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Abstract
Peanut (Arachis hypogaea L.) is a globally significant crop valued for its oil and protein content, making cultivars with high seed quality and disease resistance desirable. Genetic mapping of these traits relies on both a suitable population and accurate genotyping, however, these efforts have been hindered by the narrow genetic diversity of cultivated peanut. The objective of this dissertation is to evaluate the utility and power of an eight-way peanut multiparent advanced generation intercross (PeanutMAGIC) population in genomic studies and to compare single-reference and population-specific pangenome genotyping for PeanutMAGIC. A random subset of 310 recombinant inbred lines (RILs), termed the MAGIC Core, was selected out of the whole population of 3,187 (RILs) for phenotyping and genotyping. The MAGIC Core was phenotyped for pod and seed traits for initial population characterization and disease resistance for additional application of the population, including oleic acid, Tomato Spotted Wilt Virus (TSWV), leaf spots, and root-knot nematodes. The genomes of the eight founders of PeanutMAGIC were sequenced to construct a population-specific graph-based pangenome. This pangenome enabled a comprehensive library of over 2.7 million variants present in the population to empower genomic studies and high-resolution trait mapping. The MAGIC Core was subject to low-coverage whole-genome sequencing for single-reference and population-specific pangenome reference genotyping. The characterization study of the MAGIC Core, using pod and seed traits with single-reference genotyping calling, demonstrated that PeanutMAGIC was a well-balanced population with increased recombination that is suitable for genetic and genomic studies and breeding. Three long-standing-sought-after traits have been mapped using pangenome-based markers in genome wide association studies (GWAS), that were not found in single-reference genotyping: (1) revealed a novel third fatty acid desaturase gene (AhFAD2C) required for high oleic acid peanut and resolved the long-standing mystery of mid-oleic acid phenotypes; (2) identified a copy number variant (CNV) exclusive to the TSWV resistant founder ‘NC94022’ that contains tandem duplications of a novel glutamate receptor; (3) narrowed the root-knot nematode resistance locus to a 400kb region. These findings underscore the power of population-specific pangenomics in enhancing marker resolution, uncovering structural variants, and empowering genomic studies and trait associations.