Natural variations in the promoter alter SGT3 gene expression and affect steroidal glycoalkaloid content in potatoes

• Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers, providing a novel molecular marker for low-steroidal glycoalkaloids (SGAs) breeding. • The SGT3 promoter haplotype with (TA) 10 exhibits significantly higher transcriptional activity, correlating with high SGAs content, while the (TA) 13 haplotype is linked to low SGAs in natural germplasms.