Leptosphaeria maculans is a serious concern for canola production worldwide. For effective disease management, knowledge of the pathogen's genetic variability and population structure is a prerequisite. In this study, whole-genome sequencing was performed for 162 of 1590 L. maculans isolates collected in the years 2007–2008 and 2012–2014 in Western Canada. DNA variants in genome-wide and specific regions including avirulence (Avr) genes were characterized. A total of 31,870 high-quality polymorphic DNA variants were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants. The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations. Principal component analysis with genome-wide variants showed that the isolates collected in 2012–2014 were more genetically diverse than those collected in 2007–2008. Population structure analysis discovered three distinct sub-populations. Although isolates from Saskatchewan and Alberta were of similar genetic composition, Manitoba isolates were highly diverse. Genome-wide association study detected DNA variants in genes AvrLm4-7, Lema_T86300, and Lema_T86310 associated with the years of collection.

Leptosphaeria maculans是全球油菜生产的一个严重问题。对于有效的疾病管理，了解病原体的遗传变异性和种群结构是先决条件。在这项研究中，对 2007-2008 年和 2012-2014 年在加拿大西部收集的 1590 个L. maculans分离株中的162 个进行了全基因组测序。对全基因组和特定区域的 DNA 变体进行了表征，包括无毒 ( Avr ) 基因。共有 31,870 个高质量的多态性 DNA 变体用于研究L. maculans遗传多样性和种群结构。聚类分析表明，150 个分离株通过位于任一Avr或小的分泌蛋白编码基因，并通过全基因组变体分为 2 个主要组和 6 个亚组。核苷酸多样性和分化分析也证实了种群内和种群间的遗传变异。全基因组变异的主成分分析表明，2012-2014 年收集的分离物比 2007-2008 年收集的分离物具有更多的遗传多样性。种群结构分析发现了三个不同的亚群。尽管来自萨斯喀彻温省和阿尔伯塔省的分离株具有相似的遗传组成，但曼尼托巴省的分离株却高度多样化。全基因组关联研究检测到基因AvrLm4-7、Lema_T86300和Lema_T86310的 DNA 变异与收集年份相关。