Association mapping for seed cotton yield, yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

Association mapping has revolutionized human genetics and is increasingly used in plant genetics. It is an efficient way of determining the genetic basis of complex traits. In cotton so far numerous association mapping studies are available as compared to many other important crops. In our study, mapping was performed using cotton 63K infinium beadchip with 201 germplasm lines. Through fast STRUCTURE analysis, lines were grouped into 12 subgroups and revealed genome sharing among the groups. The critical value (R-2) was set to 0.243 as threshold to claim LD between two loci. About 3.13% marker pairs recorded significantly high LD (R-2=1), and 8.19% of marker pairs were in the range of 0.3 to 0.99R(2). In MLM, 349 significant marker-trait associations were detected as against 642 in GLM because of effectiveness in eliminating false associations in MLM. A total of 68 markers explained >10% phenotypic variation for yield and fibre quality traits. Phenotypic variation explained by markers was smaller, suggesting that they might be associated with minor QTLs.