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Seed size is an important attribute of soybean Glycine max (L.) Merr. for some food uses. The objectives of this study were to identify simple-sequence-repeat (SSR) markers associated with quantitative trait loci for seed size (SSQTL) and to compare the effectiveness of phenotypic selection and marker-assisted selection for seed size among individual F2 plants. Three small-seeded lines were crossed to parents with normal seed size to form three two-parent populations. The parents of the populations were screened with 178 SSR markers to identify polymorphism. Population 1 (Pop 1) had 75 polymorphic SSR markers covering 1306 centimorgans (cM), Pop 2 had 70 covering 1143 cM, and Pop 3 had 82 covering 1237 cM. Seed size of each population was determined with 100 F2 plants grown at Isabela, Puerto Rico, 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. Population 1 had 12 markers that individually accounted for 8.1 to 14.9% of the variation for seed size combined across environments, Pop 2 had 16 markers that individually accounted for 7.8 to 36.5% of the variation, and Pop 3 had 22 markers that individually accounted for 8.6 to 28.8% of the variation. 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. Averaged across the three populations, phenotypic selection for seed size was as effective and less expensive than marker-assisted selection.
Hoeck et al. (Wed,) studied this question.