Mapping QTLs with epistatic effects and QTL-by-environment interactions for seed coat cracking in soybeans

Abstract

Seed coat cracking (SCC) consists of irregular cracks on the surface of seed coat, giving rise to serious effects on the seed quality in soybeans. However, breeding to achieve resistance to SCC has been an arduous task due to the complicated genetic behavior and environmental interactions. Thus, this study aims to map quantitative trait loci (QTLs) controlling irregular SCC in soybeans and to study QTL-by-environment interactions. QTL analysis was conducted using an RIL population derived from Keunolkong × Sinpaldalkong. The SCC was determined at natural conditions and calculated three times by counting cracked seeds with a 100 seeds per plant basis. In the four environments, a total of 10 QTLs with additive effects were identified. Among them, three QTLs (qSCC2-1, qSCC9, and qSCC20) located on chromosomes 2, 9, and 20 showed main-additive effects explaining 9.5–19.4 % of phenotypic variances in two environments. Across environments, seven additive QTLs, four additive × environment (AE) interactions, and two pairs of epistatic QTLs and epistasis × environment interactions were identified for SCC. Similar to the results in individual environments, two major QTLs (qSCC2-1 and qSCC9) showed additive main effects explaining 10.5 and 6.5 % of phenotypic variances, respectively and significant AE interaction in 2006 Suwon. The total QTLs explained 48.0 % of the phenotypic variation, with additive effects of 33.8 %, epistatic effects of 7.6 %, and AE and AAE of 6.6 %. All in all, these results showed that both additive effects and AE interactions can serve as important genetic basis for SCC.