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Mutation in putative aminotransferase (pAMT) gene resulted in low level of spiciness in the chilli (Capsicum spp.) fruit. The study aims to identify the profile of a partial sequence of pAMT gene variation and to evaluate the total capsaicinoid content of EMS-induced chilli pepper mutants. Plant genomic DNA of EMS-induced chilli pepper mutants and control plants were amplified by using pAMT primer, then partial sequence of pAMT gene was analysed using bioinformatics program. Total capsaicinoid content of 30 DPA harvested chilli fruits was measured by using spectrophotometric method. In some mutant plants, the profile of partial sequence of pAMT gene variation detected in exon 2 and 3 was substitution and insertion respectively. Adenine substitution into guanine was detected in the G11K1 mutant plant causing alteration of amino acid lysine into glutamine, and nucleotide insertion in plants G2K1, G7K1, G7K2, G11K3 caused a frameshift mutation. Total capsaicinoid content of three genotypes of EMS-induced chilli pepper mutants were influenced by genotype interaction with EMS concentration. The highest capsaicinoid content observed in G11K0 plant was 9,992 mg g-1 Fresh Weight (FW) and the lowest capsaicinoid content of 5.407 mg g-1 FW was recorded in G7K1 plant. The alteration of partial sequence of pAMT gene did not relate to the total capsaicinoid content of mutant plant indicated that mutation detected in exon 2 and 3 of mutant plant G2K1, G7K1, G7K2, G11K1 and G11K3 did not affect the total capsaicinoid content.
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