Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotoxins are harmful for livestock and humans; therefore, many countries have strict regulatory limits for raw materials and processed food. Extensive genetic diversity is described among field populations of F. culmorum isolates for aggressiveness and production of the trichothecene mycotoxin deoxynivalenol (DON). However, the causes for this quantitative variation are not clear, yet. We analyzed 92 isolates sampled from different field populations in Germany, Russia, and Syria together with an international collection for aggressiveness and DON production in replicated field experiments at two locations in two years with two hosts, wheat and rye. The 30x coverage whole-genome resequencing of all isolates resulted in the identification of 130,389 high quality single nucleotide polymorphisms (SNPs) that were used for the first genome-wide association study in this phytopathogenic fungus. In wheat, 20 and 27 SNPs were detected for aggressiveness and DON content, respectively, of which 10 overlapped. Additionally, two different SNPs were significantly associated with aggressiveness in rye that were among those SNPs being associated with DON production in wheat. Most of the SNPs explained only a small proportion of genotypic variance (pG), however, four SNPs were associated with major quantitative trait loci (QTLs) with pG ranging from 12 to 48%. The QTL with the highest pG was involved in DON production and associated with a SNP most probably located within the Tri4 gene. The diversity of 92 isolates of F. culmorum were captured using a heuristic approach. Key phenotypic traits, SNPs, and candidate genes underlying aggressiveness and DON production were identified. Clearly, many QTLs are responsible for aggressiveness and DON content in wheat, both traits following a quantitative inheritance. Several SNPs involved in DON metabolism, among them the Tri4 gene of the trichothecene pathway, were inferred as important source of variation in fungal aggressiveness. Using this information underlying the phenotypic variation will be of paramount importance in evaluating strategies for successful resistance breeding.

中文翻译：

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通过对 92 株镰刀菌进行重测序，对小麦和黑麦赤霉病中脱氧雪腐镰刀菌烯醇的产生和侵袭性进行全基因组关联研究

Fusarium culmorum 是导致欧洲谷物赤霉病的重要病原体。这种疾病在世界范围内具有重要意义，导致产量下降、谷物质量下降和真菌毒素污染。这些霉菌毒素对牲畜和人类有害；因此，许多国家对原材料和加工食品有严格的监管限制。在 F. culmorum 分离株的野外种群中描述了广泛的遗传多样性，用于单端孢霉烯真菌毒素脱氧雪腐镰刀菌烯醇 (DON) 的侵袭性和生产。然而，这种数量变化的原因尚不清楚。我们分析了从德国、俄罗斯和叙利亚的不同野外种群采样的 92 株分离株，并在两年内在两个地点与两个宿主的重复野外实验中分析了侵略性和 DON 生产的国际收集，小麦和黑麦。对所有分离株进行 30 倍覆盖的全基因组重测序，鉴定了 130,389 个高质量的单核苷酸多态性 (SNP)，用于该植物病原真菌的首次全基因组关联研究。在小麦中，分别检测到 20 和 27 个 SNP 的侵袭性和 DON 含量，其中 10 个重叠。此外，两个不同的 SNP 与黑麦中的侵袭性显着相关，这些 SNP 与小麦中的 DON 生产相关。大多数 SNP 仅解释了一小部分基因型变异 (pG)，然而，四个 SNP 与主要数量性状基因座 (QTL) 相关，pG 范围从 12% 到 48%。具有最高 pG 的 QTL 参与 DON 生产并与最有可能位于 Tri4 基因内的 SNP 相关。使用启发式方法捕获了 92 株 F. culmorum 的多样性。确定了攻击性和 DON 产生的关键表型特征、SNP 和候选基因。显然，许多 QTL 与小麦的攻击性和 DON 含量有关，这两个性状都遵循数量遗传。一些参与 DON 代谢的 SNP，其中包括单端孢霉烯途径的 Tri4 基因，被推断为真菌侵袭性变异的重要来源。使用表型变异背后的这些信息对于评估成功的抗性育种策略至关重要。许多 QTL 与小麦的攻击性和 DON 含量有关，这两个性状都遵循数量遗传。一些参与 DON 代谢的 SNP，其中包括单端孢霉烯途径的 Tri4 基因，被推断为真菌侵袭性变异的重要来源。使用表型变异背后的这些信息对于评估成功的抗性育种策略至关重要。许多 QTL 与小麦的攻击性和 DON 含量有关，这两个性状都遵循数量遗传。一些参与 DON 代谢的 SNP，其中包括单端孢霉烯途径的 Tri4 基因，被推断为真菌侵袭性变异的重要来源。使用表型变异背后的这些信息对于评估成功的抗性育种策略至关重要。