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Sethi K., Siwach P., Verma S.K. (2017): Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations. Czech J. Genet. Plant Breed., 53: 159−167. Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibriumbased association mapping has become a powerful molecular tool to dissect and exploit genetic diversity. In the present study, population structure and marker-trait associations for fibre quality traits in genotypes belonging to six races of Gossypium arboreum were assessed. Out of 300 simple sequence repeat (SSR) markers, 100 were found polymorphic, yielding a total of 240 alleles (all polymorphic). Structure analysis revealed allelic admixtures between genotypes. A Q-matrix exhibited mixed ancestry for the majority of genotypes, the race indicum forming a significant percent ancestry for almost all genotypes. At significant threshold values of r2 ≥ 0.05, 7.37% of SSR loci showed significant linkage disequilibrium (LD), while at highly significant threshold of r2 ≥ 0.1, the value was reduced to 5.31%. LD clearly decayed within the genetic distance of 9–10 cM, with r2 ≥ 0.1. Twenty-eight SSR markers were found associated with six fibre quality traits using general linear model and mixed linear model.