QTL-seq analysis of powdery mildew resistance in a Korean cucumber inbred line

Key message QTL mapping and RT-PCR analyses identified theCsGy5G015660as a strong powdery mildew resistance candidate gene and natural variation ofCsGy5G015660allele was observed using 115 core germplasm. Powdery mildew (PM) is among the most serious fungal diseases encountered in the cultivation of cucurbits. The development of PM-resistant inbred lines is thus of considerable significance for cucumber breeding programs. In this study, we applied bulked segregant analysis combined with QTL-seq to identify PM resistance loci using F(2)population derived from a cross between two Korean cucumber inbred lines, PM-R (resistant) and PM-S (susceptible). Genome-wide SNP profiling using bulks of the two extreme phenotypes identified two QTLs on chromosomes 5 and 6, designatedpm5.2andpm6.1, respectively. The two PM resistance loci were validated using molecular marker-based classical QTL analysis:pm5.2(30%R(2)at LOD 11) andpm6.1(11%R(2)at LOD 3.2). Furthermore, reverse transcriptase-PCR analyses, using genes found to be polymorphic between PM-R and PM-S, were conducted to identify the candidate gene(s) responsible for PM resistance. We found that transcripts of the geneCsGy5G015660, encoding a putative leucine-rich repeat receptor-like serine/threonine-protein kinase (RPK2), showed specific accumulation in PM-R prior to the appearance of disease symptoms, and was accordingly considered a strong candidate gene for PM resistance. In addition, cleaved amplified polymorphic sequence markers fromCsGy5G015660were developed and used to screen 35 inbred lines. Natural variation in theCsGy5G015660allele was also observed based on analysis of a core collection of 115 cucumber accessions.Our results provide new genetic insights for gaining a better understanding of the genetic basis of PM resistance in cucumber, and pave the way for further utilization in cucumber PM resistance breeding programs.

Automated summary

Through QTL mapping and RT-PCR analyses, the CsGy5G015660 gene was identified as a strong candidate gene for powdery mildew resistance in cucumber, with natural variation observed in its allele. Two powdery mildew resistance loci were validated using molecular marker-based QTL analysis, providing new genetic insights for cucumber PM resistance breeding programs.