Quantitative trait loci for agronomic and seed quality traits in an F2 and F4:6 soybean population

Molecular breeding is becoming more practical as better technology emerges. The use of molecular markers in plant breeding for indirect selection of important traits can favorably impact breeding efficiency. The purpose of this research is to identify quantitative trait loci (QTL) on molecular linkage groups (MLG) which are associated with seed protein concentration, seed oil concentration, seed size, plant height, lodging, and maturity, in a population from a cross between the soybean cultivars ‘Essex’ and ‘Williams.’ DNA was extracted from F2 generation soybean leaves and amplified via polymerase chain reaction (PCR) using simple sequence repeat (SSR) markers. Markers that were polymorphic between the parents were analyzed against phenotypic trait data from the F2 and F4:6 generation. For the F2 population, significant additive QTL were Satt540 (MLG M, maturity, r2 = 0.11; height, r2 = 0.04, seed size, r2= 0.06], Satt373 (MLG L, seed size, r2 = 0.04; height, r2 = 0.14), Satt50 (MLG A1, maturity r2 = 0.07), Satt14 (MLG D2, oil, r2 = 0.05), and Satt251 (protein r2 = 0.03, oil, r2 =0.04). Significant dominant QTL for the F2 population were Satt540 (MLG M,height, r2 = 0.04; seed size, r2 = 0.06) and Satt14 (MLG D2, oil, r2 = 0.05). In the F4:6 generation significant additive QTL were Satt239 (MLGI, height, r2 = 0.02 at Knoxville, TN and r2 = 0.03 at Springfield, TN), Satt14 (MLG D2, seed size, r2 = 0.14 at Knoxville, TN), Satt373 (MLG L, protein, r2 = 0.04 at Knoxville, TN) and Satt251 (MLG B1, lodging r2 = 0.04 at Springfield, TN). Averaged over both environments in the F4:6 generation, significant additive QTL were identified as Satt251 (MLG B1, protein, r2 = 0.03), and Satt239 (MLG I, height, r2 = 0.03). The results found in this study indicate that selections based solely on these QTL would produce limited gains (based on low r2 values). Few QTL were detected to be stable across environments. Further research to identify stable QTL over environments is needed to make marker-assisted approaches more widely adopted by soybean breeders.