Open AccessClassification of Takifugu rubripes, T. chinensis and T. pseudommus by genotyping-by-sequencing
Author(s) -
Yeon Jung Park,
Mi Nan Lee,
Jae Koo Noh,
Eun Soo Noh,
Jung Ha Kang,
Jung Youn Park,
Eun Mi Kim
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0236483
Subject(s) - takifugu rubripes , biology , genotyping , phylogenetic tree , genetics , single nucleotide polymorphism , sanger sequencing , dna sequencing , genotype , gene
Takifugu rubripes is more expensive than other species of the genus because of its high protein content and special flavor. However, it is easily confused with imported T . chinensis and T . pseudommus because they have similar morphological characteristics. We identified single nucleotide polymorphism (SNP) markers of T . rubripes by genotyping-by-sequencing (GBS) and evaluated their ability to distinguish among T . rubripes , T . chinensis , and T . pseudommus . In all, 18 polymorphic SNPs were subjected to phylogenetic analyses of the three Takifugu species. Additionally, we subjected a second set of samples to Sanger sequencing to verify that the polymorphic SNPs could be used to evaluate the genetic variation among the three Takifugu species. A phylogenetic tree that included the analyzed sequence of set A, which is referred to as the reference sequence, and a validation sequence of set B with 18 SNPs were produced. Based on this phylogenetic tree and STRUCTURE analyses, T . rubripes , T . chinensis and T . pseudommus have low genetic variation and should be considered the same gene pool. Our findings suggest that further studies are needed to estimate the genetic association of the three Takifugu species.