A major qualitative trait locus increases antioxidant activity in testaless peanut seeds

Arachis hypogaea High Antioxidant Activity gene 1 (AhHAA1), likely encoding an anthocyanidin reductase, enhances nutritional quality of testaless peanut seeds. Improving the antioxidant activity of peanut (Arachis hypogaea) seeds is critical for extending their shelf life and enhancing their nutritional quality. Mining of genetic resources to identify loci associated with antioxidant activity could facilitate the breeding of new cultivars with high antioxidant activity in seeds. Here, we developed a population of advanced recombinant inbred lines containing 175 F_5:6 families derived from the parents 'JiHua 11' (JH11) and 'JiHuaTian 1' (JHT1). We constructed a high-resolution genetic map covering 2870.3 cM, with an average length of 143.5 cM per linkage group, using 1108 polymorphic single-nucleotide polymorphisms to identify quantitative trait loci (QTLs) associated with antioxidant activity and the contents of antioxidant components. The major QTL qIAA_A03_2 made the greatest contribution to standing genetic variation (53.75%). We mapped qIAA_A03_2 to a physical interval of approximately 80 kb on chromosome A03. Analysis of whole-genome variation between parents uncovered a strong candidate gene encoding an anthocyanin reductase, designated Arachis hypogaea High Antioxidant Activity 1 (AhHAA1). Analysis of the genotypes and phenotypes of near-inbred lines with high and low antioxidant levels as well as 50 peanut accessions suggested that AhHAA1 increases the antioxidant activity of processed testaless seeds, primarily by affecting the contents of antioxidant component_3 (AC3) and AC4. Our results provide insights into the genetic regulation of antioxidant activity in peanut seeds that can survive testa removal during processing. In addition, the polymorphic markers linked to AhHAA1 could facilitate the selection of germplasm and the breeding of peanuts with high nutritional quality via marker-assisted selection.