Breitkreuz Claudia, Schulz Philipp, Schmitt Anne-Kristin, Flath Kerstin, Vidal Tiphaine, Hubbard Amelia, Kanyuka Kostya, Stahl Andreas, Keilwagen Jens, Perovic Dragan
Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany.
Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Field Crops and Grassland, Kleinmachnow, Germany.
PLoS One. 2025 May 23;20(5):e0323046. doi: 10.1371/journal.pone.0323046. eCollection 2025.
Wheat yellow rust is one of the most destructive and rapidly evolving wheat diseases worldwide, particularly in Europe. In 2011, the previously clonal European yellow rust races were replaced by a presumably sexually derived population, characterized as the new race called 'Warrior'. This race acquired additional virulence, leading to the emergence of 'Warrior(-)' in 2013. Since 2017, Warrior(-) has undergone further diversification into subraces, named after the wheat cultivars on which they were first detected: 'Amboise', 'Benchmark' and 'Kalmar'. While none of these subraces have been directly linked to the breakdown of a specific resistance gene, they exhibit distinct infection patterns on wheat differential sets. The lack of genetic resolution required to develop reliable genetic markers for diagnosis purposes is addressed in this study. Yellow rust isolates from the 'Warrior(-)' race group were collected as part of monitoring initiatives in France, Germany, Austria, and the UK. Marker development was based on a training set of German and French isolates with known pathotypes collected between 2017 and 2021. Using genotyping-by-sequencing (GBS) and whole genome sequencing (WGS), comparisons of subraces with Fisher's exact test (case-control study) identified 14 significant single nucleotide polymorphisms (SNPs). From these, we established four functional genetic markers capable of distinguishing between the 'Amboise' and 'Benchmark' subraces, though differentiation of 'Kalmar' was not successful. These four markers were validated on two independent control groups of isolates sampled in 2021 and 2022 from the UK (n = 30) and Germany (n = 40), respectively. While subrace predictions were accurate for the German group, predictions for the UK group failed. Principal Coordinates Analysis (PCoA) of genetic distances revealed a strong origin-driven effect, further confirmed by coverage analysis of the GBS data, which demonstrated an impact on the frequency and distribution of cleavage sites. Thus, this study provides a valuable tool for future yellow rust monitoring efforts while also highlighting significant origin-dependent effects that must be considered in genetic analyses.
小麦条锈病是全球最具破坏性且进化迅速的小麦病害之一，在欧洲尤为如此。2011年，以前呈克隆性的欧洲条锈病菌小种被一个推测为有性繁殖产生的群体所取代，该群体被定为名为“勇士”的新小种。这个小种获得了额外的毒性，导致2013年出现了“勇士(-)”。自2017年以来，“勇士(-)”进一步分化为多个亚小种，以首次检测到它们的小麦品种命名：“安布瓦斯”、“基准”和“卡尔马”。虽然这些亚小种均未直接与特定抗性基因的失效相关联，但它们在小麦鉴别品种上表现出不同的侵染模式。本研究解决了开发用于诊断目的的可靠遗传标记所需的遗传分辨率不足的问题。作为法国、德国、奥地利和英国监测工作的一部分，收集了“勇士(-)”小种组的条锈病菌分离株。标记开发基于2017年至2021年间收集的具有已知致病型的德国和法国分离株训练集。使用测序基因分型(GBS)和全基因组测序(WGS)，通过费舍尔精确检验（病例对照研究）对亚小种进行比较，确定了14个显著的单核苷酸多态性(SNP)。从中，我们建立了四个能够区分“安布瓦斯”和“基准”亚小种的功能性遗传标记，不过未能成功区分“卡尔马”亚小种。这四个标记在2021年和2022年分别从英国(n = 30)和德国(n = 40)采集的两个独立分离株对照组上进行了验证。虽然对德国组的亚小种预测是准确的，但对英国组的预测失败了。遗传距离的主坐标分析(PCoA)揭示了强烈的起源驱动效应，GBS数据的覆盖分析进一步证实了这一点，该分析表明其对切割位点的频率和分布有影响。因此，本研究为未来的小麦条锈病监测工作提供了一个有价值的工具，同时也突出了在遗传分析中必须考虑的显著的起源依赖性效应。
