Pan-genomics and Comparative Genomics in Crops: Genome Diversity, Evolutionary Innovation, and Breeding Potential

Crop genomes contain extensive genetic variation that cannot be fully captured by a single reference genome. Recent advances in long-read sequencing, chromosome-level assembly, haplotype-resolved genomics, and graph-based genome representation have accelerated the development of crop pan-genomes. These resources enable systematic identification of core and dispensable genes, structural variants, presence-absence variation, copy number variation, and lineage-specific genomic regions. At the same time, comparative genomics provides a powerful framework for investigating genome evolution, gene family dynamics, chromosomal rearrangements, domestication-related changes, and the emergence of agronomically important traits. Together, pan-genomics and comparative genomics are reshaping our understanding of crop genome diversity and creating new opportunities for genetic resource utilization and molecular breeding.This Research Topic aims to address how pan-genomics and comparative genomics can deepen our understanding of crop genome diversity, evolution, and breeding potential. Although high-quality reference genomes have become available for many crop species, single-reference analyses often overlook substantial genomic variation among cultivars, landraces, wild relatives, and related species. Pan-genomic approaches can reveal the full spectrum of gene content variation and structural diversity, while comparative genomics can clarify the evolutionary processes that generated these differences. This collection seeks to bring together studies that connect genome architecture, gene repertoire variation, chromosomal evolution, and lineage-specific innovation with agronomic traits and crop improvement. By highlighting both methodological advances and biological discoveries, this Research Topic will support a more complete and evolution-informed use of crop genomic resources.We welcome Original Research, Reviews, Mini Reviews, Methods, Perspectives, and Opinion articles focused on pan-genomics and comparative genomics in crop species and their wild relatives. Topics of interest include, but are not limited to:• Chromosome-level genome assembly and haplotype-resolved genome construction, including the use of long-read sequencing, Hi-C, and optical mapping in crop species and their wild relatives• Graph-based pan-genome construction and analysis, encompassing core and dispensable genome characterization, presence-absence variation (PAV), copy number variation (CNV), and structural variant identification across diverse accessions• Comparative genomics across crop species and related taxa, including gene family dynamics, chromosomal rearrangements, synteny analysis, and whole-genome duplication events underlying evolutionary innovation• Genomic basis of agronomic traits and crop improvement, including the identification of domestication-related loci, lineage-specific genes, and the translation of pan-genomic and comparative genomic findings into breeding applicationsStudies that develop new computational methods, compare multiple crop genomes, or demonstrate how pan-genomic and comparative genomic resources can support crop improvement are particularly encouraged. Topic editors: Wei Li, Qiang He, Zhang Dan Source: https://www.frontiersin.org/research-topics/83497/pan-genomics-and-comparative-genomics-in-crops-genome-diversity-evolutionary-innovation-and-breeding-potential