Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland.
Educo BSH Ltd, Lublin, Poland.
BMC Plant Biol. 2024 Apr 17;24(1):291. doi: 10.1186/s12870-024-04960-6.
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; - log(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.
叶锈病（LR）是黑麦（Secale cereale 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（如数量性状位点（QTL）作图、候选基因表达分析和转录组测序）进行了深入研究，但黑麦对 LR 免疫反应的遗传基础仍不清楚。
利用全基因组关联研究检测控制黑麦对 LR 免疫反应的 QTL。通过杂交两个近交系：723（对 LR 敏感）和 JKI-NIL-Pr3（LR 抗性基因 Pr3 的供体），构建了 G38A 作图群体。用于基因分型的 SNP-DArT 和硅 DArT 标记。通过在接种 Puccinia recondita f. sp. secalis 的两个分离株 60/17/2.1（分离物 S）和 86/n/2.1_5x（分离物 N）后 10 和 17 天（dpi）时，对离体叶片片段的感染严重程度进行抗性表型评估。总共包括 42773 个 SNP-DArT 和 105866 个硅 DArT 标记物，其中 129 个和 140 个 SNP-DArT 和 767 个和 776 个硅 DArT 标记物与 10 和 17 dpi 时对 LR 的免疫反应显著相关（p≤0.001；-log(p)≥3.0）。大多数显著标记物被映射到 1R 染色体上。两个系统和两个时间点的共有标记物占据共有染色体位置的数量为 37 个，其中 21 个位于基因中，包括 18 个位于外显子中的标记物和 3 个位于内含子中的标记物。该基因库包括已知在 LR 反应中具有功能的蛋白质编码基因（例如，NBS-LRR 疾病抗性蛋白样蛋白和羧基末端肽酶）。
本研究通过（1）检测与黑麦 LR 免疫反应相关的两个 QTL，其中一个位于 1R 染色体的长臂上，这是新发现的，（2）将数百个与 LR 免疫反应显著相关的标记物分配到“Lo7”基因组中的基因中，以及（3）预测位于蛋白质编码基因内的 SNP-DArT 标记物多态性的潜在翻译效应，扩展和补充了黑麦对 LR 抗性的遗传基础的现有知识。
