Vuong Tri D, He Guangqi, Hu Haifei, Valliyodan Babu, Lee Dongho, Bayer Philipp E, Schapaugh William T, Hessel Rene, Edwards David, Nguyen Henry T
Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Theor Appl Genet. 2025 Sep 1;138(9):237. doi: 10.1007/s00122-025-05020-9.
The soybean [Glycine max (L.) Merr.] pangenome has been studied and shown to be an invaluable resource for investigating structural variations (SVs), from which different genomic markers were successfully developed and employed for genome-wide association studies (GWAS). Among the SVs markers, gene presence-and-absence variations (PAVs) have been developed in soybean, but have not been widely utilized for association analyses. Here, we reported GWAS and haplotype analysis of seed protein and oil content for two diverse panels, comprised over 500 soybean accessions evaluated in multiple field environments using three marker datasets, whole genome sequence (WGS)-single-nucleotide polymorphisms (SNPs), 50 K-SNPs, and PAVs. The analyses identified new quantitative trait loci (QTL) for protein and oil content, along with the validation of previously reported QTL for these traits. This includes a well-studied QTL on chromosome (Chr.) 20 and another one on Chr. 05 for protein and/or oil. Importantly, this study is the first to report a new genomic locus for both protein and oil mapped to Chr. 08. Gene ontology annotations and expression profiles suggested candidate genes. Further analyses using haplotype-based markers led to the identification of multiple haplotype blocks encompassing candidate genes. Among these, Glyma.05G243400 on Chr. 05 and Glyma.08G109900 and Glyma.08G110000 on Chr. 08 were identified as promising targets. These genes can be incorporated into soybean breeding programs to enhance the selection of desirable protein and oil phenotypes through a haplotype-based breeding approach.
大豆[Glycine max (L.) Merr.]的泛基因组已得到研究，并被证明是研究结构变异（SVs）的宝贵资源，据此成功开发了不同的基因组标记，并将其用于全基因组关联研究（GWAS）。在SVs标记中，大豆已开发出基因存在-缺失变异（PAVs），但尚未广泛用于关联分析。在此，我们报告了对两个不同群体种子蛋白质和油含量的GWAS和单倍型分析，这两个群体由500多个大豆种质组成，在多个田间环境中使用三个标记数据集进行评估，即全基因组序列（WGS）-单核苷酸多态性（SNP）、50K-SNP和PAVs。分析确定了蛋白质和油含量的新数量性状位点（QTL），同时验证了先前报道的这些性状的QTL。这包括20号染色体（Chr.）上一个经过充分研究的QTL以及5号染色体上另一个与蛋白质和/或油相关的QTL。重要的是，本研究首次报告了一个同时与蛋白质和油相关的新基因组位点，定位于8号染色体。基因本体注释和表达谱提示了候选基因。使用基于单倍型的标记进行的进一步分析导致鉴定出多个包含候选基因的单倍型块。其中，5号染色体上的Glyma.05G243400以及8号染色体上的Glyma.08G109900和Glyma.08G110000被确定为有前景的目标。这些基因可纳入大豆育种计划，通过基于单倍型的育种方法加强对理想蛋白质和油表型的选择。
