QTL-Seq: Rapid, Cost-Effective, and Reliable Method for QTL Identification

Abstract

QTL-seq is a powerful method that integrates whole-genome sequencing (WGS) with bulk-segregant analysis to rapidly and reliably identify quantitative trait loci (QTLs) associated with specific traits. This approach significantly advances traditional QTL mapping by eliminating the need for genome wide DNA markers such as SSR, RFLP, and INDELs, which are typically used in linkage-based QTL mapping. Instead, QTL-seq leverages WGS to detect all genetic variations such as SNPs, Indels, and Structural Variants across the entire genome, providing a comprehensive resource for marker development in marker-assisted selection. The QTL-seq process begins with the creation of genetically diverse mapping populations, such as F2 or RILs, followed by detailed phenotypic characterization. DNA from plants exhibiting similar phenotypes is pooled into bulk groups and sequenced, allowing for cost-effective and efficient QTL identification. Identified QTLs can be further validated through fine mapping using recombinant screenings and progeny testing, leading to the identification of candidate genes associated with traits of interest. In this study, we outline a user-friendly QTL-seq pipeline, from sequencing to data visualization, using the methodology and data provided by Takagi et al., 2013, to demonstrate its practical application. While the manuscript primarily focuses on describing the pipeline, we also conducted a case study analysis with real data to showcase its effectiveness. Our work contributes to the broader understanding of QTL-seq applications and offers practical recommendations for optimizing this method in future breeding programs.