Pathotype complexity and genetic characterization of Phytophthora sojae populations in Illinois, Indiana, Kentucky, and Ohio

Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960’s, but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps gene(s) were still effective and identifying possible population clusters. There were 218 pathotypes identified from 473 P. sojae isolates with an average of 6.7 out of 15 differential soybean lines exhibiting a susceptible response for each isolate. Genetic characterization of 103 P. sojae isolates from across Illinois, Indiana, Kentucky, and Ohio with 19 simple sequence repeat markers identified 92 multilocus genotypes. There was a moderate level of population differentiation among these four states, with pairwise FST values ranging from 0.026 to 0.246. There was also moderate to high levels of differentiation between fields, with pairwise FST values ranging from 0.071 to 0.537. Additionally, cluster analysis detected the presence of P. sojae population structure across neighboring states. The level of pathotype and genetic diversity, in addition to the identification of population clusters, supports the hypothesis of occasional outcrossing events that allow for an increase in diversity and the potential to select for a loss in avirulence to specific resistance genes within regions. The trend of suspected gene flow among neighboring fields is expected to be an ongoing issue with current agricultural practices.

大豆疫霉（Phytophthora sojae）是引发大豆疫霉根腐病（Phytophthora root and stem rot of soybean）的病原菌。自20世纪60年代起，人们便通过单一Rps基因对该病害进行防治，但该病原菌后续已对多数此类抗病基因产生适应性演化，导致这些基因丧失抗病效果。本研究旨在通过评估哪些Rps基因仍具有抗病有效性，鉴定潜在的种群聚类群，对采自伊利诺伊州、印第安纳州、肯塔基州及俄亥俄州土壤样本中的大豆疫霉的致病型与遗传多样性进行分析。研究从473株大豆疫霉分离物中鉴定出218种致病型，每株分离物在15个鉴别大豆品系中平均有6.7个表现出感病反应。研究人员利用19个简单序列重复（simple sequence repeat, SSR）标记，对来自上述四州的103株大豆疫霉分离物进行遗传特征分析，共鉴定出92个多位点基因型（multilocus genotype）。上述四个州的种群分化程度中等，两两种群间的FST值范围为0.026至0.246。不同田块间的种群分化程度则为中等至高水平，两两田块间的FST值范围为0.071至0.537。此外，聚类分析检测到相邻州间存在大豆疫霉的种群结构。致病型与遗传多样性水平，结合种群聚类群的鉴定结果，支持以下假说：偶尔发生的远交事件可提升种群多样性，并有可能在区域内筛选出对特定抗病基因丧失无致病性的菌株。当前农业生产模式下，相邻田块间疑似存在基因流的趋势或将持续存在。