Association Analysis For Seed Shape Traits And 100-seed Weight In Soybean (Glycine Max L. Merr.)

Seed size and shape traits are closely related to seed yield and appearance quality in soybean. The genetic mechanism plays an important role in the breeding of soybean. However, the results from segregation population derived from the cross between two parents were limited to the two parents, and novel alleles can not be fully mined. In this study, therefore, natural population that consists of cultivars in soybean was used to investigate the association between seed size and shape traits and molecular markers, to mine elite alleles for the above traits, and to design excellent parental combination. The results presented will provide a foundational basis of molecular breeding by design.In this study the molecular marker information of 135 SSR markers, along with phenotypic observations of yield-related traits measured in Jiangpu experimental station in 2008, in 215 soybean cultivars selected from six ecological zones of China using stratified random sampling was used to investigate the genetic mechanism of the above traits, including 100-seed weight, seed length, seed width, seed height, and their corresponding ratios (length/width, width/height and length/height). The results were as follows.First, the molecular marker information of 135 SSR markers was used to calculate population genetic characteristics, including population structure, genetic diversity and linkage disequilibrium (LD) between markers, by using the softwares of STRUCTURE 2.2, PowerMarker 3.0 and TASSEL 2.2, respectively. The results showed that:1) the population under study was partitioned into five sub-populations. When the threshold for the posterior probability that each cultivar was assigned to each sub-population was set to 0.4,73.5% of all the soybean cultivars were assigned to the four sub-populations and the remaining was composed of mixed group; 2) 890 alleles among the 135 SSR markers were observed and the number of alleles for each marker varied from one to twenty-six. The polymorphism information content (PIC) ranged from 0.02 to 0.94 except for the marker sat₂28; and 3) among 8911 loci pairs derived from 134 SSR markers,2004 (22.49%) loci pairs showed strong linkage disequilibrium (P<0.05). Note that the proportion of collinear loci pairs (34.16%) was significantly higher than that of non-collinear loci pairs (21.88%). These results in the overall population were were obviously higher than those in each sub-population.Second, the molecular marker information and phenotypic values of quantitative traits were used to carry out association analysis between marker and the trait, and to estimate the effects of both main-effect and epistatic QTL.1)31 main-effect QTL and 30 epistatic QTL for seed shape traits and 100-seed weight (LOD>2.5 and P<0.05) were detected by eBays method. The numbers of main-effect QTL detected for seed length, width, thickness, length-to-width, width-to-thickness, length-to-thickness and 100-seed weight were 2,4,6,1,7,5 and 6, respectively. The numbers of epistatic QTL detected for 100-seed weight and seed length were 29 and 1, respectively. Note that each of five markers was associated with multiple tarits.2) 168 main-effect QTL were identified by TASSEL software (P<0.05). The numbers of main-effect QTL for seed length, width, thickness, length-to-width, width-to-thickness, length-to-thickness and 100-seed weight were 26,32,28,18,22,17 and 25, respectively. Among these markers associated with the above traits, each of 86% markers was associated with more than one tarit. Obviously, the number of QTL detected by TASSEL software is more than that by the eBayes method. Therefore, the results of 100-seed weight from TASSEL software were further dissected. All the QTL detected by TASSEL were partitioned into three parts,10 QTL (40%) were confirmed by linkage analysis and previous results,9 QTL (36%) were arosen by epistatic QTL identified by eBayes approach, and 6 QTL (24%) were due to LD. In addition, evidences showed that some markers were simultaneously associated with multiple traits. This may explain the correlation between traits or pleiotropic phenomena.Finally, 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 Sat₃65, Sat₃65, Sat₂52, Sat₃72, Satt632, Sat₃72 and Sat₂56 were found to have an impact effect on seed length, width, thickness, length-to-width, width-to-thickness, length-to-thickness, and 100-seed weight, respectively. These alleles are respectively stored in the cultivars Jiaqiangniumaohuang, Zhenzhou 76065-3, Niumaohuang, Jianguochengguangbayue-huang, Shuangliuliuyuehuang, Huixuanhuang and Laoshupi. To improve the above traits in the breeding of soybean, some superior parent combinations were predicted. In these combinations, four cultivars, yafanzaodou, hefeiliangtangjiaoshuangqingdou, daqingdou and kuaidouhuang, may be available for simultaneously improving multi-traits.