Nobuaki Okamoto

Japanese amberjack/yellowtail (Seriola quinqueradiata) is a commonly cultured marine fish in Japan. For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions. In selective breeding, information of genetic markers is useful and sufficient to identify individuals carrying advantageous traits but if the aim is to determine the genetic basis of the trait, large insert genomic DNA libraries are essential. In this study, toward prospective understanding of genetic basis of several economically important traits, we constructed a high-coverage bacterial artificial chromosome (BAC) library, obtained sequences from the BAC-end, and constructed comprehensive female and male linkage maps of yellowtail using Simple Sequence Repeat (SSR) markers developed from the BAC-end sequences and a yellowtail genomic library. The total insert length of the BAC library we constructed here was estimated to be approximately 11 Gb and hence 16-times larger than the yellowtail genome. Sequencing of the BAC-ends showed a low fraction of repetitive sequences comparable to that in Tetraodon and fugu. A total of 837 SSR markers developed here were distributed among 24 linkage groups spanning 1,026.70 and 1,057.83 cM with an average interval of 4.96 and 4.32 cM in female and male map respectively without any segregation distortion. Oxford grids suggested conserved synteny between yellowtail and stickleback. In addition to characteristics of yellowtail genome such as low repetitive sequences and conserved synteny with stickleback, our genomic and genetic resources constructed and revealed here will be powerful tools for the yellowtail breeding program and also for studies regarding the genetic basis of traits.

総合学術電子ジャーナルサイト「J-STAGE」－国内で発行された学術論文全文を読むことのできる、日本最大級の総合電子ジャーナルプラットフォームです。

総合学術電子ジャーナルサイト「J-STAGE」－国内で発行された学術論文全文を読むことのできる、日本最大級の総合電子ジャーナルプラットフォームです。

Background: Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations. Results: Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots. Conclusions: The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms.

Infectious hematopoietic necrosis (IHN) is an acute, systemic, rhabdoviral disease of salmonid species. To date, the effective approach in preventing or treating this epizootic disease is unknown. In this study, a genetic cross was established to elucidate the genetic markers associated with IHN resistance in rainbow trout Oncorhynchus mykiss. An IHN-resistant paternal strain of was crossed to a susceptible maternal strain to produce a F₁generation. Mating F₁males back to the maternal strain created F₂, a backcross generation. Five backcross families were generated and IHNV was challenged on 92 individuals of each family. Linkage analysis was performed on the backcross families using 96 microsatellite markers from 25 linkage groups. LOD score as well as p values using the Pearson goodness of χ²-test were calculated to identify the chromosomal regions associated with IHN resistance. The highest LOD score of 0.952 (θ=0.39) was obtained in one backcross family. A novel chromosomal region (p = 0.011) on linkage group 2 consists of a cluster of 4 microsatellite markers, OmyFGT3TUF, OmyFGT25TUF, OmyRGT35TUF and BFRO0001, and they were identified as a potential region for quantitative trait loci of IHN resistance in rainbow trout.