Abstract
Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.
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NCBI Reference Sequence
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Acknowledgements
We thank J. Ross-Ibarra (University of California, Davis) and J.-Y. Li (Chinese Academy of Agricultural Sciences (CAAS)) for critical comments, D. DellaPenna (Michigan State University) for assistance in β-carotene pathway analysis and the three anonymous referees for their constructive comments. We thank F. Cunningham (University of Maryland) for providing the pAC-BETA plasmid. This work was supported by funding from the National Program on Key Basic Research Projects in China (the 973 Program; 2012CB113900), the National Natural Science Foundation of China (NSFC; 31225025) the National High-Tech Research Development Program in China (the 863 Program; 2010AA10A108 and 2012AA100101), and other NSFC grants (31030057, 30972011, 31101550, 31071797, 31171961, 31272161 and 31322047), the Chinese Ministry of Agriculture (the 948 program; 2008-Z42), the Chinese Ministry of Finance (1251610601001) and CAAS (seed grant to S.H.).
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S.H. and Z.Z. conceived and designed the experiments. J.Q., D.S., H.M., X.G., S.W., Y.L., T.L., Y.S., X.Y., H.C., X.X., K.H., J.C. and L.T. performed the experiments. Z.Z., J.Q., X. Liu, B.X., X. Li, P.Z., J.Y., Y.D., Z.F., L.M., T.S., S.S.R., W.J.L., S.K. and S.H. analyzed the data. S.H., Z.Z., X. Liu and J.Q. wrote the manuscript. Z.F., T.S., S.S.R., W.J.L. and S.K. revised the manuscript.
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Supplementary information
Supplementary Text and Figures
Supplementary Note, Supplementary Tables 2, 3, 5, 6 and 14, and Supplementary Figures 1–14 (PDF 4631 kb)
Supplementary Table 1
Summary of the sampled core collection (XLS 63 kb)
Supplementary Table 4
Presence and absence variation (PAV) genes identified in the core collection of 115 cucumber accessions (XLS 144 kb)
Supplementary Table 7
The SNP loci chosen for validation by PCR and Sanger sequencing (XLS 57 kb)
Supplementary Table 8
Putative regions identified to be under domestication sweeps (XLS 74 kb)
Supplementary Table 9
Genes within the putative regions identified to be under domestication sweeps (XLS 541 kb)
Supplementary Table 10
Summary of the genes present within Bt region (XLS 79 kb)
Supplementary Table 11
Highly differentiated regions across the cultivated groups (XLS 58 kb)
Supplementary Table 12
Genes located in the highly differentiated regions (XLS 1100 kb)
Supplementary Table 13
Genes containing nonsynonymous SNPs of significantly high FST values (XLS 443 kb)
Supplementary Dataset
Supplementary dataset for Supplementary Figures 1–5 and 7–10 (XLSX 6505 kb)
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Qi, J., Liu, X., Shen, D. et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45, 1510–1515 (2013). https://doi.org/10.1038/ng.2801
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DOI: https://doi.org/10.1038/ng.2801
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