The 6 bp exon deletion in StMYBA1 affects the expression of genes related to anthocyanin biosynthesis in potato

Abstract Differential coloration of potato tuber skin is an important agronomic trait. However, its genetic regulatory mechanism remains unclear. In this study, an F₁ segregation population was constructed, and segregation in tuber skin coloration was observed. Using bulked segregant analysis by sequencing (BSA-seq) combined with fine mapping, a major quantitative trait locus (QTL) was mapped to a 52.24–53.08 Mb interval on Chr10. Within this region, StMYBA1, an R2R3-MYB transcription factor, emerged as the key candidate gene. Notably, a 6-bp (CTCCTC) deletion in the exon of StMYBA1 caused the loss of two proline residues, which was strongly associated with the absence of differential skin coloration. Further investigations demonstrated that overexpression of StMYBA1 markedly enhanced anthocyanin accumulation in both leaves and tubers. In transgenic lines, delphinidin content in leaves increased by 216.6%–297.4%, and after five days of light exposure, tuber eyes and heels exhibited a pronounced purple pigmentation. Consistently, key anthocyanin biosynthetic genes, including StANS and StF3′H, were significantly upregulated. Dual-luciferase assays further confirmed that StMYBA1 promotes anthocyanin biosynthesis by activating the MYB transcription factor StAN2 and its downstream targets. Importantly, the 6-bp deletion partially attenuated StMYBA1 regulatory activity, as reflected by reduced activation of several anthocyanin-related promoters and moderately lower anthocyanin accumulation in transient assays, while DNA-binding activity was retained. Collectively, these findings provide new insights into the regulatory role of StMYBA1 in potato anthocyanin biosynthesis and identify a potentially useful genetic target for potato quality improvement.