Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness

Cardiorespiratory fitness (CRF) is a heritable trait associated with improved metabolic health and reduced mortality. To identify regulatory mechanisms associated with CRF variation, we generated and integrated 546 transcriptomic and epigenomic (chromatin accessibility and histone marks) profiles from 128 genetically heterogeneous rats selectively bred for high and low running capacity, a model that mirrors CRF-associated traits in humans. We found that selection for high CRF led to genetic convergence in skeletal muscle regulatory regions linked to genes involved in lipid metabolism and angiogenesis. We validated thousands of these genetic effects through generation and integration of 426 genotype, gene expression, and chromatin accessibility profiles in an independent HCRxLCR F2 population (n=147). Together, these 972 omics profiles show that genetic variation reshapes the chromatin landscape to support energy metabolism and oxygen delivery in skeletal muscle and overall CRF, offering a molecular framework to identify targets that reduce cardiometabolic disease risk.