Association Analysis Of Early Maturity, Yield And Fiber Quality Traits In Upland Cotton Using Ssr Markers

Upland cotton is one of the widely cultivated cotton species in China. The seversituation that the increasing population and the decreasing cultivated areas has generated aserious influence on planting the upland cotton. Nowadays, it becomes a significant target incotton breeding that breeding the new upland cotton cultivars with features of early maturity,high yield and high quality. Conventional breeding methods have two main disadvantages:long period and low efficiency. Compared with those, it can not only shorten the breedingtime but improve the breeding efficiency by using molecular markers that tightly linked toQTL (Quantitative trait locus) in marker-assisted selection breeding.In this study,186samples of upland cotton cultivars (or lines) which selected fromfour cotton growing regions in China and the United States were used to performassociation analysis of17traits related to early maturity, yield and fiber quality using284SSR (Simple sequence repeat) loci obtained from103polymorphic SSR markers. Penotypesof the17tratis were indentified at two sowing dates. General linear model (GLM) andmixed linear model (MLM) were used to do association analysis by TASSEL5.0software.The research objectives are as follows: detecting SSR loci that significantly associated withtraits, and laying a foundation for maker-assisted selection in the upland cotton breeding.The main results were as follows:1. The results of phenotypic statistic analysis and variance analysis of17traits in186tested materials showed that the varieties had extensive phenotypic diversity, so they couldbe used in association analysis. The results of correlation analysis showed that the traitsrelated to early maturity were positively correlated at P＜0.01level.2. Genetic diversity analysis showed that a total of284alleles were obtained from103polymorphism SSR primers for the186tested materials, with an average of2.76alleles perSSR primers. Polymorphism information content (PIC) of primers ranged from0.348to0.953, with an average of0.706. And it showed that the selected primers could provideextensive genetic information.3. SM (Simple matching coefficients of similarity) among varieties were calculated byNTSYS software showed that similarity coefficients ranged from0.348to0.953, with an average of0.668. Besides, similarity coefficients less than0.669accounted for70.95percent. Cluster analysis based on Nei’s genetic distance detected two subgroups in the186upland cotton cultivars (or lines), and showed that the results basically agreed with thepedigrees.4. Population structure that analyzed by STRUCTURE2.3.4software showed that the186samples were divided into2subgroups (POP-1and POP-2) with100and86samples,respectively.5. Association analysis using GLM and MLM was performed by TASSEL5.0software,and the phenotypic effect values of partial SSR loci that associated with traits werecalculated.(1). Association analysis using GLM showed that62SSR loci significantly (P＜0.01)associated with15traits at two sowing dates were detected. Among them,44SSR locisignificantly associated with two or more traits simultaneously, which might be theinteraction of pleiotropic genes or QTLs. Besides, this phenomenon might be the hereditarybasis of correlation between traits.(2). Association analysis using MLM showed that8SSR loci significantly (P＜0.01)associated with6traits at two sowing dates were detected.(3).7SSR loci significantly associated with traits were detected by both GLM andMLM at two sowing dates and showed that the7SSR loci were stable and reliable.(4). Phenotypic effect values of partial SSR loci that associated with traits werecalculated. This study detected7SSR loci (DPL0524-185, HAU3318-299, MGHES-73-352,NAU1042-247, NAU1102-236, NAU3820-131and NAU3913-378) that associated withtwo or more traits related to early maturity and showed negative phenotypic effect (positiveeffect to pre-frost yield). Therefore, the7SSR loci could be used for maker-assistedselection in short season cotton breeding after the further study.