Design Breeding Framework in Potato ( Solanum tuberosum L.) Based on Phased Pangenomes and Multi‐Omics—A Review

ABSTRACT Potato is one of the most important non‐cereal food crops worldwide, yet its genetic improvement has long been constrained by a highly heterozygous autotetraploid genome, tuber‐based clonal propagation, self‐incompatibility and the accumulation of deleterious mutations. Over the past decade, long‐read sequencing, Hi‐C‐assisted assembly, haplotype resolution, pangenome construction, phylogenomics and multi‐omics approaches have shifted potato research from single‐reference genomics towards phased pangenomes and genome‐informed design breeding. Long‐read sequencing has resolved haplotype structures in both diploid and tetraploid potatoes, while pangenome analyses have revealed extensive structural variation and deleterious mutation landscapes. These genomic resources are now being applied to hybrid potato breeding and trait‐targeted improvement. They have also connected genomic resources with disease resistance, tuber micronutrient accumulation and nutritional quality improvement. This review synthesizes these developments and argues that potato research is converging on a new framework: genetic resource exploration, phased pangenome construction, deleterious‐variant identification, candidate‐gene validation, haplotype design and molecular breeding application. Future work will need to combine wild resource utilization, structural‐variant analysis, multi‐omics integration, mineral‐nutrition improvement and functional validation to move potato from a traditional clonal crop towards a more analysable, predictable and designable crop system.