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.
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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.
The authors declare no competing financial interests.
Supplementary Figures 1–12, Supplementary Tables 10–12 and 17, and Supplementary Note (PDF 16895 kb)
Details on 300 Cajanus accessions (breeding lines, landraces and wild species accessions) including biological status, species, geographical region, country and state. (XLSX 20 kb)
Details on raw sequencing data generated on 292 Cajanus accessions. (XLSX 30 kb)
Identification and distribution of molecular variation (SNPs and indels) among 11 pseudomolecules CcLG01 to CcLG11 and unanchored genome sequence as CcLG0. (XLSX 21 kb)
Nonsynonymous-to-synonymous ratio in breeding lines, landraces and wild species in 1-Mb non-overlapping windows. (XLSX 17 kb)
Non-synonymous to synonymous ratio in breeding lines, landraces and wild species in 10 Kb non-overlapping windows (XLSX 1172 kb)
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)
Structural variations (CNVs and PAVs) identified in breeding lines as compared to the reference genome. (XLSX 29 kb)
Structural variations (CNVs and PAVs) identified in landraces as compared to the reference genome. (XLSX 24 kb)
Structural variations (CNVs and PAVs) identified in wild species accessions as compared to the reference genome. (XLSX 24 kb)
ROD values calculated during domestication (wild species versus landraces) and breeding (landraces versus breeding lines) at 10-kb non-overlapping windows. (XLSX 582 kb)
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)
Genes that played an important role in domestication of crop species and their homologs in Cajanus. (XLSX 23 kb)
Trait phenotyping data used for GWAS. (XLSX 59 kb)
MTAs identified for target traits with P values. (XLSX 43 kb)
Number of favorable alleles identified in Cajanus accessions for detected MTAs in each trait. (XLSX 31 kb)
The distribution of favorable alleles for 17 MTAs detected for 100-seed weight in Cajanus accessions. (XLSX 25 kb)
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)
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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). https://doi.org/10.1038/ng.3872
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