar 

  10. 10

    Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Tang, H., Peng, J., Wang, P. & Risch, N.J. Estimation of individual admixture: analytical and study design considerations. Genet. Epidemiol. 28, 289–301 (2005).

    Article  Google Scholar 

  12. 12

    Van der Maesen, L.J.G. Cajanus DC and Atylosia W. & A. (Leguminosae) (Agricultural University Wageningen Papers) (Wageningen Universiteit Project, 1986).

  13. 13

    Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408–414 (2015).

    CAS  Article  Google Scholar 

  14. 14

    Wang, Q., Tian, F., Pan, Y., Buckler, E.S. & Zhang, Z. A SUPER powerful method for genome wide association study. PLoS One 9, e107684 (2014).

    Article  Google Scholar 

  15. 15

    Sladek, R. et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881–885 (2007).

    CAS  Article  Google Scholar 

  16. 16

    Gudbjartsson, D.F. et al. Variants conferring risk of atrial fibrillation on chromosome 4q25. Nature 448, 353–357 (2007).

    CAS  Article  Google Scholar 

  17. 17

    McPherson, R. et al. A common allele on chromosome 9 associated with coronary heart disease. Science 316, 1488–1491 (2007).

    CAS  Article  Google Scholar 

  18. 18

    Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445–449 (2007).

    CAS  Article  Google Scholar 

  19. 19

    Pinto, D. et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368–372 (2010).

    CAS  Article  Google Scholar 

  20. 20

    Stefansson, H. et al. Large recurrent microdeletions associated with schizophrenia. Nature 455, 232–236 (2008).

    CAS  Article  Google Scholar 

  21. 21

    McCarthy, S.E. et al. Microduplications of 16p11.2 are associated with schizophrenia. Nat. Genet. 41, 1223–1227 (2009).

    CAS  Article  Google Scholar 

  22. 22

    Diskin, S.J. et al. Copy number variation at 1q21.1 associated with neuroblastoma. Nature 459, 987–991 (2009).

    CAS  Article  Google Scholar 

  23. 23

    Horiguchi, G., Gonzalez, N., Beemster, G.T., Inzé, D. & Tsukaya, H. Impact of segmental chromosomal duplications on leaf size in the grandifolia-D mutants of Arabidopsisthaliana. Plant J. 60, 122–133 (2009).

    CAS  Article  Google Scholar 

  24. 24

    Xiao, H., Jiang, N., Schaffner, E., Stockinger, E.J. & van der Knaap, E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319, 1527–1530 (2008).

    CAS  Article  Google Scholar 

  25. 25

    Maron, L.G. et al. Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc. Natl. Acad. Sci. USA 110, 5241–5246 (2013).

    CAS  Article  Google Scholar 

  26. 26

    Chia, J.M. et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44, 803–807 (2012).

    CAS  Article  Google Scholar 

  27. 27

    Saxena, R.K., Edwards, D. & Varshney, R.K. Structural variations in plant genomes. Brief. Funct. Genomics 13, 296–307 (2014).

    Article  Google Scholar 

  28. 28

    Upadhyaya, H.D. et al. Pigeonpea composite collection and identification of germplasm for use in crop improvement programmes. Plant Genet. Resour. 9, 97–108 (2011).

    CAS  Article  Google Scholar 

  29. 29

    Meyer, R.S. & Purugganan, M.D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840–852 (2013).

    CAS  Article  Google Scholar 

  30. 30

    Weller, J.L. et al. A conserved molecular basis for photoperiod adaptation in two temperate legumes. Proc. Natl. Acad. Sci. USA 109, 21158–21163 (2012).

    CAS  Article  Google Scholar 

  31. 31

    Tajima, F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–460 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    Weir, B.S. & Cockerham, C.C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).

    CAS  Google Scholar 

  33. 33

    Upadhyaya, H.D. & Gowda, C.L.L. Managing and Enhancing the Use of Germplasm—Strategies and Methodologies (International Crops Research Institute for the Semi-Arid Tropics, 2009).

  34. 34

    Bradbury, P.J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).

    CAS  Article  Google Scholar 

  35. 35

    Xu, X. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30, 105–111 (2011).

