Cotton (Gossypium spp.) genetic mapping often involves the development, genotyping and phenotyping of F2 or recombinant inbred lines (RIL) derived from an F1 cross between different cultivars or species. For these mapping populations there is an extreme disequilibrium between linked loci and there should be no effects of population structure use of the random sampling, or disequilibrium between non-linked loci, thus the detection and approximate mapping of quantitative trait loci (QTL) is favored. Association mapping in complex-pedigree populations relevant for plant breeding could prove useful for detecting a higher number of QTLs than in F2- and RIL-derived populations. Advances in the use of Gossypium hirsutum (Upland cotton) breeding require an understanding of the relatedness and ancestry of upland cotton accessions, and identification of simple sequence repeat (SSR) markers associated with agronomically important traits, such as resistance to biotic stresses. Two-hundred G. hirsutum accessions (TX) have been evaluated for resistance to reniform nematodes and these will be genotyped with SSR markers. The general linear model method will be used to disclose marker–trait associations. Marker–trait associations will be investigated by fitting single marker regression models for phenotypic traits on marker band intensities with correction for population structure. This study illustrates the potential of association mapping in allotetraploid cotton, because existing phenotypic data, a varied number of SSR markers, and a pioneering statistical analysis, has identified interesting associations.
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