Identification of quantitative trait loci (QTLs) for seed protein concentration in soybean and analysis for additive effects and epistatic effects of QTLs under multiple environments

Soybean protein concentration is a key trait driver of successful soybean quality. A recombination inbred lines derived from a cross between 'Charleston' and 'Dongnong594', were planted in three environments across four years in China. Then, the genetic effects were partitioned into additive main effects, epistatic main effects and their environment interaction effects by using composite interval mapping, multiple interval mapping and composite interval mapping in a mixed linear model. Forty-three quantitative trait loci QTLs were identified on 17 of 20 soybean chromosomes excluding Ch 7, Ch 8 and Ch 17. Two QTLs showed a good stability across multiple environments, qPRO20-1 was detected under four environments, which explained 4.4-9.95% phenotypic variances and the allele was from 'Charleston' among four environments. qPRO7-5 was detected under three environments, which explained 7.2-14.5% phenotypic variances and the allele was from 'Dongnong 594', three pathway genes of protein biosynthesis were detected in the interval of qPRO7-5. The additive main-effect QTLs contributed more phenotypic variation than the epistasis and environmental interaction. This indicated that it is feasible by marker-assisted selection to improve soybean protein concentration.