Genome-wide association study of sugar content and development of diagnostic KASP markers in peanut (Arachis hypogaea L.)

Background Sugar content is a critical factor influencing the quality of peanut kernels, determining the sweetness and taste of peanuts, which in turn affects consumer acceptance and market value. However, the genetic mechanisms underlying sugar content in peanut kernels remain poorly understood. Results In this study, GWAS analysis was conducted using 103 peanut germplasm resources with significant differences in total sugar content (TSC), soluble sugar content (SSC), and sucrose content (SC). The variation ranges for the three traits were 6.48%~26.10%, 5.22%~17.29%, and 2.01%~7.97%, respectively. Based on genome-wide association analysis, 98, 122, and 148 SNPs significantly associated with TSC, SSC, and SC were identified, respectively. Among them, 42 SNPs on chromosome A05 contributed 9.60%~20.29% phenotypic variance to SC. Further analysis detected 21 pleiotropic SNPs, including 2 SNPs significantly associated with both TSC and SC, and 18 SNPs significantly associated with both SSC and SC. Among the 21 multi-environment co-localized SNPs, 6 SNPs were consistently detected across three environments, with phenotypic explanation rates ranging from 10.03% to 20.29%. Based on the genome-wide association analysis results, within the decay region of two significant SNPs (AX-176820713 and AX-176816968), one SWEET gene ( Arahy . 78PE2K ) and two STP genes ( Arahy.KFDF05 and Arahy . IG4CN6 ) were identified as participating in sugar metabolism. qRT-PCR results showed that the expression levels of Arahy . 78PE2K and Arahy.KFDF05 were significantly upregulated in high-sugar varieties, while the expression level of Arahy . IG4CN6 was significantly downregulated. The KASP marker qK-SCB03.1 (AX-176816968), developed based on the genome-wide association analysis and qRT-PCR results, can distinguish germplasm sugar content types, providing an important theoretical basis and technical support for peanut sugar content improvement and molecular marker-assisted breeding. Conclusions This study provides comprehensive insights into the identification and application of SNPs, candidate genes, and KASP molecular markers associated with peanut sugar content. It offers valuable theoretical support and genetic resources for molecular breeding projects aimed at improving peanut seed sugar content and developing high-sugar peanut varieties.