Detection of genes associated with soybean protein content using a genome-wide association study
Year: 2025
Type: article
Abstract: The protein content in soybean seeds serves as a crucial measure of soybean quality. Breeding high-protein varieties remains the most cost-effective and efficient approach to increasing soybean protein levels. Nevertheless, limited research has focused on identifying the genes responsible for high protein content among the diverse soybean cultivars. To address this gap, a genome-wide association study (GWAS) was conducted on 455 soybean varieties with varying protein content to predict and validate novel genes involved in regulating protein levels in soybean seeds. Protein content data were obtained from three distinct environments, along with three environmental variables derived from oil content, which is closely related to protein levels. Genotyping was performed using the SoySNP180k BeadChip, yielding genotype data for 63,306 non-redundant single nucleotide polymorphisms (SNPs). Five multi-locus GWAS methods were employed, resulting in the identification of 81 significant quantitative trait nucleotides (QTNs), of which 37 QTNs detected across different methods and environments were further analyzed. Moreover, the simulation platform Blib was used to conduct single-crossing simulation breeding on 81 QTN loci for actual breeding prediction. Haplotype analysis based on re-sequencing data confirmed 2 genes closely linked to protein synthesis, providing a theoretical basis for breeding high-protein soybean varieties and developing molecular breeding strategies. In this study, a total of 81 QTNs associated with soybean protein content were identified via five distinct GWAS mapping methods. Among these, 37 QTN loci were consistently localized through multiple approaches. The nine QTN loci that were reliably localized across various methods and environments were linked to the genes Glyma.11G094400 and Glyma.20G223200, which are involved in protein synthesis in soybean. The results from this investigation offer a theoretical basis for the development of high-protein soybean varieties and for molecular breeding techniques. If the advantageous haplotypes of protein-related genes identified in the results of this study are applied to high-protein soybean breeding via molecular markers, the efficiency of high-protein soybean breeding could be greatly improved.
Source: Plant Molecular Biology
Authors: Zhiyuan Yu, Bo Hu, Hailong Ning, Wen-Xia Li
Institution: Northeast Agricultural University
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: hybrid
Estimated APC paid: $4,590
OpenAlex ID: W4408744333