Gossypium hirsutum races are believed to be potential reservoirs of desirable traits, which can play crucial roles to overcome the existing narrow genetic base of modern Upland cotton cultivars.  However, prior to utilizing the races in cotton improvement programs, understanding their genetic constitutions is needed.  Thus, this study used molecular and morphological techniques to characterize 110 G. hirsutum germplasm including 109 semi-wild accessions and one Upland cotton cultivar, CRI12.  In the study, 104 SSR markers detected 795 alleles, with an average of 7.64 alleles per marker, ranging from 3 to 14, and average polymorphism information content (PIC) value of 0.71.  And 96 of the markers were found to be highly informative, with PIC value≥0.50.  Pairwise genetic similarity coefficient across the accessions ranged from 0.19 to 1.00, with an average value of 0.46.  Morphological characterization was done using fiber length, fiber strength, micronaire, fiber uniformity index, and fiber elongation.  Pairwise taxonomic distance within the accessions ranged from 0.17 to 3.41, with a mean of 1.33.  The SSR and fiber quality traits data set based unweighted pair group method of arithmetic mean (UPGMA) analysis grouped the accessions into 7 and 12 distinct clusters, respectively, that corresponds well with the results of principal component analysis (PCA).  Our study revealed the existence of vast molecular and morphological diversities within the accessions and provided valuable information on each semi-wild accession for quick and better informed germplasm utilization in cotton breeding programs.   

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium (LD). This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism (PIC=0.53) was found, and three groups were detected (K=3) with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model (GLM) and mixed linear model (MLM) (P 0.01). The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci (QTLs) information for marker-assisted selection.