**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 GOAL OF THE PROJECT IS TO DEVELOP A STATE-OF-THE-ART BREEDING SYSTEM THAT WILL ACCELERATE THEGENETIC GAIN OF ONE OF THE MOST ECONOMICALLY IMPORTANT AND GENETICALLY VULNERABLE MAJOR US CROPS,UPLAND COTTON. WE WILL LEVERAGE EXISTING GENOMIC RESOURCES, WITH NEW ONES CREATED HERE, TO DEVELOPPRACTICAL TOOLS THAT ADDRESS THE NEEDS OF PRODUCERS, PROCESSORS, AND CONSUMERS. THIS WORK ADDRESSES THE COMMODITY BOARD CO-FUNDING TOPIC 'INITIATE INCREMENTAL DEVELOPMENT OF A PANGENOME AND HAPLOTYPE DATABASE FOR GOSSYPIUM HIRSUTUM UPLAND COTTON BREEDING.' THIS EFFORT, LED BY USDA-ARS, INCLUDES A PARTNERSHIP BETWEEN A PROMINENT PUBLIC COTTON BREEDER, A LEADING GENOME ANALYST, AND A DISTINGUISHED REPRESENTATIVE OF U.S. COTTON PRODUCERS WITH THE GOAL OF ENABLING HAPLOTYPE-ASSISTED BREEDING FOR UPLAND COTTON. WE WILL DO THIS BY:1. BUILDING A DYNAMIC AND EXPANDABLE HAPLOTYPE DATABASE FOR IMPROVED UPLAND COTTON.2. DEVELOPING AND OPTIMIZING SNP-BASED GENOMIC PREDICTION MODELS FOR COTTON PRODUCTIVITY TRAITS OF VARYING HERITABILITY.3. INTEGRATING HAPLOTYPE INFORMATION FOR ENHANCED GENOMIC SELECTION IN A CONTEMPORARY PUBLICCOTTON BREEDING PROGRAM.THE STRUCTURE OF COTTON BREEDING PROGRAMS IS RIPE FOR A REORGANIZATION OF RESOURCES THAT CAPITALIZES ON ASSESSING GENETIC VARIATION THROUGH A PANGENOME LENS AND HARNESSING IT THROUGH PREDICTIVE BREEDING. THIS PROJECT WILL DELIVER A PUBLICLY AVAILABLE DATABASE OF HAPLOTYPES AND PREDICTION MODELS, ALONG WITH A BLUEPRINT ON HOW TO DEPLOY THEM, TO DRIVE COTTON'S GENETIC GAIN. THIS NEW INFORMATION WILL HAVE A PROFOUND EFFECT ON COTTON BREEDING PROGRAMS THAT WILL RESULT IN THE DEVELOPMENT OF IMPROVED CULTIVARS TO ENHANCE THE PROFITABILITY OF U.S. GROWERS.