Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics

Abstract

The medaka is becoming an attractive model organism for the study of vertebrate early development and organogenesis and large-scale mutagenesis projects that are aimed at creating developmentally defective mutants are now being conducted by several groups in Japan. To strengthen the study of medaka developmental genetics, we have conducted a large-scale isolation of ESTs from medaka embryos and developed tools that facilitate mutant analysis. In this study, we have characterized a total of 132,082 sequences from both ends of cloned insert cDNAs from libraries generated at different stages of medaka embryo development. Clustering analysis with 3-prime sequences finally identified a total of 12,429 clusters. As a pilot analysis, 924 clusters were subjected to in situ hybridization to determine the spatial localization of their transcripts. Using EST sequence data generated in the present study, a 60-mer oligonucleotide microarray with 8,091 unigenes (Medaka Microarray 8K) was constructed and tested for its usefulness in expression profiling. Furthermore, we have developed a rapid and reliable mutant mapping system using a set of mapped EST markers (M-marker 2003) that covers the entire medaka genome. These resources will accelerate medaka mutant analyses and make an important contribution to the medaka genome project.

Genetic Analysis of Craniofacial Traits in the Medaka

“…The genetic correlation was estimated from the phenotypic variance and covariance of F 1 and F 2 progeny (Ukai 2002). A total of 304 markers, composed of 48 M-marker 2003 (Kimura et al 2004) and 256 newly mapped markers (Kimura et al 2005), were used to map the quantified craniofacial traits. The genotype data are those described in Kimura et al (2005).…”

Phenotypic analysis of a novel chordin mutant in medaka

“…Medaka is thought to be a model organism complimentary to zebrafish because it is evolutionarily distant to zebrafish and has a different organization of the genome, which is more similar to Fugu (reviewed in Kimura et al, 2004). In addition to completion of the medaka draft genome (Kasahara et al, 2007), a large number of medaka mutants has been isolated from natural population or from ethylnitrosourea (ENU) -induced mutagenesis screening (Ishikawa, 2000;Loosli et al, 2000;Furutani-Seiki et al, 2004; H.T., unpublished data; many of them can be browsed at National BioResource Project Medaka in Japan at http:// shigen.lab.nig.ac.jp/medaka).…”

An autosomal locus controls sex reversal in interspecific XY hybrids of the medaka fishes

“…Individual PCR conditions were optimized for each primer pair, and products were digested with restriction enzymes if necessary. Separation of PCR products was performed by conventional polyacrylamide gel electrophoresis (Kimura et al, 2004).…”