QTN mapping, gene prediction and molecular design breeding of seed protein content in soybean

Soybean seeds contain approximately 40% protein, making soybeans an important source of plant-based protein. Research on QTN mapping, molecular design breeding and mining of genes related to seed protein formation provides guiding significance for the analysis of the underlying genetic mechanisms of seed protein formation and the selection of high-protein varieties. The seed protein contents (SPCs) of 144 lines of a soybean four-way recombinant inbred line (FW-RIL) population were determined in 8 environments. A three-variance component multisite random effects mixed linear model (3VmrMLM) was used to conduct a genome-wide association study on protein content. A single detected QTN explained 0.53%–3.37% of the phenotypic variation. A molecular-assisted selection breeding model containing the 18 QTNs explained 51.97% of the phenotypic variation in protein content. Eight biparental and five tri-parental crosses that produced excellent lines with the greatest protein content-related genotype values that could be generated by phenotypic and molecular-assisted selection were screened. An LD block of 17 QTNs (QEIs) was identified, and one key candidate gene related to protein formation was predicted by haplotype analysis. The proportion of Hap 1 varieties in the spring-sowing soybean region in North China was lower than those in the Huang-Huai-Hai soybean region in Central China and the multiripe soybean region in South China. The proportion of Hap 1 varieties among the wild varieties and landraces was greater than that among the improved varieties. The results of this study provide important insights into the genetic basis of soybean protein content and information to aid in molecular design breeding methods to improve protein content.