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Dive into the research topics where Kanako Fuji is active.

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Featured researches published by Kanako Fuji.


BMC Genomics | 2010

A second generation genetic linkage map of Japanese flounder ( Paralichthys olivaceus )

Cecilia Castaño-Sánchez; Kanako Fuji; Akiyuki Ozaki; Osamu Hasegawa; Takashi Sakamoto; Kagayaki Morishima; Ichiro Nakayama; Atsushi Fujiwara; Tetsuji Masaoka; Hiroyuki Okamoto; Kengo Hayashida; Michihira Tagami; Jun Kawai; Yoshihide Hayashizaki; Nobuaki Okamoto

BackgroundJapanese 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.ResultsSex-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.ConclusionsThe 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.


BMC Genomics | 2010

Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus

Takashi Koyama; Shuichi Asakawa; Takayuki Katagiri; Atsushi Shimizu; Fernand F. Fagutao; Rapeepat Mavichak; Mudjekeewis D. Santos; Kanako Fuji; Takashi Sakamoto; Toshihide Kitakado; Hidehiro Kondo; Nobuyoshi Shimizu; Takashi Aoki; Ikuo Hirono

BackgroundHigher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome.ResultsMj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences.ConclusionsOur results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.


PLOS ONE | 2013

Quantitative Trait Loci (QTL) Associated with Resistance to a Monogenean Parasite (Benedenia seriolae) in Yellowtail (Seriola quinqueradiata) through Genome Wide Analysis

Akiyuki Ozaki; Kazunori Yoshida; Kanako Fuji; Satoshi Kubota; Wataru Kai; Jun-ya Aoki; Yumi Kawabata; Junpei Suzuki; Kazuki Akita; Takashi Koyama; Masahiro Nakagawa; Takurou Hotta; Tatsuo Tsuzaki; Nobuaki Okamoto; Kazuo Araki; Takashi Sakamoto

Benedenia infections caused by the monogenean fluke ectoparasite Benedenia seriolae seriously impact marine finfish aquaculture. Genetic variation has been inferred to play a significant role in determining the susceptibility to this parasitic disease. To evaluate the genetic basis of Benedenia disease resistance in yellowtail (Seriola quinqueradiata), a genome-wide and chromosome-wide linkage analyses were initiated using F1 yellowtail families (n = 90 per family) based on a high-density linkage map with 860 microsatellite and 142 single nucleotide polymorphism (SNP) markers. Two major quantitative trait loci (QTL) regions on linkage groups Squ2 (BDR-1) and Squ20 (BDR-2) were identified. These QTL regions explained 32.9–35.5% of the phenotypic variance. On the other hand, we investigated the relationship between QTL for susceptibility to B. seriolae and QTL for fish body size. The QTL related to growth was found on another linkage group (Squ7). As a result, this is the first genetic evidence that contributes to detailing phenotypic resistance to Benedenia disease, and the results will help resolve the mechanism of resistance to this important parasitic infection of yellowtail.


Marine Biotechnology | 2011

Linkage Mapping of Toll-Like Receptors (TLRs) in Japanese Flounder, Paralichthys olivaceus

Seong Don Hwang; Kanako Fuji; Tomokazu Takano; Takashi Sakamoto; Hidehiro Kondo; Ikuo Hirono; Takashi Aoki

Toll-like receptors (TLRs) are responsible for the recognition of specific pathogen-associated molecular patterns and consequently activate signal pathways leading to inflammatory and interferon responses. The region surrounding several TLRs was previously found to be associated with resistance to specific disease. Hence, we determined the location of 11 TLRs in Japanese flounder (Paralichthys olivaceus) using polymorphic microsatellite markers. TLR1 and TLR3 were located on linkage group (LG) 21 and 7, respectively. Membrane TLR5 and soluble TLR5 were mapped to LG22. TLR7 and TLR8 were mapped to LG3. TLR9 was found on LG1 and TLR14 and TLR21 were located on the same linkage group, LG10. TLR22 was found on LG8. Interestingly, TLR2 was mapped with the previously reported Poli9-8TUF microsatellite marker which is tightly associated with lymphocystis virus disease resistance. Therefore, TLR2 is a candidate gene for resistance to lymphocystis disease. These results imply that the location of a TLR associated with a particular disease may be valuable for the research on the relationship between host immune response and disease resistance.


