Next-generation sequencing for genetic and genomic characterization of horticultural crops

Abstract

Horticultural crops such as fruits, vegetables and ornamentals are disproportionately difficult to improve through conventional breeding because of long juvenility, high heterozygosity, polyploidy, clonal propagation and structurally complex genomes. Next-Generation Sequencing (NGS) has addressed several of these constraints by enabling rapid, cost-effective genome and transcriptome characterisation and its scope now extends well beyond first-generation whole-genome sequencing to telomere-to-telomere (T2T) and haplotype-resolved assemblies, graph-based pan-genomes, long-read and single-cell/spatial transcriptomics, whole-genome bisulfite and chromatin-accessibility profiling and genotyping platforms that underpin marker-assisted selection, genomic selection and genome-wide association studies. Integration of NGS with precision genome-editing tools, including base editing, prime editing and Cas12-based multiplexing, has further shortened the path from gene discovery to trait deployment. This review synthesises these developments specifically as they apply to horticultural crops, evaluates the comparative strengths, costs and limitations of current sequencing platforms and genotyping strategies, and identifies persistent bottlenecks arising from genome complexity, structural variation and the computational demands of multi-omics data integration. We also examine emerging opportunities in artificial-intelligence-assisted genomic prediction, digital and predictive breeding and microbiome-informed crop management and outline a conceptual framework linking sequencing technologies to functional validation and breeding application. Rather than a general survey, this review positions itself against recent NGS-in-plants literature by focusing on the technology-to-breeding translation gap that is most acute in horticultural species, and by highlighting where evidence remains preliminary.