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11, 01, and 22, respectively. With respect to flounder�Cmedaka genome synteny, the alignment of 6,463 orthologues on the 24 flounder chromosomes revealed an obvious syntenic relationship with the 24 corresponding chromosomes of medaka. Except for some chromosomes with minor multi-chromosome hits (S6 Kinase an orthologous match between two species. Pol, Paralichthys olivaceus; Dre, Danio rerio; Ola, Oryzias latipes ... 4.?Discussion 4.1. High-resolution genetic map construction using RAD-based SNPs Genetic maps constructed using molecular markers are important for genomic and genetic analyses of individual species. SNPs are particularly attractive for genetic map construction, because they represent the most common type of DNA polymorphism in the genome and are amenable to high-throughput genotyping.17 In the present study, ?950 million RAD tags were generated from 2 Japanese flounder parents and 216 offspring individuals. We discovered 13,362 novel SNPs evenly distributed throughout http://www.selleckchem.com/products/LY294002.html the entire Japanese flounder genome, providing thereby a large number of genetic variation resources for future genome selection and genome-wide association studies. Among the identified SNPs, 12,712 SNPs were successfully genotyped and assigned to 24 LGs corresponding to the 24 chromosome pairs of the Japanese flounder genome. The total length of the resulting map was 3,497.29 cM, with an average marker spacing of 0.47 cM. Four genetic maps of Japanese flounder have been previously constructed using various markers,7�C10 but those maps are characterized by relatively larger genetic intervals and/or non-uniform marker distributions. The most recent genetic map10 containing 1,487 SSRs with an average interval of 1.22 cM was formerly the densest reported flatfish linkage map and worthy of acclaim. However, whole genome-level analyses such as genome-wide association selleck kinase inhibitor studies were still not practical using this map because of the limits imposed by the types of markers and their associated genotyping methods.23 The denser SNP-based genetic map constructed in this study thus has greatly expanded application. It represents a considerable improvement over previous flounder genetic linkage maps based on SSR and AFLP markers. Most LGs on our genetic map were considered to be saturated with an even distribution of three types of SNPs, namely, maternal heterozygous, paternal heterozygous, and double heterozygous SNPs; a few LGs, such as LG8, LG9, LG11, LG18, LG19, were not, however, revealing a complex genome containing regions enriched in repeat sequences and transposable elements.