Association mapping and favourable allele exploration for plant architecture traits in upland cotton (Gossypium hirsutum L.) accessions

Association mapping based on linkage disequilibrium (LD) is a promising tool to identify genes responsible for quantitative variations underlying complex traits. The present paper presents an association mapping panel consisting of 172 upland cotton ( Gossypium hirsutum L.) accessions. The panel was phenotyped for five cotton plant architecture traits across multiple environments and genotyped using 386 simple sequence repeat (SSR) markers. Of these markers, 101 polymorphic SSR markers were used in the final analysis. There were abundant phenotypic variations within this germplasm panel and a total of 267 alleles ranging from two to seven per locus were identified in all collections. The threshold of LD decay was set to r 2 = 0·1 and 0·2, and the genome-wide LD extended up to about 13–14 and 6–7 cM, respectively, providing the potential for association mapping of agronomically important traits in upland cotton. A total of 66 marker–trait associations were detected based on a mixed linear model, of which 35 were found in more than one environment. The favourable alleles from 35 marker loci can be used in marker-assisted selection of target traits. Both the synergistic alleles and the negative alleles for some traits, especially plant height and fruit branch angle, can be utilized in plant architecture breeding programmes according to specific breeding objectives.