Initial stage of genetic mapping in Ciona intestinalis.

The use of classic genetics is emerging in the ascidian Ciona intestinalis; recent advances in genomics and high-quality developmental and evolutionary studies have made this animal an attractive model for research purposes. Genetic mapping in Ciona will likely make a major contribution to ascidian genomics and developmental biology by providing support for genome assembly and annotation and for the isolation of genes with particular mutations, while construction of genetic maps advances classic genetics in this species. Two major issues must be overcome before fine genetic maps can be constructed: the choice of proper genetic backgrounds and the establishment of laboratory strains. A high degree of polymorphism is useful for genetic mapping if we consider particular combinations of genetic backgrounds and techniques, although it is necessary to pay attention to the confused classification of C. intestinalis. Thus, it is preferred to establish laboratory strains instead of using samples with various genetic backgrounds. As these issues are unresolved, only amplified fragment length polymorphism-based maps have been created, while bulk segregant analysis is expected to isolate markers flanking mutant loci. However, rich genomic resources should facilitate the next stage of genetic map construction based on type I markers using coding sequences. The meiotic events that occur in crossing experiments for mapping purposes should shed light on population genetics and speciation issues. The results of such investigations may provide feedback for comparative genomics and developmental genetics in the near future.