QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

Abstract

QTL mapping using NGS-assisted BSA was successfully applied to an F population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis. Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F confirmed dm2.2 (R = 10.8-24 %) and dm5.2 (R = 14-27.2 %) as major QTLs and dm4.1 (R = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R = 28.2 %) was detected by the conventional QTL method using an F population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

Identification of novel loci and candidate genes for cucumber downy mildew resistance using GWAS

“…Four QTLs (dm2.1, dm4.1, dm5.1, and dm6.1) were detected by the cross between DM-resistant inbred line WI7120 and susceptible '9930', and dm4.1 and dm5.1 were major effect QTLs [13]. Five QTLs (dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1) were found using NGSassisted BSA, and dm2.2 and dm5.2 were major effect loci for DM resistance [14]. reported that dm5.1, dm5.2, and dm5.3 were major-effect QTLs contributing to DM resistance.…”

Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays

“…Combining the BSA strategy with a high-throughput NGS technology is a common practice for gene identification and QTL mapping. Many studies have outlined methodologies and applications of high-throughput sequencing in BSA for qualitative and quantitative traits (Abe et al, 2012; Takagi et al, 2013; Win et al, 2016). …”

QTLseqr: An R Package for Bulk Segregant Analysis with Next‐Generation Sequencing

“…In plant breeding research, the main pipeline used for BSA, termed QTL‐seq, was developed by Takagi et al (2013) and has been widely used in several crops for many traits (e.g., Das et al, 2014; Lu et al, 2014; Win et al, 2016; and many others). Takagi and colleagues define the ∆(SNP‐index) for each SNP as the difference of the low value bulk SNP‐index from the high value bulk SNP‐index.…”