You Hee Jin, Zhao Ruihua, Choi Yu-Mi, Kang In-Jeong, Lee Sungwoo
Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea.
Plants (Basel). 2024 Dec 15;13(24):3501. doi: 10.3390/plants13243501.
(Kauffman and Gerdemann) is an oomycete pathogen that threatens soybean ( L.) production worldwide. The development of soybean cultivars with resistance to this pathogen is of paramount importance for the sustainable management of the disease. The objective of this study was to identify genomic regions associated with resistance to isolate 40468 through genome-wide association analyses of 983 soybean germplasms. To elucidate the genetic basis of resistance, three statistical models were employed: the compressed mixed linear model (CMLM), Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK), and fixed and random model circulating probability unification (FarmCPU). The three models consistently identified a genomic region (3.8-5.3 Mbp) on chromosome 3, which has been previously identified as an cluster. A total of 18 single nucleotide polymorphisms demonstrated high statistical significance across all three models, which were distributed in eight linkage disequilibrium (LD) blocks within the aforementioned interval. Of the eight, LD3-2 exhibited the discernible segregation of phenotypic reactions by haplotype. Specifically, over 93% of accessions with haplotypes LD3-2-F or LD3-2-G displayed resistance, whereas over 91% with LD3-2-A, LD3-2-C, or LD3-2-D exhibited susceptibility. Furthermore, the BLINK and FarmCPU models identified new genomic variations significantly associated with the resistance on several other chromosomes, indicating that the resistance observed in this panel was due to the presence of different alleles of multiple genes. These findings underscore the necessity for robust statistical models to accurately detect true marker-trait associations and provide valuable insights into soybean genetics and breeding.
考夫曼氏菌和格德曼氏菌是一种卵菌病原体，威胁着全球大豆（Glycine max (L.)）的生产。培育对这种病原体具有抗性的大豆品种对于该病害的可持续管理至关重要。本研究的目的是通过对983份大豆种质进行全基因组关联分析，确定与对分离株40468抗性相关的基因组区域。为了阐明抗性的遗传基础，采用了三种统计模型：压缩混合线性模型（CMLM）、贝叶斯信息与连锁不平衡迭代嵌套关键路径法（BLINK）以及固定和随机模型循环概率统一法（FarmCPU）。这三种模型一致地在3号染色体上鉴定出一个基因组区域（3.8 - 5.3兆碱基对），该区域先前已被确定为一个抗性簇。共有18个单核苷酸多态性在所有三种模型中都显示出高度统计学意义，它们分布在上述区间内的8个连锁不平衡（LD）块中。在这8个LD块中，LD3 - 2通过单倍型表现出明显的表型反应分离。具体而言，超过93%具有单倍型LD3 - 2 - F或LD3 - 2 - G的种质表现出抗性，而超过91%具有LD3 - 2 - A、LD3 - 2 - C或LD3 - 2 - D的种质表现出易感性。此外，BLINK和FarmCPU模型在其他几条染色体上鉴定出了与抗性显著相关的新基因组变异，表明该群体中观察到的抗性是由于多个抗性基因存在不同等位基因所致。这些发现强调了使用稳健统计模型准确检测真实标记 - 性状关联的必要性，并为大豆遗传学和育种提供了有价值的见解。
