Simons Kristin J, Oladzad Atena, Lamppa Robin, McClean Phillip E, Osorno Juan M, Pasche Julie S
Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.
Department of Plant Pathology, North Dakota State University, Fargo, ND, United States.
Front Plant Sci. 2021 Feb 26;12:621097. doi: 10.3389/fpls.2021.621097. eCollection 2021.
Dry bean ( L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by pv. . A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7-36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8-27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91-23.36 and Pv11:52.4. A ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies.
菜豆（L.）是一种重要的全球豆类作物，对由 pv. 引起的普通细菌性疫病（CBB）具有低到中等水平的抗性。对来自北达科他州立大学菜豆育种项目的总共852个基因型（品种、初级和高级育种系）进行了测试，以评估它们作为全基因组关联研究（GWAS）群体的有效性，从而确定与抗CBB相关的基因组区域，利用相关标记进行标记辅助育种（MAB），并鉴定候选基因。在生长室中对这些基因型在单叶期和三叶期的抗病性进行了评估。在单叶期，35%的基因型具有抗性，而在三叶期，25%的基因型具有抗性。使用Illumina平台对从每个基因型生成的文库进行测序。在对序列质量、读取深度和次要等位基因频率进行筛选后，分别将41,998个单核苷酸多态性（SNP）和30,285个SNP用于中美洲和安第斯基因库的GWAS。来自安第斯基因库的靠近SAP6分子标记的Pv10远端附近的一个区域解释了26.7 - 36.4%的抗性变异。来自中美洲基因库的三到七个区域贡献了25.8 - 27.7%的抗性，最显著的峰值也在SAP6标记附近。与CBB抗性相关的总共八个区域中的六个可能是先前遗传研究中确定的数量性状位点的物理位置。与CBB抗性相关的两个新位置位于Pv10:22.91 - 23.36和Pv11:52.4。Pv10上的一个直系同源基因成为CBB抗性的候选基因。Pv07上一个SNP的状态与易感性相关。其随后在MAB中的应用将使初级和高级田间产量试验中当前的品系数量减少多达14%，并且仅淘汰易感基因型。这些结果提供了一个基础SNP数据集，增进了我们对菜豆中CBB抗性的理解，并影响育种项目中的资源分配，因为育种群体可用于双重目的：品种开发以及遗传研究。
