Discovery of a novel CnAMADH2 allele associated with higher levels of 2-acetyl-1-pyrroline (2AP) in yellow dwarf coconut (Cocos nucifera L.)

Abstract

Aromatic coconut is a special type of dwarf coconut containing a pleasant pandan-like aroma in its meat and water. 2-Acetyl-1-pyrroline (2AP) is a major constituent of the aroma in coconut and in other plants. A single nucleotide change in the coding sequence of CnAMADH2 has been associated with 2AP biosynthesis in aromatic ‘green’ dwarf coconut. However, this variant is not present in an aromatic ‘yellow’ dwarf coconut, suggesting that an alternative allele of amino aldehyde dehydrogenase 2 (CnAMADH2) is associated with the aroma in this variety. Here, we characterized CnAMADH2 in the aromatic yellow coconut to identify a novel aromatic allele. Compared with the aromatic green dwarf coconut and non-aromatic coconut, a single nucleotide change (G-to-A) was identified in exon 9 of CnAMADH2 in this yellow coconut causing an amino acid change (H299R). The H299R amino acid substitution resides at a highly conserved region of the ALDH cysteine (C) active site. According to the 3-D structural modeling results, this mutation could cause a reduction of aminoaldehyde dehydrogenase (AMADH) activity, thus increasing 2AP. This novel allele is likely associated with a higher level of 2AP. Functional markers specific to each of the two alleles of CnAMADH2 associated with the aroma trait in coconut were developed and successfully used to discriminate aromatic from non-aromatic coconut varieties. These markers would be useful for an aromatic coconut breeding program and for quality control of aromatic coconut production and cultivation.