ADVANCING KNOWLEDGE OF EQUINE HEALTH, DEVELOPMENT AND REPRODUCTION THROUGH GENOMIC PREDICTION AND CLINICAL DIAGNOSES IS HIGHLY DEPENDENT UPON AN ACCURATE REFERENCE GENOME. OUR GOAL IS TO IMPROVE THE QUALITY AND COMPLETENESS OF THE REFERENCE SEQUENCE OF EQUINE SEX CHROMOSOMES (~8% OF THE GENOME), WITH A FOCUS ON THEIR UNIQUE STRUCTURAL AND FUNCTIONAL FEATURES THAT CANNOT BE RESOLVED BY CURRENT WHOLE GENOME SEQUENCING APPROACHES. THESE SPECIFICALLY INCLUDE STRUCTURALLY COMPLEX REPETITIVE GENE ARRAYS ON BOTH SEX CHROMOSOMES. OUR RATIONALE FOR UNDERTAKING THIS RESEARCH IS THAT THESE COMPLEX GENOMIC REGIONS COMPRISE SUBSTANTIAL REAL ESTATE ON THE SEX CHROMOSOMES, AND HARBOR BIOLOGICALLY IMPORTANT GENES AND REGULATORY ELEMENTS THAT INFLUENCE TRAITS OF ECONOMIC INTEREST, INCLUDING REPRODUCTION, NEUROBIOLOGY, GROWTH, AND IMMUNITY. A HIGH-QUALITY GENOME ASSEMBLY IS ALSO A PREREQUISITE FOR MORE COMPLETE AND ACCURATE FUNCTIONAL ANNOTATION OF THE EQUINE GENOME (FAANG INITIATIVE). WE WILL PRODUCEHIGHLY ACCURATE SEX CHROMOSOME SEQUENCES BY UTILIZING A SUITE OF COST-EFFECTIVE AND COMPLEMENTARY APPROACHES, INCLUDING CDNA SELECTION AND LONG-READ SEQUENCING OF CLONE TILING PATHS. THE PROPOSED ACTIVITIES BUILD AND EXPAND UPON OUR PRODUCTIVE PRIOR AND RECENTLY COMPLETED RESEARCH ON MAMMALIAN SEX CHROMOSOMES. THE PROJECT DIRECTLY ADDRESSES ANIMAL HEALTH AND PRODUCTION AND ANIMAL PRODUCTS PRIORITY AREA #1201 TOOLS AND RESOURCES BY GENERATING TOOLS AND EXPERIMENTAL PROTOCOLS WHICH CAN BE APPLIED TO ADVANCE BASIC BIOLOGY AND IMPROVE ANIMAL HEALTH AND PRODUCTION.