** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** INEXPENSIVE AND ACCURATE HIGH THROUGHPUT SEQUENCING HAS MADE IT POSSIBLE TO BEGIN TO UNDERSTAND THEGENETIC BASIS OF HEALTH AND PERFORMANCE IN ANIMALS. IN AGRICULTURAL APPLICATIONS, THESE DATA HAVEEXPOSED THE LIMITATIONS OF A SINGLE REFERENCE GENOME FOR A SPECIES. IT IS NOW FEASIBLE TO CREATE MANYREFERENCE GENOMES OF INDIVIDUAL BREEDS, PROVIDING FOR THE IMPACT OF BREED-SPECIFIC GENETIC,EPIGENETIC, AND STRUCTURAL DIFFERENCES TO BE ELUCIDATED. A PAN-GENOME ALLOWS FOR THE INTEGRATION OFMULTIPLE REFERENCE GENOMES WITH THEIR ASSOCIATED ANNOTATION AND VARIANT DATA TO FACILITATE DISCOVERY.OUR LONG-TERM GOAL IS TO PROVIDE TOOLS AND READILY ACCESSIBLE DATA TO EXPEDITE EFFORTS TO CONNECTGENOME TO PHENOME. IN THIS PROPOSAL WE WILL BUILD UPON PRIOR COMMUNITY EFFORTS TO ADDRESS OUR GOALBY: 1) CREATING A PANGENOME FROM ACCURATE, HAPLOTYPE-RESOLVED GENOME ASSEMBLIES OF 13 TARGETBREEDS AND 3 RELATED EQUIDS, 2) ANNOTATE THE PANGENOME USING TISSUE-SPECIFIC TRANSCRIPTOMIC ANDEPIGENETIC DATA, AND 3) DEVELOPING AND MAKING AVAILABLE AN INTEGRATIVE GENOMICS PORTAL. AS ANOUTCOME OF THIS WORK, IN LINE WITH FAIR PRINCIPLES, WE WILL HAVE TOOLS NECESSARY FOR ANYONE TOQUICKLY AND EASILY ACCESS COMMUNITY-GENERATED GENOMICS DATA WITHOUT BIOINFORMATICS TRAINING. THEMETHODOLOGY DEVELOPED FOR ANALYSES AND DATA ACCESS CAN BE APPLIED ACROSS SPECIES. OUR TEAM ISWELL-POSITIONED TO DO THIS WORK, WHICH FITS INTO THE BLUEPRINT AREA OF DEVELOPING ADVANCED GENOMICTOOLS, TECHNOLOGIES, AND RESOURCES FOR AGRICULTURAL ANIMALS, GIVEN OUR PRIOR EXPERIENCE INHAPLOTYPE-RESOLVED GENOME ASSEMBLY AND BIOINFORMATIC METHODOLOGY, A SIGNIFICANT AMOUNT OF DATA ONHAND, AND THE SUPPORT OF A HIGHLY COLLABORATIVE COMMUNITY.

University Of Kentucky Research Foundation, The

Investigators