Genetic Regulation of Major Immunogenic Protein Accumulation in Peanut Seeds

Peanut is a major oilseed crop in the U.S., which ranks third globally in production, with South Carolina ranking sixth nationally. In 2025, U.S. peanut production is projected to reach a record 7.4 billion pounds. Despite their economic and nutritional value, peanuts are unsuitable for 1–2% of the U.S. population due to allergy and anaphylaxis, making reduced-allergen peanuts a critical priority. This study aimed to identify peanut lines with reduced Ara h1, h2, h3, and h6 levels and to elucidate their genetic regulation using genome-wide association studies (GWAS). Ninety-two accessions from the U.S. peanut mini-core collection were screened using ELISA and SDS-PAGE, and data were analyzed with 5,532 SNP markers. Substantial phenotypic diversity was observed. Twenty-three extreme lines were further evaluated by RP-UPLC, and nine by LC-MS. GWAS identified 165 marker–trait associations (MTAs) across raw and log-transformed data, with 13 MTAs common to both datasets, including shared associations between Ara h1–h2 and Ara h2–h6. MTAs were grouped into protein quantitative loci (PQLs), revealing six trans -PQLs and cis -PQLs for five of eight Ara h genes. Seed-expressed candidate transcription factors and pleiotropic PQLs were identified. These findings support marker-assisted breeding and advance understanding of Ara h protein regulation.