** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** THE ECONOMIC IMPORTANCE OF U.S. CATTLE PRODUCTION NECESSITATES DISCOVERY OF FUNCTIONAL ELEMENTS IN THE BOVINE GENOME THAT REGULATE PRODUCTION, REPRODUCTION AND WELLBEING. TO DATE, ASSEMBLIES OF PAN-GENOMES, PAN-EPIGENOMES AND PAN-CHROMATIN ARCHITECTURES OF BOVINE/RUMINANT SPECIES HAVE BEEN INITIATED TO UNDERSTAND GENOME STRUCTURES, VARIATION AND ACCESSIBILITY. THEREFORE, THE GOAL OF OUR BOVINE PAN-TRANSCRIPTOME INITIATIVE IS TO BUILD THE GENOME-PHENOME BRIDGES AND THUS TAKE GENOME ANNOTATION, SELECTION AND DESIGN TO THE NEXT LEVEL IN THE SPECIES. BRIEFLY, BOVINE PAN-TRANSCRIPTOMES WILL BE CONSTRUCTED USING BOTH LONG- AND SHORT-READ SEQUENCING STRATEGIES TO COLLECT FULL-LENGTH SINGLE TRANSCRIPTS AND THEIR EXPRESSION COUNTS. IN OBJECTIVE 1, WE WILL DEVELOP EVOLUTIONARILY DIVERSE PAN-TRANSCRIPTOMES INVOLVING FOUR RUMINANT SPECIES TO DISCOVER THE TRANSCRIPTOME SWEEPS THAT DRIVE PHENOTYPIC DIVERGENCE IN EACH SPECIES AND IDENTIFY THE EVOLUTIONARY GENOME-PHENOME PATTERNS AMONG DIFFERENT SPECIES. IN OBJECTIVE 2, WE WILL ESTABLISH ECONOMICALLY IMPORTANT PAN-TRANSCRIPTOMES IN CATTLE BY TARGETING PARASITE INFECTION AND DARK CUTTING BEEF IN BOTH USA AND AUSTRALIA TO EXPLORE PHENOTYPE AS A FUNCTION OF GENOTYPES, RNA VARIANTS, ENVIRONMENTS AND THEIR INTERACTIONS. OVERALL, THE PROPOSED RESEARCH WILL ALLOW US TO DEVELOP A BOVINE PAN-TRANSCRIPTOME RESOURCE IN GENERAL AND UNDERSTAND THE ORIGINS OF SPECIES DIVERGENCE, SEXUAL DIMORPHISMS AND DISEASE/STRESS RESISTANCE IN PARTICULAR. WE BELIEVE THAT USE OF RNA VARIANTS TO BRIDGE THE GENOME AND PHENOME AND THEN IMPROVE EFFICIENCY OF GENOME-WIDE ASSOCIATION STUDIES OPENS NEW RESEARCH FRONTS, LEADING TO THE DEVELOPMENT OF NOVEL STRATEGIES TO UNDERSTAND GENOME-PHENOME RELATIONSHIPS FOR BROAD BENEFITS TO SOCIETY.