Uncovering microsatellite markers linked with agronomic, yield and quality traits of upland cotton (Gossypium hirsutum L.)

High yield and fiber quality of upland cotton has been remained main focus of breeding programs. Breeders use various methods like interspecific hybridization, conventional hybridization with exotic germplasm, production of transgenic plants and mutagenesis in order to introduce variation in cotton, so that, they can use this change for development of cotton. This can only be possible with developments in the fields of biotechnology and molecular biology and exploring quantitative trait loci (QTL). To explore QTLs which has strong linkage to yield, agronomic, morphological and fiber quality traits, 80 SSR markers have been used in present study to find out the QTLs in the genetic structure of 100 Gossypium hirsutum accessions. Among the 80 SSR markers only 20 showed strong association with traits under study. The range of P value was 1.66E-13 to 2.69E-04 and of R2 was 0.13-0.44. Three markers, CIR0307, NAU5383 and NAU5499 were linked with fiber fineness; MGHES0034 and NAU5480 with fiber uniformity; BNL3594 and JESPR0153 with fiber strength and seed cotton yield; NAU2038 and BNL1066 showed their association with fiber elongation. Structure analysis was conducted with the aid of model-based software STRUCTURE of 100 cotton genotypes which showed a little admixture. The highest ..K value was observed at K = 6 which divided the genotypes into two subgroups; Group I had 45 cotton genotypes and Group II carried 55 cotton genotypes. The QTLs having strong linkage with desire traits will help the breeders to use information of QTLs for cotton improvement by marker assisted selection (MAS) program.. KEYWORDS :SSR markers, Gossypium hirsutum, QTLs, Fiber, Yield traits.