Molecular marker analysis of seed size in soybean

Seed size is an important attribute of soybean [Glycine max (L.) Merr.] for some food uses. The objectives of this study were to identify markers associated with quantitative trait loci for seed size (SSQTL), determine the influence of the environment on expression of the marker-SSQTL associations, and compare the efficiency of phenotypic selection and marker-assisted selection for the trait. Three small-seeded lines were crossed to a line or cultivar with normal seed size to form three two-parent populations. The parents of the populations were screened with 178 simple sequence repeat (SSR) markers to identify polymorphism. Population 1 (Pop 1) had 75 polymorphic SSR markers covering 1306 cM, population 2 (Pop 2) had 70 covering 1143 cM, and population 3 (Pop 3) had 82 covering 1237 cM. Seed size of each population was determined with 100 F2 plants grown at Ames, IA, and their F2-derived lines grown in two replications at three environments. Single-factor analysis of variance and multiple regression were used to determine significant marker-SSQTL associations. Pop 1 had 12 markers that individually accounted for 8 to 17% of the variation for seed size, Pop 2 had 16 markers that individually accounted for 8 to 38% of the variation, and Pop 3 had 22 markers that individually accounted for 8 to 29% of the variation. Four of the 12 markers in Pop 1, four in Pop 2, and one in Pop 3 had significant associations with SSQTL across four environments, while five loci in Pop 1, seven in Pop 2, and eight in Pop 3 had significant associations in more than one environment. Three marker loci that had significant SSQTL associations in this study also were significant in previous research and 13 markers had unique SSQTL associations. The relative effectiveness of phenotypic and marker-assisted selection among F2 plants varied for the three populations. On the average, phenotypic selection for seed size was as effective and less expensive than marker-assisted selection