Genome-wide Association Study,Fine Mapping And Domestication Analysis Of Seed Shape Traits In Soybean (Glycine Max L. Merr.)

Seed size and shape traits as critical components of soybean yield are closely related to seed yield and appearance quality in soybean.Therefore,it is important in theory and application to dissect their genetic foundation and mine corresponding elite alleles.Meanwhile,these traits are important domestication traits,which have significantly changed in the process of domestication from wild to cultivated soybean.The related study would enhance our understanding to the mechanism of domestication.Based on preliminary studies in our group,this study focuses on seed size and shape traits in three aspects,including association mapping,fine mapping and domestication study.As for association mapping,257 soybean cultivars were sampled from six soybean ecological zones in China by stratified sampling method,and measured for seed length,width,thickness,and their corresponding ratios from 2008 to 2010.These traits observations along with the information of 135 molecular markers were used to carry out association mapping using epistatic association mapping.The associated loci were used to mine elite alleles,design excellent parental combination,pyramid elite alleles and predict candidate genes.As for fine mapping,7 heterozygous plants in F2:6 populations in the target intervals satt331-satt592 were used to construct 356 RHL-F2 individuals,named population I;and 168 recombinants in F2:6 populations in the same target intervals were used to construct populations II and III.The lasso and composite interval mapping approaches were used to fine map quantitative trait loci（QTL）for two indicators of these above traits in the three populations.The detected loci were used to mine candidated genes.As for domestication study,14 wild soybeans,45 landraces and 30 released cultivars were used as materials to investigate domestication mechanisms of these traits using phenotypic analysis,partial correlation analysis and factor analysis.The main conclusions are as follows:1.A total of 59 main-effect QTL and 31 environment-by-QTL interactions for seed shape traits were detected by the eBayes method.Among them,25 markers were associated with two or more traits simultaneously and some closely linked markers were associated with multiple traits;80 QTL（90%）can be confirmed by E-cMLM analysis method.The heritabilities of qSL-5,qSW-7e,qST-5-2 and qSLW-2 were greater than 10%.Then elite alleles were mined and superior parent combinations were predicted,according to the results of association mapping by the eBayes method.By estimating the effects of alleles of detected QTL,novel alleles of satt453（307）,sat₂56（313）,sat₂56（313）,satt459（189）,satt102（154）,and satt565（174）were found to have an impact effect on seed length,width,thickness,length-to-width,width-to-thickness and length-to-thickness,respectively.These alleles are respectively stored in the cultivars of Yanqing,Yixingwuhuangdou,Shangqiu7605,Sudouyihao,Hefeiliangtangqiaoshuangqingdou and Deqingxiangzhudou.To improve the above traits in the breeding of soybean,some superior parent combinations were predicted,eg.Zhenghezhibanzi × Nannongdahuangdou in seed length.The new variety pyramiding 42 elite alleles was the combinations of Lindoul 0,Deqingxiangzhudou,Ninghaixiazhidou,Zhenghezhibanzi,0803,Shangqiu7605 and 0831.Then the collinearity analysis was carried out between the soybean genome and the known seed shape genes of Arabidopsis,rice,maize and wheat.A total of 28 candidate genes were found to be around the associated markers in this study.2.Markers associated with SL were O19 and S21/satt331 from lasso method and S21-S22 and O23-O19 from CIM method;marker associated with SW was O19/O21 from lasso method and O23-O19/O19-O21 from CIM method;and markers associated with SLW were O19,O21 and S21/satt331 from lasso method,and O23-O19 and S21-S22/satt331-S21 from CIM method.It indicates that one QTL responsive for SL,SW and SLW is located marker interval S21-S22,and the other for SL and SLW is located marker interval O23-O19/O19-O21.According to the annotation project database,Glyma10g35240 and Glyma10g34980 might be the most likely candidate genes for seed shape traits.3.Results showed that 100-seed weight was significantly correlated with seed length,width and thickness traits in the cultivated soybeans but not with seed length in the wild soybeans.And length-to-width was a main trait in the first factor of factor analysis in wild soybean but not in the cultivated soybean.It showed that seed length and length-to-width traits have significant changes in the process of soybean domestication.