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Capsinoids are the class of secondary metabolites identified in non-pungent peppers exhibiting the same bioactive properties as capsaicinoid. Previously, it has been demonstrated that capsinoid production is controlled by the capsaicin synthase (CS) gene and the putative-aminotransferase (pAMT) gene. In this study, we report that C. chinense ‘SNU11-001’ containing high levels of capsinoid has an early stop codon in pAMT resulted from 403 bp and 8 bp insertions deletion in the third and sixth exons. In order to know whether CS expression is correlated with the level of capsinoid, CS and pAMT expressions were determined using SNU11-001 and four Capsicum accessions with different pungency level. RT-PCR analysis showed higher transcription levels of CS in pungent accessions but no clear differences in pAMT expression. To investigate the effect of the substitution of the pAMT allele of C. chinense ‘Habanero’ with the dysfunctional pAMT allele of SNU11-001, an F2 population was constructed by a cross between aforementioned parental lines. Molecular markers were developed to distinguish CS and pAMT genotypes of SNU11-001 and Habanero and F2 plants were genotyped. All F2 plants having the pAMT genotype of SNU11-001 contained high levels of capsinoid while very low levels of capsaicinoid. There was no significant difference in levels of capsinoid among the F2 plants regardless of CS genotypes. This may be due to strong CS expression of both parental lines. In conclusion, our results show that it is possible to develop a new Habanero cultivar with high capsinoid content by introducing a dysfunctional pAMT allele.

Substitution of a Dysfunctional pAMT Allele Results in Low-Pungency but High Levels of Capsinoid in Capsicum chinense ‘Habanero’