J Integr Plant Biol. ›› 2019, Vol. 61 ›› Issue (8): 929-942.DOI: 10.1111/jipb.12723

Special Issue: Plant genomics

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Genomic divergence in cotton germplasm related to maturity and heterosis

Shoupu He1,2†, Gaofei Sun1,3†, Longyu Huang2†, Daigang Yang2, Panhong Dai2, Dayun Zhou2, Yuzhen Wu2, Xiongfeng Ma2, Xiongming Du1,2, Shoujun Wei2*, Jun Peng2* and Meng Kuang1,2*   

  1. 1Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang 455000, China
    2Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
    3Department of Computer Science and Information Engineering/Data Mining Institute, Anyang Institute of Technology, Anyang 455000, China

    These authors contributed equally to the work.
    Email: Meng Kuang (kuangmeng007@163.com, Dr. Kuang is fully responsible for the distribution of all materials associated with this article); Jun Peng (jun_peng@126.com); Shoujun Wei (weisj@cricaas.com.cn)
  • Received:2018-08-03 Accepted:2018-09-17 Online:2018-09-25 Published:2019-08-01


Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high‐quality single‐nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage‐specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity‐related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage‐specific regions and heterozygous loci, in the high‐yield hybrids, suggests a role for these regions in cotton heterosis.

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