Mapping and Functional Characterization of Homologous Genes AhSUCA06 and AhSUCA16 Underlying Sucrose, Oil and Protein Contents in Peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) is an important oilseed and cash crop, and seed sucrose content (SSC), seed oil content (SOC) and seed protein content (SPC) are key determinants of seed flavour, texture, and overall quality. Identifying quantitative trait loci (QTLs) and candidate genes associated with SSC, SOC and SPC is therefore of considerable importance for peanut genetics and breeding. In this study, two recombinant inbred line (RIL) populations derived from reciprocal crosses between the lines Jihuatian1 (JHT1) and PI478819 (PI) were used to detect major QTLs for SSC, SOC and SPC through bulked segregant analysis combined with whole-genome sequencing (BSA-seq). Multiple lines of evidence supported the homologous gene pair AhSUCA06 and AhSUCA16 as candidate genes underlying the epistatic QTLs qA06.1 and qA16.1, which exhibited major and stable effects across multiple phenotypic evaluations. Furthermore, the function of AhSUCA06 was validated through CRISPR/Cas9-mediated genetic transformation. Subcellular localization assays using GFP fusion proteins, together with dual-luciferase reporter assays, demonstrated that AhSUCA06 and AhSUCA16—both containing a DUF7950 domain of previously unknown function—localize to the nucleus and act as transcriptional repressors. In addition, DAP-seq analysis suggested that these genes may regulate pathways related to glycolysis and gluconeogenesis. Overall, this study provides new insights into the molecular mechanisms underlying the regulation of SSC, SOC and SPC in peanut and offers valuable information to support the genetic improvement of seed quality traits in peanut breeding programs.