Identification of candidate genes GmSPC2-1 and development of functional molecular markers for protein content in...

Seed protein content (SPC) is a crucial quantitative trait that determines both the quality and commercial value of soybean. However, research on the genes and molecular markers that influencing protein content remains limited. In this study, we utilized a Recombinant Inbred Line (RIL) population derived from a cross between Heihe 36 and Dongnong L13 as experimental material. Based on the Single nucleotide polymorphism binning (SNP-bin) genetic map and SPC data from three environments, we mapped Quantitative Trait Loci (QTLs) for SPC, identified candidate genes, and developed molecular markers. A total of eight QTLs were mapped across five chromosomes, each explaining between 0.93% and 27.04% of the phenotypic variance (PVE). Among these, qSPC-2-1 was identified as a major-effect locus (PVE = 27.04%), while qSPC-15-1 and qSPC-15-4 were classified as novel loci. Through tissue expression analysis, functional annotation, and haplotype analysis, we identified GmSPC2-1 (Glyma.02G255800), which encodes an amino acid transporter, as the most likely candidate gene regulating soybean protein content in the qSPC-2-1 interval. The Hap2 haplotype of this gene was associated with higher SPC. Derived Cleaved Amplified Polymorphic Sequence (dCAPS) markers were developed and validated based on variant sites in the coding regions of candidate genes. This study provides new genetic resources for breeding protein-rich soybean varieties and molecular markers to support marker-assisted selection.

The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01722-0.