Genetic Structure And Association Analysis Of Superior Germplasm Resources In Domesticated Upland Cotton (Gossypium Hirsutum L.)

The gene flow pattern and genetic structure of cultivated domestication crops are little determined,especially for economically important crops like cotton.Furthermore,the marker-assisted breeding of cotton are largely lags behind the other major crops due to limited information of association loci of fiber yield and quality traits.In this study,we investigated the genetic structure and gene flow pattern of upland cotton superior germplasm resources and performed association analysis of 15 agronomic traits(including ten yield components and five fiber quality traits)using the nineteen microsatellites and two nuclear markers.The results showed that the upland cotton accessions have the low level of genetic diversity(Simple sequence repeats,Polymorphism information content = 0.427)and nucleotide variability(Pi = 0.01330),while extensive gene flow occurred among different ecological geographic regions.Bayesian clustering analysis indicated that there were no obvious geographic population groups in the sampled cotton resources.The extensive genetic exchanges and gene flow among different areas were occurred,which may resulted from the frequently introgression and pollen migration introduced by human transferences.The association analysis further showed that the 82 marker–trait associations were significantly and which of the proportion of phenotypic variations explained by markers ranged from 3.04% to 47.14%.Interestingly,nine SSR loci were detected in more than one environment condition.In addition,fourteen SSR loci were co-associated with two or more different traits.It was noteworthy that NAU4860 and NAU5077 loci simultaneously associated with three fiber quality traits(uniformity index,specific breaking strength and micronaire value)and detected at least in two environments.In conclusions,these finds provides new insights into the population genetic structure and genetic exchange pattern of cultivated cotton superior accessions.The quantitative trait loci of domestication cotton identified will also be very useful for improvement of yield and fiber quality in the future cotton molecular breeding programs.