Czech J. Genet. Plant Breed., 2017, 53(4):159-167 | DOI: 10.17221/142/2016-CJGPB

Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populationsOriginal Paper

Khushboo SETHI1, Priyanka SIWACH*,1, Surender Kumar VERMA2
1 Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
2 Central Institute of Cotton Research, Regional Station, Sirsa, Haryana

Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibrium-based 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.

Keywords: general linear model; genetic distance; genetic diversity; mixed linear model; simple sequence repeat

Published: December 31, 2017  Show citation

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SETHI K, SIWACH P, VERMA SK. Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations. Czech J. Genet. Plant Breed. 2017;53(4):159-167. doi: 10.17221/142/2016-CJGPB.
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