The First Identification of the Gene Conferring Aroma in Tree Plant, Coconut (Cocos nucifera)

The aroma contributed by the potent volatile compound 2-acetyl-1-pyrroline (2AP) is an economically important trait in several crops including aromatic rice and soybean. The genes conferring this trait have been identified in rice (OsBADH2) by a positional cloning and in soybean (GmAMADH2) by a similarity search the genome for the rice orthologous gene. The lack of function of the gene has been reported contributing to the 2AP biosynthesis in both rice and soybean. Aromatic coconut, which the meat of young endosperm and juice can be consumed fresh, is also found to produce and accumulate 2AP. Due to the lack of complete genome sequence of coconut (Cocos nunifera), the identification of the aromatic gene by a similarity search is not possible. In this study, we constructed two RNA-seq libraries from immature endosperms of non-aromatic and aromatic coconut, sequenced them by HiSeq 2500 system, Illumina, and performed a de novo assembly of the transcriptome data in order to identify the aromatic gene. The candidate gene, CnuAMADH2, was characterized and compared between non-aromatic and aromatic coconut. A base substitution from G to C in the coding sequence that causes one amino acid change, from alanine to proline, was revealed in the aromatic coconut. A functional marker for the aromatic trait was developed and verified in a collection of coconut germplasm. The result was clearly shown that all of the aromatic coconut accessions contain the same mutation in the gene CnuAMADH2. Our results confirmed that plants share the orthologous gene for the aromatic trait. This study firstly reported the gene that confers aroma in the tree plant, coconut.