From High-Density Genomic Mapping to Precision Molecular Breeding: A Comprehensive Review of Capsicum Genomic...

The genus Capsicum comprises several species that are vital vegetable and spice crops cultivated worldwide, possessing significant economic, nutritional, and ornamental value due to their diverse fruit morphologies, colors, spiciness levels, and stress resistance. Historically, the large genome size (approximately 3 Gb) and high proportion of repetitive sequences (over 80% transposable elements) have constrained in-depth analysis of structural variations and functional genes within Capsicum species. However, recent advances in long-read sequencing, Hi-C scaffolding, and genome assembly have enabled the production of multiple high-quality and telomere-to-telomere (T2T) Capsicum genomes, which have ushered in a new era of research at the nuclear, organellar, and pan-genome levels. The publication of these omics resources has greatly expanded our understanding of the evolution of agronomically and environmentally relevant traits in peppers and their wild relatives. This review systematically summarizes recent progress in reference genomes, pan-genomes, and organellar genomes of the genus Capsicum, highlighting the enhancement of key breeding trait analyses through omics data, and outlines future integrated breeding strategies to provide theoretical and methodological references for genetic improvement and molecular breeding in pepper.