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Genome-wide association study of yield components and fibre quality traits in a cotton germplasm diversity panel

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Abstract

A genome-wide association study (GWAS) was conducted on a diversity panel of 103 cotton accessions over three seasons to determine genetic contributions to a range of cotton yield components including fibre quality, plant architecture and stomatal conductance traits. The accessions covered breeding lines, released cultivars and some obsolete cultivars that contributed significantly to modern breeding pools. They were genotyped with Illumina’s CottonSNP63 K single nucleotide polymorphism (SNP) assay. Broad-sense heritability was low for yield component traits (\(h_{B}^{2}\) = 0.14–0.43), except for gin turnout and boll weight (\(h_{B}^{2}\)) = 0.74 and 0.59, respectively), and low to high for fibre quality traits (\(h_{B}^{2}\) = 0.26–0.89). Population structure analysis revealed extensive admixture and cryptic relatedness amongst the accessions. Genome-wide linkage disequilibrium (LD) analyses showed LD decayed, on average, within a physical distance of 5 Mbp and reduced to 2 Mbp at r 2 ≥ 0.2, suggesting that few markers are necessary for association mapping in cotton. A mixed linear model accounting for population structure and cryptic relatedness identified 17 and 50 significant SNP associations for fibre length and micronaire, respectively. GWAS failed to detect significant associations in other traits, with the contribution of any single SNP to the phenotypic falling below 5%. This may be due to the low level of DNA polymorphism in cotton and/or insufficient resolution provided by the cotton SNP chip. Whole genome sequencing combined with whole genomic selection approaches that do not require prior knowledge about the effect or function of individual SNPs may be better suited than GWAS for trait dissection and prediction in cotton breeding.

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Acknowledgements

This study was financially supported by Cotton Breeding Australia, a joint venture between CSIRO and Cotton Seed Distributors. The authors would like to thank technical staff of CSIRO cotton breeding group, particularly Alan Thompson, Kay Smith, Sandra Megann, Jo Price and Kellie Cooper, as well as Vanessa Gillespie and Ray Yuan of the Cotton Marker Disease team, for their invaluable contribution to this work. Andrew Spriggs provided bioinformatics support. We also thank Rowan Bunch and Dr. Bill Barendse for processing and help with the analysis of the Illumina CottonSNP63 K assays. We thank Drs. Linda Broadhurst and James Kajik for their comments and suggestions on earlier versions of this paper.

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  1. CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT, 2601, Australia

    Washington Gapare, Qian-Hao Zhu, Danny Llewellyn & Iain Wilson

  2. CSIRO Agriculture and Food, Locked Bag 59, Narrabri, NSW, 2390, Australia

    Warren Conaty, Shiming Liu & Warwick Stiller

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  1. Washington Gapare
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Gapare, W., Conaty, W., Zhu, QH. et al. Genome-wide association study of yield components and fibre quality traits in a cotton germplasm diversity panel. Euphytica 213, 66 (2017). https://doi.org/10.1007/s10681-017-1855-y

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