Washington State University

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.