Upland cotton is the most important natural-fiber crop. The genomic variation of diverse germplasms and alleles underpinning fiber quality and yield should be extensively explored. Here, we resequenced a core collection comprising 419 accessions with 6.55-fold coverage depth and identified approximately 3.66 million SNPs for evaluating the genomic variation. We performed phenotyping across 12 environments and conducted genome-wide association study of 13 fiber-related traits. 7,383 unique SNPs were significantly associated with these traits and were located within or near 4,820 genes; more associated loci were detected for fiber quality than fiber yield, and more fiber genes were detected in the D than the A subgenome. Several previously undescribed causal genes for days to flowering, fiber length, and fiber strength were identified. Phenotypic selection for these traits increased the frequency of elite alleles during domestication and breeding. These results provide targets for molecular selection and genetic manipulation in cotton improvement.
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We thank the National Mid-term Gene Bank for Cotton at the Cotton Research Institute, Chinese Academy of Agricultural Sciences, for providing the original collection seeds. We thank T. Zhang for releasing resequencing data for wild cotton accessions. This work was supported by the Fund of the China Agriculture Research System (CARS18-08) and the Science and Technology Support Program of Hebei Province (16226307D) to Z.M.; the National Major Science and Technology Program (2016ZX08005003-005) to X.W.; the National Key Research and Development Program (2016YFD0100203) to X.D., (2016YFD0101405) to Y.Z., and (2016YFD0100306) to S.H.; and the National Science and Technology Support Program (2013BAD01B03) to X.D.
The authors declare no competing financial interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figures 1–23 and Supplementary Tables 3, 6, 8, 9, 11–13 and 15
The list of 419 cotton accessions used in this study and their sequenced information
Statistics of different SNP mutation types for 419 accessions
Tracy-Widom statistics of eigenvalues from PCA analysis of 419 accessions
The ancestry proportion estimates for each accession when the ancestral population was specified as three
Number of SNP variation of different genes between core collection and wild races
List of the associated SNPs and genes for 13 traits
SNPs, elite alleles and their frequency of 13 traits in wild races, early- and modern-varieties
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Ma, Z., He, S., Wang, X. et al. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet 50, 803–813 (2018). https://doi.org/10.1038/s41588-018-0119-7
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