Identification of Wild Segments Related to High Seed Protein Content Under Multiple Environments and Analysis of Its Candidate Genes in Soybean

Annual wild soybean is characterized by a high protein content. To elucidate the genetic basis, this study utilized a chromosome segment substitution line population (177 lines) constructed with cultivated soybean NN1138-2 as the recipient and wild soybean N24852 as the donor. Phenotypic analyses across three environments revealed significant variation in protein content ranging from 42.86% to 49.08%, with a high heritability of 0.70, indicating strong genetic control. Through high-throughput sequencing, six wild segments associated with high protein content were detected on chromosomes 3, 6, 9, 15, and 20, with phenotypic variation explained (PVE) by individual segments ranged from 3.58% to 22.46%, with segments on chromosomes 9, 15, and 20 as large-effect segments with PVE > 10%. All wild segments exhibited positive additive effects (0.42–1.09%), consistent with the characteristic of a high protein content in wild soybean. Compared with previous studies, five segments overlapped with reported loci, while qPro6.1 on chromosome 6 was a novel discovery. Integration of genomic and transcriptomic data identified 10 genes involved in nucleic acid binding, transmembrane protein transport, and amino acid synthesis pathway, with homologs validated in soybean, rice, and rapeseed. This research deepens the understanding of wild soybean’s high protein and offers new gene resources for breeding high-protein cultivated soybean.