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Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

Author

Listed:
  • Zhaoen Yang

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Xiaoyang Ge

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Zuoren Yang

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Wenqiang Qin

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Gaofei Sun

    (Anyang Institute of Technology)

  • Zhi Wang

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Zhi Li

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Ji Liu

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Jie Wu

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Ye Wang

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Lili Lu

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Peng Wang

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Huijuan Mo

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Xueyan Zhang

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • Fuguang Li

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

Abstract

Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Here, we use single-molecule long read and Hi-C sequencing technologies to assemble genomes of the two upland cotton cultivars TM-1 and zhongmiansuo24 (ZM24). Comparisons among TM-1 and ZM24 assemblies and the genomes of the diploid ancestors reveal a large amount of genetic variations. Among them, the top three longest structural variations are located on chromosome A08 of the tetraploid upland cotton, which account for ~30% total length of this chromosome. Haplotype analyses of the mapping population derived from these two cultivars and the germplasm panel show suppressed recombination rates in this region. This study provides additional genomic resources for the community, and the identified genetic variations, especially the reduced meiotic recombination on chromosome A08, will help future breeding.

Suggested Citation

  • Zhaoen Yang & Xiaoyang Ge & Zuoren Yang & Wenqiang Qin & Gaofei Sun & Zhi Wang & Zhi Li & Ji Liu & Jie Wu & Ye Wang & Lili Lu & Peng Wang & Huijuan Mo & Xueyan Zhang & Fuguang Li, 2019. "Extensive intraspecific gene order and gene structural variations in upland cotton cultivars," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10820-x
    DOI: 10.1038/s41467-019-10820-x
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    Cited by:

    1. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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