Integration of Pangenomics into Modern Plant Breeding

In plant science, the advent of pangenomics has fundamentally transformed our understanding of genetic diversity and adaptation. Traditional breeding has often relied on a limited pool of elite germplasms, leading to systems that, while productive, are highly uniform and susceptible to environmental and biological threats. Current research emphasizes the necessity of moving beyond a single reference genome model to fully capture the breadth of allelic variation underlying important agronomic traits. Recent studies in both major and orphan crops highlight the value of the core, accessory, and unique genomic components revealed through pangenome analyses. Yet, the adoption of pangenomics remains uneven, with significant gaps in methodology, scalability, and integration with other omics approaches limiting its widespread use and the realization of its full potential.As researchers expand the pangenomic approach, vital questions remain regarding how best to assemble, interpret, and apply the data generated. Modern advances are increasingly integrating genomics with big-data pipelines, genome-wide association studies, and innovative genotyping methods— trends that promise holistic and actionable insights into genetic structure, plant function, and environmental adaptation. Despite these developments, the technical challenges of reliably predicting gene presence or absence, understanding structural variations, and achieving computational efficiency persist. Furthermore, the integration of pangenomics with other omics disciplines, such as transcriptomics and metabolomics, offers exciting prospects for deciphering complex biological interactions directly relevant to crop resilience and productivity.This Research Topic aims to anticipate and define the future landscape of plant pangenomics by showcasing cutting-edge methodologies, theoretical advances, and cross-disciplinary integrations. By cultivating a platform for the latest research on cost-effective genotyping, data analysis pipelines, and the synergistic integration of omics sciences, this collection seeks to inform, inspire, and connect experts and non-experts alike. It intends to highlight innovative uses of pangenomics for both major and orphan crops, explore methods for constructing robust pangenomes, and examine strategies for maintaining genetic diversity and promoting resilience in agricultural ecosystems.This Research Topic will consider studies that span fundamental advances and applied research integrating pangenomics into plant science, with a focus on the practical boundaries and innovative intersections with breeding, bioinformatics, and agriculture. The scope includes, but is not limited to, the following themes:• Mechanisms that shape pangenomes• Integrative studies uniting pangenomics with GWAS, QTL mapping, and genomic selection for breeding applications• Development and benchmarking of pangenome construction methods• Integration of pangenomics with other omics disciplines, including metagenomics• The interplay between pangenomics and the rhizosphere• Strategies and impacts of pangenomics in the adoption of orphan crops• Applications and future prospects of pangenomics in forestryWe welcome submissions of the following article types: Brief Research Report, Correction, Editorial, FAIR² DATA Direct Submission, FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Policy and Practice Reviews, Review, Systematic Review, Technology and Code. Topic editors: Leonardo Alfredo Ornella, OSVAL A. MONTESINOS-LOPEZ, Monica Balzarini Source: https://www.frontiersin.org/research-topics/78036/integration-of-pangenomics-into-modern-plant-breeding