| Cotton is the primary source of natural fiber crop in the world. Resulting from its high-yield ability and adaptability to diverse ecologies, cotton breeding programs have focused on improving Upland cotton(G. hirsutum L.). However, the narrow genetic base of the primary cotton gene pool has been impeding improvement efforts at large. With main objectives to explore the genetic diversity, to identify quantitative traits loci(QTLs) of economic importance,and to facilitate simultaneous improvement of fiber yield and quality traits, 302 elite Upland cotton germplasms(253 from China, 25 from the USA, and 24 from other countries), were evaluated under varied natural environments of Yellow River and Yangtze River valley, China from 2012 to 2013 and genotyped using 198 genome-wide simple sequence repeats(SSRs)markers. The whole panel, inferred, and geographic origin-based populations were studied. The SSR markers amplified 897 alleles in the whole panel, of which 77.7% were polymorphic. The number of alleles varied from 2 to 12(mean 4.53). The polymorphic information content values ranged from 0.371 to 0.019(mean 0.225). Germplasms of Chinese origin had the highest level of SSR polymorphisms(Gene diversity = 0.268, polymorphic information content = 0.218).Genetic distances in the whole panel ranged from 0.451 to 0.052(mean 0.270). American-origin germplasms had the highest mean genetic distance(0.274). The model-based Bayesian(MBB)analysis of population genetic structure revealed that the whole panel germplasm could be grouped into three sub-populations. The molecular variation which accounted for differences between MBB populations was 4%(p < 0.001), demonstrating the existence of a population structure. The pair-wise relative kinship varied from 0 to 0.867, of which 51.91% pairs of cotton germplasms had zero kinship values. Only 1.59% of the total SSR loci pairs showed significant(p < 0.001) linkage disequilibrium(LD, r2). A mean r2 of 0.5582(p < 0.001) was obtained in the linked marker pairs, which was higher than that of an unlinked marker pairs and panel population,indicating that physical linkage strongly influences LD in the cotton panel. Genome-wide LD decays within the genetic distance of ~30–32 c M with r2= 0.1, whereas it was reduced to ~1–2c M at r2= 0.2, demonstrating the potential for association mapping of important traits in cotton breeding program. The results of combined analysis of variance for the ten fiber yield and quality traits revealed significant(p ≤ 0.01) variations in main effects of genotypes(G), environments(E), and genotype by environment interactions(G × E). Among studied phenotypic traits, the mean performance for lint percentage, fiber length, and micronaire ranged from 42.94% to28.25%, from 32.86 to 24.33 mm, and from 5.90 to 3.70 μg inch-1, respectively. Simple linear correlation coefficients(r) study revealed strongest positive associations(0.199 to 0.795, p < 0.01)among quality traits. Estimates of the broad-sense heritability(H2) of fiber yield and fiber quality traits ranged from 75.18 to 97.08%. The mixed linear model(MLM) analysis detected 102marker-trait associations(p < 0.01) among 41 SSR markers and 10 traits, including 11 for plant height(PH), 8 for boll number(NB), 10 for boll weight(BW), 9 for lint percentage(LP), 9 for fiber length(FL), 13 for micronaire(Mic), 17 for fiber strength(FS), 8 for fiber elongation(FE),7 for length uniformity index(UI), and 10 for fiber uniformity ratio(UR). The proportion of phenotype variation explained by SSR loci ranged from 1.8 to 8.9%, with a mean of 3.5%. More than half(51%) of the significant QTL detected were favorable alleles, the highest QTL number being for Mic(12), followed by FS(8) and BW(7). Overall, Genome-wide SSR revealed a considerable amount of genetic diversity in the elite Upland cotton germplasms and permitted exploration of favorable QTL, which may have great potentials for developing improved Upland cotton cultivars in future breeding program, such as marker assisted selection(MAS). |
PDF Full Text Request