Advances in Pangenome Construction and Analysis for Horticultural Crop Genomics

Abstract

Pangenomics is transforming crop science by overcoming the limitations of single-reference genomes and capturing the full spectrum of genetic diversity across elite cultivars, landraces, wild relatives, and related taxa. This review outlines the evolution from linear references to graph-based pangenomes that resolve structural variation, presence-absence variation, and lineage-specific genes. We evaluate major pangenome construction strategies and enabling sequencing technologies, including high-fidelity long reads and chromosome-scale assemblies. We further discuss how integrating pangenomics with association mapping, genomic selection, and CRISPR-based editing accelerates allele discovery, precision introgression, and breeding for adaptation, resilience, and domestication-related traits. Case studies in horticultural crops show how pangenome approaches uncover the genetic basis of fruit quality, flavor, shelf life, stress tolerance, and domestication-related traits often overlooked by single-reference genomes. By capturing extensive structural and allelic diversity across diverse germplasm, pangenomics provides a powerful framework for precision breeding and sustainable improvement of horticultural species.