Comparative transcriptome profiling of vanilla (Vanilla planifolia) capsule development provides insights of vanillin...

Vanillin is the most abundant volatile compound in natural vanilla extract and the primary metabolite from an economic perspective. Natural vanilla is the second most expensive spice in the world and the most profitable crop adapted to the warm tropics. Despite its global popularity, vanilla is mainly cultivated from vegetatively propagated clones and insufficient modern plant breeding has been achieved. One of the breeding objectives is to increase the vanillin concentration in the cured vanilla capsules. The vanillin biosynthesis pathway has not been thoroughly deciphered and multiple hypotheses are considered.

A comparative transcriptomic approach between two accessions with contrasting vanillin content was used to fill in knowledge gaps on vanillin biosynthesis and identify potential candidate genes affecting vanillin accumulation. Out of the 59,128 genes known in vanilla, putative positive and negative regulators that influence vanillin accumulation through pathway modulation, precursor sequestration or enzymatic efficiency were identified. Differentially expressed genes were identified using three specific comparisons on accession, tissue type and developmental stage of capsule. Each comparison was analyzed separately focusing specifically on the accession contrast. BLAST annotation of differentially expressed genes provided protein identities that were mapped to the prominent vanillin biosynthetic pathways proposed by previous studies.

Enzymes from the lignin biosynthetic pathway were found to be negatively correlated to vanillin accumulation in vanilla cured capsules. There were 656 differentially expressed genes shared among all three comparisons and included β-glucosidase, cytochrome P450 and PAL amongst others. These results identify gene targets that could lead to higher vanillin content in vanilla cured capsules.