The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome-wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non-BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates.

中文翻译：

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GWAS揭示了尾孢叶斑病病原体中快速进化的候选无毒效应子

最近在甜菜杂交种中培育的主要抗性基因BvCR4对由真菌病原体Cercospora beticola引起的Cercospora叶斑病具有高水平的抗性。通过在瑞士自然疾病压力下进行的现场试验，研究了克服BvCR4的病原体菌株的出现。在升高的人工疾病压力下进行的现场试验中评估了这些菌株的一部分的毒力。我们创建了新的C. beticola参考基因组，并绘制了在瑞士和德国收集的 256 个分离株的全基因组序列。将它们与毒力表型相结合，进行三项独立的全基因组关联研究（GWAS），以确定候选无毒基因。我们鉴定了一个与无毒力相关的基因座，其中包含一个名为AvrCR4的推定无毒效应基因。所有强毒分离株要么缺乏AvrCR4，要么在该基因内具有非同义突变。AvrCR4存在于来自非BvCR4杂交体的所有 74 个分离株中，而来自BvCR4杂交体的 89 个分离株中的 33 个带有缺失。我们还将 190 个美国公开分离株的基因组数据映射到我们新的参考基因组。在美国，来自非BvCR4杂种的95 个独特分离株中仅发现了一个 AvrCR4 缺失。AvrCR4是无毒效应子的一个独特例子，其中有毒等位基因最近才出现。这些很可能是在部署BvCR4后从现有的遗传变异中选出的。AvrCR4的鉴定将能够对C. beticola种群进行实时筛查，以发现有毒菌株的出现和传播。