Horticultural crops, including fruits, vegetables, ornamental plants, and tea plants, are vital for economic and nutritional sustainability, yet their cultivation is severely hampered by abiotic stresses such as heat, cold, and salinity. The advent of the grapevine genome in 2007 initiated the genomic era for horticultural species. This milestone facilitated the use of genome-wide association studies (GWAS) to decode the complex phenotypic diversity of these crops. Unlike traditional methods, GWAS utilizes natural genetic diversity to identify quantitative trait loci linked to key traits, offering a high-resolution approach for dissecting traits such as stress resistance, quality, and yield. This review highlights the innovative workflows and technical advancements in GWAS applications for horticultural crops, covering aspects including population design, high-throughput phenotyping, sophisticated statistical modeling, and their applications in horticultural plants. Notably, the integration of multi-omics approaches has enhanced our understanding of the genetic mechanisms underlying critical horticultural traits. Future directions aim at harnessing technological innovations, cross-omics synthesis, and precision breeding strategies to optimize trait selection and expedite the development of resilient cultivars. Consequently, GWAS serves as a crucial bridge linking genomic variation to practical applications in horticultural improvement, enabling a paradigm shift toward predictive breeding and sustainable agricultural practices.

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