Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA.
G3 (Bethesda). 2022 Jul 29;12(8). doi: 10.1093/g3journal/jkac148.
Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew. It carries 2 powdery mildew resistance-associated genetic loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. The purpose of this study was to identify candidate resistance genes associated with each haplotype of the 2 loci. Both haplotypes of each resistance-associated locus were identified, phased, and reconstructed. Haplotype phasing allowed the identification of several structural variation events between haplotypes of both loci. Combined with a manual refinement of the gene models, we found that the heterozygous structural variants affected the gene content, with some resulting in duplicated or hemizygous nucleotide-binding leucine-rich repeat genes. Heterozygous structural variations were also found to impact the domain composition of some nucleotide-binding leucine-rich repeat proteins. By comparing the nucleotide-binding leucine-rich repeat proteins at Run1.2 and Run2.2 loci, we discovered that the 2 loci include different numbers and classes of nucleotide-binding leucine-rich repeat genes. To identify powdery mildew resistance-associated genes, we performed a gene expression profiling of the nucleotide-binding leucine-rich repeat genes at Run1.2b and Run2.2 loci with or without powdery mildew present. Several nucleotide-binding leucine-rich repeat genes were constitutively expressed, suggesting a role in powdery mildew resistance. These first complete, haplotype-resolved resistance-associated loci and the candidate nucleotide-binding leucine-rich repeat genes identified by this study are new resources that can aid the development of powdery mildew-resistant grape cultivars.
圆叶 muscadinia 品种 Trayshed 是葡萄白粉病抗性的宝贵资源。它携带 2 个与白粉病抗性相关的遗传基因座，第 12 号染色体上的 Run1.2 和第 18 号染色体上的 Run2.2。本研究的目的是鉴定与 2 个基因座的每个单倍型相关的候选抗性基因。鉴定、分相和重建了每个抗性相关基因座的两个单倍型。单倍型分相允许鉴定两个基因座的单倍型之间的几个结构变异事件。结合对基因模型的手动细化，我们发现杂合结构变异影响了基因的含量，有些导致重复或半合子核苷酸结合亮氨酸重复基因。还发现杂合结构变异会影响一些核苷酸结合亮氨酸重复蛋白的结构域组成。通过比较 Run1.2 和 Run2.2 基因座上的核苷酸结合亮氨酸重复蛋白，我们发现这两个基因座包括不同数量和类别的核苷酸结合亮氨酸重复基因。为了鉴定与白粉病抗性相关的基因，我们对 Run1.2b 和 Run2.2 基因座上的核苷酸结合亮氨酸重复基因进行了白粉病存在或不存在的基因表达谱分析。几个核苷酸结合亮氨酸重复基因持续表达，表明它们在白粉病抗性中发挥作用。这些完整的、单倍型解析的抗性相关基因座和本研究中鉴定的候选核苷酸结合亮氨酸重复基因是新的资源，可以帮助开发对白粉病具有抗性的葡萄品种。
