Genomics in Perennial Crops: From Genetic Resources to Domestication and Breeding

Perennial crops play a fundamental role in food production, ecosystem services, and the development of more sustainable agricultural systems. However, compared with major annual crops, many perennial species remain underexplored and face substantial challenges in genetic characterization, domestication, and breeding. Long generation cycles, high heterozygosity, complex reproductive systems, and strong genotype-by-environment interactions can limit the efficiency of conventional breeding approaches. At the same time, advances in high-throughput sequencing and genomic technologies are expanding our ability to characterize genetic diversity and understand the genomic basis of complex traits. These developments create new opportunities to accelerate the conservation, domestication, and genetic improvement of both established and underutilized perennial crops.Despite recent advances, genomic resources and breeding strategies remain unevenly distributed among perennial species. While some economically important crops benefit from extensive genomic and breeding resources, many underutilized, orphan, and emerging perennial species remain at early stages of genetic characterization and domestication. Bridging the gap between the characterization of genetic resources and their effective use in breeding remains a major challenge. This Research Topic aims to bring together advances in genomics that can support the transition from genetic resource characterization to the domestication and improvement of perennial crops. By integrating approaches such as population and landscape genomics, genome-wide association studies, genomic prediction, pangenomics, and other emerging genomic tools, we aim to highlight strategies for identifying useful genetic variation, understanding adaptation, accelerating pre-breeding, and improving complex traits. We particularly encourage studies that demonstrate how genomic information can be translated into practical applications for crop domestication, breeding, conservation, and adaptation to changing environments.We welcome original research articles, reviews, methods, perspectives, and other article types relevant to the application of genomics in perennial crops. Contributions may focus on established, underutilized, orphan, or emerging perennial species. Topics include, but are not limited to: • Genetic diversity, germplasm characterization, and conservation genomics; • Population and landscape genomics; • Reference genomes, pangenomes, and structural variation; • GWAS and the genetic architecture of complex traits; • Multi-trait and integrative genomic approaches; • Genomic prediction and selection; • Pre-breeding and the use of wild relatives; • Genomics-assisted and de novo domestication; • Genotype-by-environment interactions, adaptation, and climate resilience; • Integration of genomics with phenomics and other omics approaches; • Genomic tools and strategies for perennial crop breeding and improvement. This Research Topic seeks to provide a platform for integrating genomic advances across diverse perennial species and promoting their application from genetic resource characterization to domestication and crop improvement. Topic editors: Evellyn G.O. Couto, Eveline Teixeira Caixeta Source: https://www.frontiersin.org/research-topics/86475/genomics-in-perennial-crops-from-genetic-resources-to-domestication-and-breeding