Identification and characterization of a novel leaky vanillin aminotransferase (vamt) allele, affecting capsaicinoid composition in chili pepper (Capsicum chinense).

Capsaicinoids and their low pungent analogs are the important compounds to determine quality of chili pepper fruit in food industrial and medical purposes. Our previous screening for chili pepper bio-resources has shown that the pungent accession 'Charapita' (CH) (Capsicum chinense) has a unique composition with a higher capsinoid content. This study aimed to identify the mutation responsible for the high capsinoid content in CH. QTL analysis was performed using F₂ population between Red Habanero (RH) and CH, and it detected a major QTL on chromosome 3. Further genetic analysis showed that the QTL was narrowed down to approximately 400 kb region, which includes VAMT (vanillin aminotransferase). Allelism test demonstrated that CH possesses a leaky vamt allele. The sequencing analysis revealed that CH-type vamt allele has a unique amino acid substitution (G373E) due to a SNP in exon 15. CH-type vamt decreased pungency by 50%, and increased capsinoid content about three times compared with RH-type. We designated the CH-type allele as vamt ^L3. There was no difference in the expression levels of VAMT or other capsaicinoid biosynthetic genes between RH and CH. The vanillylamine synthesis activity was evaluated with crude extract from placental tissue. It showed that the activity in CH was 30 times less compared with RH. Given that the enzyme activity significantly decreased without transcriptional change, G373E likely reduces VAMT activity, conferring the characteristic composition of capsaicinoids and capsinoids. The novel vamt allele (vamt ^L3) will contribute to manipulate pungency level and capsinoid content in chili pepper breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01595-9.