Pangenomics and Functional Genomics in Grasses: From Structural Variation to Climate-Resilient Breeding

Grasses (Poaceae) are among the most important plant groups for global food security, livestock production, bioenergy, and ecosystem sustainability. Advances in long-read sequencing, chromosome-scale assembly, and graph-based genomics have revealed that single reference genomes capture only a fraction of species-wide diversity. Structural variations, including insertions, deletions, duplications, inversions, and presence–absence variants, can influence gene content, regulation, adaptation, and agronomic performance. However, pangenomic studies across grasses remain unevenly distributed, with major staple crops receiving greater attention than wild relatives and orphan crops. Moreover, the functional interpretation of pangenomic variation remains limited, particularly for traits associated with drought, heat, salinity, nutrient limitation, yield stability, and resource-use efficiency. Integrating pangenome resources with functional genomics and breeding is therefore essential to translate genome diversity into climate-resilient agricultural innovation.This Research Topic aims to advance the understanding of pangenomic diversity and its functional consequences across the grass family. It will bring together genome biologists, geneticists, breeders, computational scientists, and other researchers to examine how pangenome assemblies and comparative analyses reveal species-wide variation; how structural variants and gene-content differences contribute to agronomically important traits; and how functional genomics can clarify the regulatory mechanisms underlying stress tolerance, yield, development, and adaptation. The Research Topic will also explore how pangenomic information can support genomic selection, marker-assisted breeding, gene editing, and the improvement of underutilized crops and wild genetic resources. By connecting methodological innovation with experimental validation and translational applications, it seeks to accelerate fundamental discovery and enable more effective breeding strategies for sustainable agriculture under changing climatic conditions.To gather further insights into pangenomics, functional genomics, and breeding applications across major grasses, wild relatives, and orphan crops, we welcome articles addressing, but not limited to, the following themes:• Pangenome assembly and comparative genomics across grass species• Structural variation discovery, genotyping, and functional characterization• Functional genomics and gene regulatory networks associated with stress tolerance, yield, and developmental plasticity• Pangenome-informed genomic selection and marker-assisted breeding• Applications of pangenomic diversity in gene editing and trait improvement• Genetic resources from wild relatives and orphan or underutilized grass crops• Climate resilience to drought, heat, salinity, nutrient limitation, and other environmental stresses• Integration of pangenomic data with transcriptomics, epigenomics, phenomics, and environmental data• Novel computational approaches for graph genomes, reference-free analysis, annotation, and variant interpretation• Experimental strategies for validating candidate genes, regulatory elements, and structural variants-------We welcome contributions from researchers across the field, and we are glad to support you as you prepare your submission. If you would like early feedback on whether your planned manuscript fits the scope of this Research Topic, please write to us at plantscience@frontiersin.org before submitting. A quick check at this stage helps confirm your work is a strong fit and can save you time later in the process.To take part, click “Participate in this topic” at the top right of this page, then confirm through the “Participate” link in the follow-up email. This lets us know to expect your contribution, keeps you informed of key deadlines, and gives you access to resources that guide you through submission. We would also be glad to talk with you about possible routes for support with the Article Processing Charge (APC).We look forward to your participation and to building a vibrant, cohesive Research Topic together. Topic editors: Weixiong Long, Salih KAFKAS, Qiang He, Minqiang Tang Source: https://www.frontiersin.org/research-topics/84645/pangenomics-and-functional-genomics-in-grasses-from-structural-variation-to-climate-resilient-breeding