title: De novo transcriptome assembly and identification of the gene conferring a "pandan-like" aroma in coconut (Cocos nucifera L.).
abstract: Thailand's aromatic coconut (Cocos nucifera L.) is a special type of green dwarf coconut, the liquid endosperm of which is characterized by a pleasant "pandan-like" aroma due to the presence of 2-acetyl-1-pyrroline (2AP). The aim of this study was to perform a de novo assembly of transriptome from C. nucifera endosperm and to identify the gene responsible for 2AP biosynthesis. CnAMADH2 was identified as an ortholog of the rice aromatic gene and a G-to-C substitution found in exon 14 was associated with 2AP content in the aromatic green dwarf coconut accessions. The base substitution caused an amino-acid change, alanine-to-proline, at position 442 (P442A). The presence of P at this position might alter the steric conformation at the loop region and subsequently result in an unstabilized dimer conformation that could lower AMADH enzyme activity. Among AMADH/BADH protein sequences in different plant species, the P442A mutation was found exclusively in aromatic coconut. The PCR marker developed based on this sequence variation can perfectly detect the aromatic and non-aromatic alleles of the gene. This study confirms the hypothesis that plants may share a mechanism of 2AP biosynthesis. This is the first identification of the gene associated with 2AP biosynthesis in a tree plant.
authors.affiliation: Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, 10900, Thailand.
authors.forename: Chatree
authors.initials: C
authors.lastname: Saensuk
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand.
authors.forename: Samart
authors.initials: S
authors.lastname: Wanchana
authors.affiliation: Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
authors.forename: Kiattawee
authors.initials: K
authors.lastname: Choowongkomon
authors.affiliation: Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
authors.forename: Sugunya
authors.initials: S
authors.lastname: Wongpornchai
authors.affiliation: Chumphon Horticultural Research Center, Department of Agriculture, Bangkok, 10900, Thailand.
authors.forename: Tippaya
authors.initials: T
authors.lastname: Kraithong
authors.affiliation: Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
authors.forename: Wachiraya
authors.initials: W
authors.lastname: Imsabai
authors.affiliation: Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
authors.forename: Ekawat
authors.initials: E
authors.lastname: Chaichoompu
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand.
authors.forename: Vinitchan
authors.initials: V
authors.lastname: Ruanjaichon
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand.
authors.forename: Theerayut
authors.initials: T
authors.lastname: Toojinda
authors.affiliation: Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
authors.forename: Apichart
authors.initials: A
authors.lastname: Vanavichit
authors.affiliation: Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand. Electronic address: arikit@gmail.com.
authors.forename: Siwaret
authors.initials: S
authors.lastname: Arikit
mesh_terms: D053898:Biosynthetic Pathways; D003059:Cocos / Q000235:genetics* / Q000378:metabolism; D018744:DNA, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D008958:Models, Molecular; D009812:Odorants; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D011758:Pyrroles / Q000737:chemistry / Q000378:metabolism*; D020539:Sequence Analysis, Protein
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D011758:Pyrroles; D010088:Oxidoreductases; C426303:2-acetyl-1-pyrroline
keywords: 2-acetyl-1-pyrroline; AMADH; Aroma; BADH; Coconut; RNA-seq