    CAS  Article  Google Scholar 

  36. 36

    Lipka, A.E. et al. GAPIT: genome association and prediction integrated tool. Bioinformatics 28, 2397–2399 (2012).

    CAS  Article  Google Scholar 

  37. 37

    Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).

    CAS  Article  Google Scholar 

Download references


The authors are thankful to the US Agency for International Development (USAID) for providing financial support to R.K.V. The authors would like to thank A. Gafoor, B. Poornima and P. Bajaj for their support in this work. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium.

Author information




R.K.V., R.K.S., Y.Y., C.K., D.K., J.K., S.A., V.K., J.-S.K. and W.Z. contributed to generation of whole-genome resequencing data. H.D.U. and R.K.V. contributed genetic material. H.D.U., G.A., K.N.Y. and S.M. performed phenotyping. R.K.V., R.K.S., H.D.U., A.W.K., C.K., A.R., D.K., J.K., S.A., J.-S.K., R.V.P., E.v.W. and S.K.D. worked on different analyses. R.K.V. and R.K.S. together with C.K., A.R., J.-S.K., R.V.P. and E.v.W. wrote and finalized the manuscript. R.K.V. and R.K.S. directed the project, and R.K.V. conceived and designed the study.

Corresponding author

Correspondence to Rajeev K Varshney.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–12, Supplementary Tables 10–12 and 17, and Supplementary Note (PDF 16895 kb)

Supplementary Table 1

Details on 300 Cajanus accessions (breeding lines, landraces and wild species accessions) including biological status, species, geographical region, country and state. (XLSX 20 kb)

Supplementary Table 2

Details on raw sequencing data generated on 292 Cajanus accessions. (XLSX 30 kb)

Supplementary Table 3

Identification and distribution of molecular variation (SNPs and indels) among 11 pseudomolecules CcLG01 to CcLG11 and unanchored genome sequence as CcLG0. (XLSX 21 kb)

Supplementary Table 4

Nonsynonymous-to-synonymous ratio in breeding lines, landraces and wild species in 1-Mb non-overlapping windows. (XLSX 17 kb)

Supplementary Table 5

Non-synonymous to synonymous ratio in breeding lines, landraces and wild species in 10 Kb non-overlapping windows (XLSX 1172 kb)

Supplementary Table 6

19 genomic regions (R1 to R19) showing high (>2.5) nonsynonymous-to-synonymous ratio in breeding lines, landraces and wild species in 1-Mb non-overlapping windows. (XLS 1068 kb)

Supplementary Table 7

Structural variations (CNVs and PAVs) identified in breeding lines as compared to the reference genome. (XLSX 29 kb)

Supplementary Table 8

Structural variations (CNVs and PAVs) identified in landraces as compared to the reference genome. (XLSX 24 kb)

Supplementary Table 9

Structural variations (CNVs and PAVs) identified in wild species accessions as compared to the reference genome. (XLSX 24 kb)

Supplementary Table 13

ROD values calculated during domestication (wild species versus landraces) and breeding (landraces versus breeding lines) at 10-kb non-overlapping windows. (XLSX 582 kb)

Supplementary Table 14

FST values for ROD regions with maximum values calculated in a pairwise manner for landraces versus breeding lines and wild species versus landraces. (XLSX 119 kb)

Supplementary Table 15

Genes that played an important role in domestication of crop species and their homologs in Cajanus. (XLSX 23 kb)

Supplementary Table 16

Trait phenotyping data used for GWAS. (XLSX 59 kb)

Supplementary Table 18

MTAs identified for target traits with P values. (XLSX 43 kb)

Supplementary Table 19

Number of favorable alleles identified in Cajanus accessions for detected MTAs in each trait. (XLSX 31 kb)

Supplementary Table 20

The distribution of favorable alleles for 17 MTAs detected for 100-seed weight in Cajanus accessions. (XLSX 25 kb)

Supplementary Table 21

MTAs identified in GWAS for different target traits and their corresponding structural variations (CNVs and PAVs) in breeding lines, landraces and wild species accessions. (XLSX 61 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Varshney, R., Saxena, R., Upadhyaya, H. et al. Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits. Nat Genet 49, 1082–1088 (2017).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing