** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** CHILE PEPPERS (CAPSICUM SPP.) ARE KNOWN FOR THEIR CULINARY USES, AND MEDICINAL AND HEALTH BENEFITS. THEY ARE CONSIDERED AS THE SIGNATURE CROP OF NEW MEXICO, WITH THE STATE BEING THE TOP PRODUCER IN THE UNITED STATES IN 2019 AT ~63,000 TONS OF TOTAL PRODUCTION (USDA NASS 2019). INCREASING THE NUTRITIONAL QUALITY AND YIELD OF CHILE PEPPERS IN NEW MEXICO AND ACROSS THE UNITED STATES WILL BENEFIT GROWERS, PRODUCERS, AND CONSUMERS. THE GENETICS OF NUTRITIONAL CONTENT AND YIELD IN NEW MEXICAN CHILE PEPPERS IS CURRENTLY NOT WELL UNDERSTOOD. NOVEL GENOMICS APPROACHES SUCH AS GENOME-WIDE ASSOCIATION STUDIES (GWAS) AND GENOMIC SELECTION (GS) TOGETHER WITH HIGH-THROUGHPUT PHENOTYPING STRATEGIES CAN FACILITATE THE BREEDING AND DEVELOPMENT OF CHILE PEPPERS WITH IMPROVED NUTRITIONAL CONTENT AND YIELD THROUGH A BROADER UNDERSTANDING OF THE GENETIC MECHANISMS UNDERPINNING THESE TRAITS. THE OBJECTIVES OF THIS RESEARCH ARE: 1) IDENTIFY GENETIC LOCI LINKED WITH NUTRITIONAL QUALITY, FRUIT MORPHOLOGY, ANDYIELD-RELATED TRAITS IN NEW MEXICAN CHILE PEPPERS USING GWAS; 2) IMPLEMENT GS FOR CHILE PEPPER YIELD, NUTRITIONAL QUALITY, AND FRUIT MORPHOLOGY AND EVALUATE THE EFFECTS OF DIFFERENT PARAMETERS ON GS ACCURACY; AND 3) DEVELOP MOLECULAR MARKERS FOR ALLELES THAT IMPROVE FRUIT MORPHOLOGY, NUTRITIONAL QUALITY, AND YIELD IN CHILE PEPPERS. IMPLEMENTING GENOMICS-ASSISTED APPROACHES TO DISSECT THE GENETIC BASIS OF NATURAL VARIATION FOR FRUIT AND YIELD-RELATED TRAITS IN NEW MEXICAN CHILE PEPPERS WILL ACCELERATE THE DEVELOPMENT OF GENETICALLY IMPROVED CULTIVARS. THE FAVORABLE ALLELES IDENTIFIED FROM THIS PROJECT CAN BE INTRODUCED IN OTHER CHILE PEPPER BREEDING PROGRAMS IN THE UNITED STATES TO ACCELERATE AND FACILITATE THE GENETIC IMPROVEMENT OF EXISTING GERMPLASM.