Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI).

Publisher Summary This chapter focuses on the current status of medaka genetics and genomics. The egg-laying killifish medaka, Oryzias latipes, is an old (100 years) and well-established genetic model system for developmental genetics and many other areas of biological and environmental research. Genetics in medaka offers several advantages; for example, the availability of divergent, completely inbred strains and a genome of only 800 Mb, less than half the size of the zebrafish genome. Also, as a practical aspect, the sexes are easily distinguished in medaka, in contrast to zebrafish, facilitating breeding in general and genetic studies in particular. Like zebrafish, medaka is suitable for forward genetics based on chemically induced mutations and might even be advantageous in certain aspects. The medaka genome is less than half the size of the zebrafish genome and is highly polymorphic in nucleotide sequences without large-scale rearrangements. Although the comparison of all mutant phenotypes in medaka and zebrafish is not possible, it is clear that many mutants in medaka display phenotypes previously undescribed in zebrafish. Transposable elements are a major source of mutations. Large-scale medaka expressed sequence tag (EST) analysis and gene mapping are essential for positional cloning of the genes responsible for mutants and the genomewide comparison of linkage relationships among vertebrate species. The development of bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) cloning systems has revolutionized genome analysis in vertebrates. Chromosome analysis of medaka started long before the emergence of mammalian cytogenetics.