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《Journal of Yangzhou University(Agricultural and Life Science Edition)》 2010-02
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Association analysis of starch pasting characteristic traits with SSR markers in waxy corn in Jiangsu province

ZHANG Dan1,LIU Li-jun1,XUE Lin2,LI Jian3,XU Chen-wu1(1.Key Lab of Crop Gen and Physiol of Jiangsu Prov,Yangzhou Univ,Yangzhou 225009,China;2.Inst of Agric Sci of the Coastal District of Jiangsu Prov,Rugao 226541,China;3.Inst of Agric Sci of Rugao City,Rugao 226500,China)  
53 waxy corn inbreds and 30 waxy corn hybrids were selected as materials.Based on the data of starch pasting characteristic traits,analysis of phenotypic variation was carried out.91 pairs of SSR polymorphism markers were used to scan the genome of waxy corn.With the genotype and phenotype data genetic diversity analysis were also carried out.To perform association analysis,53 waxy corn inbreds and 30 waxy corn hybrids were combined as one population and analyzed for linkage disequili-brium(LD) of pairwise loci and population structure,then for association between SSR loci and starch pasting characteristic traits under TASSEL GLM(general linear model) program.The results were as follow: ① Differences among the tested materials were very significant in starch pasting characteristic traits.② 433 specific DNA bands were detected in waxy corn inbreds.1~10 polymorphic fragments were amplified stably by each primer with an average of 5 fragments.The value of polymorphism information content(PIC) for each SSR locus varied from 0 to 0.841 with an average of 0.573.While in hybrids,403 specific DNA bands were detected.1~10 polymorphic fragments were amplified by each primer with an average of 4 fragments.The value of PIC for each SSR locus varied from 0 to 0.841 with average of 0.562.③ The cluster results of starch pasting characteristic traits and SSR markers had a certain degree of similarity.④ LD was detected among syntenic SSR markers and the loci pairs with D′0.5 was 10.31% of the total.⑤ Genetic structure analysis showed that the combined population was composed of 9 subpopulations.The 26 SSR loci with a total of 91 loci were found to be associated with 7 starch pasting characteristic traits.⑥ There were 11 loci associated simultaneously with two or more traits,which might be the genetic reason of positive correlation among traits as well as the pleiotropic effects of gene(s).⑦ The total interpretation rate of phenotypic variability of markers associated with starch pasting characteristic traits were all at a high level,part of them were more than 100%,indicating the high false positive in association analysis,so the mathematical approach of association analysis had yet to be further improved.
【Fund】: 国家重点基础研究发展计划项目(973-2006CB101700);; 江苏省高校自然科学研究重大项目(09KJA210002);; 江苏省农业科技自主创新资金项目[CX(09)637];; 江苏省高新技术研究计划项目(BG2005309)
【CateGory Index】: S513
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