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.…

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.