Leaf rust (LR) is among the most destructive fungal diseases of rye (Secale cereale L.). Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear. A genome-wide association study was employed to detect QTLs controlling the immune response to LR of rye. A mapping population, G38A, was constructed by crossing two inbred lines: 723 (susceptible to LR) and JKI-NIL-Pr3 (a donor of the LR resistance gene Pr3). For genotyping, SNP-DArT and silico-DArT markers were used. Resistance phenotyping was conducted by visual assessment of the infection severity in detached leaf segments inoculated with two isolates of Puccinia recondita f. sp. secalis, namely, 60/17/2.1 (isolate S) in the main experiment and 86/n/2.1_5x (isolate N) in the validation experiment, at 10 and 17 days post-infection (dpi), respectively. In total, 42,773 SNP-DArT and 105,866 silico-DArT markers were included in the main analysis including isolate S, of which 129 and 140 SNP-DArTs and 767 and 776 silico-DArTs were significantly associated (p ≤ 0.001; − log10(p) ≥ 3.0) with the immune response to LR at 10 and 17 dpi, respectively. Most significant markers were mapped to chromosome 1R. The number of common markers from both systems and at both time points occupying common chromosomal positions was 37, of which 21 were positioned in genes, comprising 18 markers located in exons and three in introns. This gene pool included genes encoding proteins with a known function in response to LR (e.g., a NBS-LRR disease resistance protein-like protein and carboxyl-terminal peptidase). This study has expanded and supplemented existing knowledge of the genetic basis of rye resistance to LR by (1) detecting two QTLs associated with the LR immune response of rye, of which one located on the long arm of chromosome 1R is newly detected, (2) assigning hundreds of markers significantly associated with the immune response to LR to genes in the ‘Lo7’ genome, and (3) predicting the potential translational effects of polymorphisms of SNP-DArT markers located within protein-coding genes.

中文翻译：

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通过精密作图鉴定与黑麦叶锈病抗性相关的数量性状位点

叶锈病 (LR) 是黑麦 (Secale Greeke L.) 最具破坏性的真菌病害之一。尽管使用各种分析和方法学方法进行了深入研究，例如数量性状基因座 (QTL) 作图、候选基因表达分析和转录组测序，但黑麦对 LR 免疫反应的遗传基础仍不清楚。采用全基因组关联研究来检测控制黑麦 LR 免疫反应的 QTL。通过杂交两个自交系构建了作图群体 G38A：723（对 LR 敏感）和 JKI-NIL-Pr3（LR 抗性基因 Pr3 的供体）。对于基因分型，使用了 SNP-DArT 和 silico-DArT 标记。通过视觉评估接种两种隐秘柄锈菌 f 分离株的分离叶段的感染严重程度来进行抗性表型分析。 sp。 secalis，即主实验中的 60/17/2.1（分离株 S）和验证实验中的 86/n/2.1_5x（分离株 N），分别在感染后 10 天和 17 天 (dpi)。总共，42,773 个 SNP-DArT 和 105,866 个 silico-DArT 标记物被纳入包括分离株 S 在内的主要分析中，其中 129 和 140 个 SNP-DArT 以及 767 和 776 个 silico-DArT 显着相关 (p ≤ 0.001；− log10(p ) ≥ 3.0) 分别在 10 和 17 dpi 时对 LR 产生免疫反应。最重要的标记被定位到染色体 1R。两个系统和两个时间点占据共同染色体位置的共同标记数量为 37 个，其中 21 个位于基因中，其中 18 个位于外显子，3 个位于内含子。该基因库包括编码具有已知响应LR功能的蛋白质的基因（例如NBS-LRR抗病蛋白样蛋白和羧基末端肽酶）。本研究通过(1)检测了两个与黑麦LR免疫反应相关的QTL，其中一个位于1R染色体长臂上的QTL是新检测到的，(2 ) 将数百个与 LR 免疫反应显着相关的标记分配给“Lo7”基因组中的基因，以及 (3) 预测位于蛋白质编码基因内的 SNP-DArT 标记多态性的潜在翻译效应。