Population Structure and Association Analysis of Traits in Summer Soybeans

The summer soybeans (Glycine max (L.) Merr.) in Hebei Province, China, which have adapted to different environments, show extraordinarily rich genetic diversity and extensive species variation. The objectives of this study were to analyze the population structure of summer soybean using simple sequence repeat (SSR) markers and to identify the SSR markers associated with specific traits. A set of 135 SSR markers was used to analyze 50 soybean cultivars, of which 47 cultivars were from 10 breeding institutions in Hebei Province and three cultivars were introductions from the United States. Software tools, the TASSEL, DARwin, and STRUCTURE, were used to analyze linkage disequilibrium (LD) and genetic structure. In addition, an association analysis between the molecular markers and the phenotypic values of 15 agronomic and quality traits was performed. The yield-related agronomic traits included plant height, bottom pod height, effective branch number, number of nodes on main stem, pod number per plant, seed number per plant, one-seed pods, two-seed pods, three-seed pods, four-seed pods, seed weight per plant, 100-seed weight, and yield. The quality traits included crude protein content and crude fat content. The following results were obtained from the analysis. First, principal component analysis (PCA) indicated that a significant correlation existed between the cultivar distribution and the breeding institutions or breeding areas. Second, 63.86% of pairs of SSR loci exhibited certain levels of LD. The fragment between loci Satt557 and Satt371 in the C2 LG had a genetic distance of 33.29 cM and featured strong LD (r ² > 0.33). Third, the genetic-structure analysis revealed that the population was composed of two subpopulations, which related to their parental pedigrees. In addition, 70 SSR markers were found to be associated with 13 agronomic traits; 49 SSR markers have not been reported previously. The SSR markers identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of soybean for yield and quality.