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

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Abstract

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.

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Acknowledgements

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).

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Authors and Affiliations

  1. College of Agronomy, Xinjiang Agricultural University, Nanchang Road 42, Ürümqi, Xinjiang, China

    XianTao Ai & YanYing Qu

  2. Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, Xinjiang, China

    XianTao Ai, YaJun Liang, JunDuo Wang, JuYun Zheng, ZhaoLong Gong, JiangPing Guo & XueYuan Li

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  1. XianTao Ai
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  2. YaJun Liang
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  3. JunDuo Wang
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  5. ZhaoLong Gong
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  7. XueYuan Li
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Correspondence to XueYuan Li or YanYing Qu.

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10709_2017_9976_MOESM1_ESM.tif

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)

Supplementary material 2 (XLS 49 KB)

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Ai, X., Liang, Y., Wang, J. et al. Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data. Genetica 145, 409–416 (2017). https://doi.org/10.1007/s10709-017-9976-8

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  • DOI: https://doi.org/10.1007/s10709-017-9976-8

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