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Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

Abstract

The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243 G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.

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Fig. 1: Genomic divergence and geographic-relationship analysis.
Fig. 2: GaKASIII regulates cotton seed oil content.
Fig. 3: A genetic locus that underwent geographical isolation confers resistance to fusarium wilt disease.
Fig. 4: Both GWAS and QTL analysis identified the same region in the G. arboreum genome as being potentially important for seed fuzz development.

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Acknowledgements

This work was supported by funding from the National Natural Science Foundation of China (grants 31621005 to F. Li and 90717009 to Y.Z.), the National Key Technology R&D Program, the Ministry of Science and Technology (2016YFD0100203 to X.D. and 2016YFD0100306 to S. He), the National Science and Technology Support Program, the Ministry of Agriculture (2013BAD01B03 to X.D.), the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS to S. Huang), and the leading talents of Guangdong Province Program (00201515 to S. Huang).

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F. Li, Y.Z., X.D., and T.L. conceived and designed the research. F. Li and S. Huang managed the project. T.L., N.L., M.L., F. Liu, F.W., H. Zheng., and G.S. performed the genome sequencing, assembly, and bioinformatics. X.D., S. He, J.S., Z.Y., X.M., X.Z., Y.J., Z. Pan., W.G., Z.L., H. Zhu., L.M., D.Y., Q.G., Z. Peng., L.W., S.X., and X.W. prepared the samples, performed phenotyping, and contributed to data analysis. Y.Z. designed the molecular experiments, and Z.Y. and G.H. performed the molecular experiments and led interpretation of the molecular-data analysis. S. He, Z.Y., and G.H. prepared the figures and tables. Y.Z., S. He, G.H., Z.Y., T.L., S. Huang, H.S., C.L., and W.F. wrote and revised the manuscript.

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Correspondence to Tao Lin, Yuxian Zhu or Fuguang Li.

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Du, X., Huang, G., He, S. et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet 50, 796–802 (2018). https://doi.org/10.1038/s41588-018-0116-x

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