Zhao Xunchao, Zhu Hanhan, Liu Fang, Wang Jie, Zhou Changjun, Yuan Ming, Zhao Xue, Li Yongguang, Teng Weili, Han Yingpeng, Zhan Yuhang
Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
Daqing Branch, Heilongjiang Academy of Agricultural Science, Daqing 163711, China.
Plants (Basel). 2024 Apr 17;13(8):1128. doi: 10.3390/plants13081128.
Protein content (PC) is crucial to the nutritional quality of soybean [ (L.) Merrill]. In this study, a total of 266 accessions were used to perform a genome-wide association study (GWAS) in three tested environments. A total of 23,131 high-quality SNP markers (MAF ≥ 0.02, missing data ≤ 10%) were identified. A total of 40 association signals were significantly associated with PC. Among them, five novel quantitative trait nucleotides (QTNs) were discovered, and another 32 QTNs were found to be overlapping with the genomic regions of known quantitative trait loci (QTL) related to soybean PC. Combined with GWAS, metabolome and transcriptome sequencing, 59 differentially expressed genes (DEGs) that might control the change in protein content were identified. Meantime, four commonly upregulated differentially abundant metabolites (DAMs) and 29 commonly downregulated DAMs were found. Remarkably, the soybean gene , which is homologous with Arabidopsis hydroxyproline-rich glycoproteins (HRGPs), may play an important role in improving the PC. Additionally, was divided into two main haplotype in the tested accessions. The PC of haplotype 1 was significantly lower than that of haplotype 2. The results of this study provided insights into the genetic mechanisms regulating protein content in soybean.
蛋白质含量（PC）对大豆[（L.）Merrill]的营养品质至关重要。在本研究中，共使用266份种质在三个测试环境中进行全基因组关联研究（GWAS）。共鉴定出23131个高质量单核苷酸多态性（SNP）标记（最小等位基因频率≥0.02，缺失数据≤10%）。共有40个关联信号与蛋白质含量显著相关。其中，发现了5个新的数量性状核苷酸（QTN），另外32个QTN被发现与大豆蛋白质含量相关的已知数量性状位点（QTL）的基因组区域重叠。结合GWAS、代谢组和转录组测序，鉴定出59个可能控制蛋白质含量变化的差异表达基因（DEG）。同时，发现了4种常见上调的差异丰富代谢物（DAM）和29种常见下调的DAM。值得注意的是，与拟南芥富含羟脯氨酸糖蛋白（HRGP）同源的大豆基因可能在提高蛋白质含量方面发挥重要作用。此外，在测试的种质中被分为两个主要单倍型。单倍型1的蛋白质含量显著低于单倍型2。本研究结果为大豆蛋白质含量调控的遗传机制提供了见解。
