, Volume 145, Issue 4–5, pp 409–416 | Cite as

Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data

  • XianTao Ai
  • YaJun Liang
  • JunDuo Wang
  • JuYun Zheng
  • ZhaoLong Gong
  • JiangPing Guo
  • XueYuan LiEmail author
  • YanYing QuEmail author
Original Paper


Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.


Genetic diversity Population structure Molecular variance Genome-wide SNP markers Gossypium hirsutum L. 



We thank all our collaborators who made the work on cotton genetics a rewarding experience. This work was supported by the National Natural Science Foundation of China (31360351).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10709_2017_9976_MOESM1_ESM.tif (5.3 mb)
Supplementary Fig. 1 a Histogram of allele frequencies for the complete panel of G. hirsutum germplasms. b Histogram of allele frequencies for the Chinese panel of G. hirsutum germplasms. (TIF 5433 KB)
10709_2017_9976_MOESM2_ESM.xls (50 kb)
Supplementary material 2 (XLS 49 KB)


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • XianTao Ai
    • 1
    • 2
  • YaJun Liang
    • 2
  • JunDuo Wang
    • 2
  • JuYun Zheng
    • 2
  • ZhaoLong Gong
    • 2
  • JiangPing Guo
    • 2
  • XueYuan Li
    • 2
    Email author
  • YanYing Qu
    • 1
    Email author
  1. 1.College of AgronomyXinjiang Agricultural UniversityÜrümqiChina
  2. 2.Institute of Economic CropsXinjiang Academy of Agricultural SciencesÜrümqiChina

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