title: Single base substitution causing the fragrant phenotype and development of a type-specific marker in aromatic coconut (Cocos nucifera).
abstract: The fragrance gene, betaine aldehyde dehydrogenase 2 (Badh2), has been well studied in many plant species. The objectives of this study were to clone Badh2 and compare the sequences between aromatic and non-aromatic coconuts. The complete coding region was cloned from cDNA of both aromatic and non-aromatic coconuts. The nucleotide sequences were highly homologous to Badh2 genes of other plants. Badh2 consisted of a 1512-bp open reading frame encoding 503 amino acids. A single nucleotide difference between aromatic and non-aromatic coconuts resulted in the conversion of alanine (non-aromatic) to proline (aromatic) at position 442, which was the substrate binding site of BADH2. The ring side chain of proline could destabilize the structure leading to a non-functional enzyme. Badh2 genomic DNA was cloned from exon 1 to 4, and from exon 5 to 15 from the two coconut types, except for intron 4 that was very long. The intron sequences of the two coconut groups were highly homologous. No differences in Badh2 expression were found among the tissues of aromatic coconut or between aromatic and non-aromatic coconuts. The amino acid sequences of BADH2 from coconut and other plants were compared and the genetic relationship was analyzed using MEGA 7.0. The phylogenetic tree reconstructed by the Bayesian information criterion consisted of two distinct groups of monocots and dicots. Among the monocots, coconut (Cocos nucifera) and oil palm (Elaeis guineensis) were the most closely related species. A marker for coconut differentiation was developed from one-base substitution site and could be successfully used.
authors.affiliation: Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.
authors.forename: A
authors.initials: A
authors.lastname: Vongvanrungruang
authors.affiliation: Division of Genetics, Department of Science, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand.|Research Unit of Genetic Technology and Applications, Department of Science, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand.
authors.forename: C
authors.initials: C
authors.lastname: Mongkolsiriwatana
authors.affiliation: Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.
authors.forename: T
authors.initials: T
authors.lastname: Boonkaew
authors.affiliation: Functional Food Unit, Division of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok, Thailand.
authors.forename: O
authors.initials: O
authors.lastname: Sawatdichaikul
authors.affiliation: Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.|Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Chatuchak, Bangkok, Thailand.|Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.
authors.forename: K
authors.initials: K
authors.lastname: Srikulnath
authors.affiliation: Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand fscisrp@ku.ac.th.|Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Chatuchak, Bangkok, Thailand fscisrp@ku.ac.th.|Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand fscisrp@ku.ac.th.
authors.forename: S
authors.initials: S
authors.lastname: Peyachoknagul
mesh_terms: D000595:Amino Acid Sequence; D050728:Betaine-Aldehyde Dehydrogenase / Q000235:genetics*; D003059:Cocos / Q000201:enzymology / Q000235:genetics*; D005091:Exons; D017343:Genes, Plant; D009812:Odorants; D010641:Phenotype; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins; D050728:Betaine-Aldehyde Dehydrogenase