Whole-genome resequencing in horticultural crops: transitioning from variant discovery to breeding application

The developments in whole-genome resequencing (WGR) have opened up unparalleled avenues for genetic, breeding, and evolutionary studies of horticultural crops. This review systematically analyzes 499 WGR studies, demonstrating a paradigm shift from single-variant analysis toward integrated multi-variant approaches. By screening high-quality integrated genomic variants—including SNPs, InDels, and SVs—researchers have conducted genome-wide association studies (GWAS), QTL mapping, and bulk segregant analysis (BSA-seq). These approaches have provided comprehensive insights into the genetic basis of major agronomic traits across five key categories: fruit appearance, leaf, flower, functional nutrition, and plant architecture. Moreover, WGR has facilitated significant breakthroughs in elucidating the domestication mechanisms of horticultural crops, particularly by revealing the distinct evolutionary pathways underlying stress resistance and economic traits. Looking forward, long-read sequencing and pan-genome construction, along with the establishment of shared phenotypic-variant databases, will further enhance the capture of comprehensive genetic variation. Emerging analytical approaches, including k-mer-based association studies, epigenome-wide association studies (EWAS), and haplotype-based GWAS, are expected to accelerate the discovery of genes and QTLs. These genomic resources provide essential foundations for marker-assisted selection (MAS), significantly improving breeding efficiency. The synergistic integration of WGR with genome editing and machine learning is catalyzing the transition from conventional breeding to precision molecular design breeding, ultimately enabling more accurate and effective genetic improvement strategies for horticultural crops.