QTL Sequencing in Plant Breeding: A Comprehensive Review

Quantitative trait loci sequencing (QTL-seq) is a novel technology that combines traditional QTL mapping with next-generation sequencing, making the identification of genomic loci associated with complex traits more efficient and accurate. This methodology employs bulk segregant analysis along with whole-genome sequencing to detect candidate genomic regions and underlying genes with reduced effort, lower cost, and higher precision compared to conventional approaches. QTL-seq not only enhances resolution and accuracy in detecting polygenic loci but also enables the identification of low-frequency alleles and fine genetic variations, thereby offering a clearer understanding of trait architecture. Its advantages over traditional QTL mapping include faster detection, higher efficiency, and broader applicability across different crops, including those with complex polyploid genomes. Despite its potential, QTL-seq faces challenges such as dependency on high-quality reference genomes and limited detection power for rare variants. Nevertheless, its adaptability has already been demonstrated in marker-assisted selection and genomic prediction, thus accelerating crop improvement. This review comprehensively discusses the principles, scope, advantages, limitations, and future directions of QTL-seq, highlighting its role in advancing both genetic studies and applied plant breeding.