DNA Microarray for Rapid Detection of Mitochondrial DNA Haplotypes of Chum Salmon

Abstract

For use in genetic stock identification, we developed an oligonucleotide (DNA) microarray hybridization method for rapid and accurate detection of nucleotide sequence variations in 20 previously identified variable nucleotide sites in about 500 bp within the 5' half of the control region of mitochondrial DNA of chum salmon (Oncorhynchus keta). The method includes immobilization of synthesized oligonucleotides containing respective polymorphic sites on a glass slide precoated with polycarbodiimide resin, a 2-hour hybridization with DNA microarray of biotinylated polymerase chain reaction fragments spanning the 5' variable portion followed by short washing, and visualization of hybridization signals by conventional ABC method and scanner-assisted computation of signal intensity on a computer. The entire process of hybridization and detection was completed within 4 hours. The resulting DNA microarray could detect all of the single nucleotide mutations and therefore could be used to identity the sequence variations defining 30 mtDNA haplotypes of chum salmon as revealed previously by nucleotide sequence analysis.

Activity of the pituitary–gonadal axis is increased prior to the onset of spawning migration of chum salmon

“…An oligonucleotide microarray that detects these SNPs was developed for rapid identification of these chum salmon haplotypes (Moriya et al, 2004). In the present study, the mtDNA haplotype of individual pre-migratory fish was identified by this technique.…”

“…1A). Japanese populations were identified on the basis of mitochondrial DNA (mtDNA) haplotypes that were determined with DNA microarray (Moriya et al, 2004). In autumn, homing adults were collected along their migratory pathway in the Ishikari River-Ishikari Bay system in Hokkaido, Japan.…”

Gene Expression Patterns During the Larval Development of European Sea Bass (Dicentrarchus Labrax) by Microarray Analysis

“…There is indeed a consensus that regulation of gene expression is a fundamental mechanism underlying the complex processes of cell differentiation and morphogenesis during ontogenesis of an organism. Recently, microarrays have dramatically accelerated many types of investigations in marine organisms, been especially used for comparative genomic hybridization (Fish; Moriya et al, 2004 and2007) and for monitoring the expression levels of thousands of genes simultaneously in order to study the effects of certain treatments (Algae; Jamers et al, 2006), diseases (Crustaceans; Wang et al, 2006) and transgenesis manipulation (Mori et al, 2007) on transcriptome. Over the last two decades, studies based on whole-body or tissue-specific microarray approaches have investigated gene expression profiles during embryogenesis in several species (Drosophila, White et al, 1999;Xenopus, Baldessari et al, 2005;mouse, Tanaka et al, 2000) including fish (zebrafish, Ton et al, 2002;sea bream, Sarropoulou et al, 2005).…”

Nonrandom distribution of chum salmon stocks in the Bering Sea and the North Pacific Ocean estimated using mitochondrial DNA microarray

“…Preparation of the DNA microarray for the 30 mtDNA haplotypes was described previously [8,9]. In brief, each synthesized 17-to 20-mer oligomer contained the previously identified single-nucleotide mutation or no mutation [5,6] in the middle of the sequence.…”

“…Recently, we developed a DNA microarray for rapid and accurate identification of all the single-nucleotide polymorphisms (SNPs) occurring in the 20 variable sites of the 5 0 half of chum salmon mtDNA control region [8], which defines all 30 mtDNA haplotypes of three clades (A, B, and C) as described previously [6]. Noticeable features of this method include immobilization of oligomers containing the SNP sites with an appropriate length on a resin-precoated glass slide, quick hybridization with labeled target fragments amplified by polymerase chain reaction (PCR), and optical signal detection by conventional histochemical coloring method without an expensive fluorescence image detector.…”