Marine Biotechnology | 2015

Identification of Sex-Linked SNPs and Sex-Determining Regions in the Yellowtail Genome

Takashi Koyama; Akiyuki Ozaki; Kazunori Yoshida; Junpei Suzuki; Kanako Fuji; Jun-ya Aoki; Wataru Kai; Yumi Kawabata; Tatsuo Tsuzaki; Kazuo Araki; Takashi Sakamoto

Unlike the conservation of sex-determining (SD) modes seen in most mammals and birds, teleost fishes exhibit a wide variety of SD systems and genes. Hence, the study of SD genes and sex chromosome turnover in fish is one of the most interesting topics in evolutionary biology. To increase resolution of the SD gene evolutionary trajectory in fish, identification of the SD gene in more fish species is necessary. In this study, we focused on the yellowtail, a species widely cultivated in Japan. It is a member of family Carangidae in which no heteromorphic sex chromosome has been observed, and no SD gene has been identified to date. By performing linkage analysis and BAC walking, we identified a genomic region and SNPs with complete linkage to yellowtail sex. Comparative genome analysis revealed the yellowtail SD region ancestral chromosome structure as medaka-fugu. Two inversions occurred in the yellowtail linage after it diverged from the yellowtail-medaka ancestor. An association study using wild yellowtails and the SNPs developed from BAC ends identified two SNPs that can reasonably distinguish the sexes. Therefore, these will be useful genetic markers for yellowtail breeding. Based on a comparative study, it was suggested that a PDZ domain containing the GIPC protein might be involved in yellowtail sex determination. The homomorphic sex chromosomes widely observed in the Carangidae suggest that this family could be a suitable marine fish model to investigate the early stages of sex chromosome evolution, for which our results provide a good starting point.


BMC Genomics | 2014

Construction of a radiation hybrid panel and the first yellowtail ( Seriola quinqueradiata ) radiation hybrid map using a nanofluidic dynamic array

Jun-ya Aoki; Wataru Kai; Yumi Kawabata; Akiyuki Ozaki; Kazunori Yoshida; Tatsuo Tsuzaki; Kanako Fuji; Takashi Koyama; Takashi Sakamoto; Kazuo Araki

BackgroundYellowtail (Seriola quinqueradiata) are an economically important species in Japan. However, there are currently no methods for captive breeding and early rearing for yellowtail. Thus, the commercial cultivation of this species is reliant upon the capture of wild immature fish. Given this, there is a need to develop captive breeding techniques to reduce pressure on wild stocks and facilitate the sustainable development of yellowtail aquaculture. We constructed a whole genome radiation hybrid (RH) panel for yellowtail gene mapping and developed a framework physical map using a nanofluidic dynamic array to use SNPs (single nucleotide polymorphisms) in ESTs (expressed sequence tags) for the DNA-assisted breeding of yellowtail.ResultsClonal RH cell lines were obtained after ionizing radiation; specifically, 78, 64, 129, 55, 42, and 53 clones were isolated after treatment with 3,000, 4,000, 5,000, 6,000, 8,000, or 10,000 rads, respectively. A total of 421 hybrid cell lines were obtained by fusion with mouse B78 cells. Ninety-four microsatellite markers used in the genetic linkage map were genotyped using the 421 hybrid cell lines. Based upon marker retention and genome coverage, we selected 93 hybrid cell lines to form an RH panel. Importantly, we performed the first genotyping of yellowtail markers in an RH panel using a nanofluidic dynamic array (Fluidigm, CA, USA). Then, 580 markers containing ESTs and SNPs were mapped in the first yellowtail RH map.ConclusionsWe successfully developed a yellowtail RH panel to facilitate the localization of markers. Using this, a framework RH map was constructed with 580 markers. This high-density physical map will serve as a useful tool for the identification of genes related to important breeding traits using genetic structural information, such as conserved synteny. Moreover, in a comparison of 30 sequences in the RH group 1 (SQ1), yellowtail appeared to be evolutionarily closer to medaka and the green-spotted pufferfish than to zebrafish. We suggest that synteny analysis may be potentially useful as a tool to investigate chromosomal evolution by comparison with model fish.


Aquaculture | 2006

Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus)

Kanako Fuji; Kazunobu Kobayashi; Osamu Hasegawa; Maria Raquel Moura Coimbra; Takashi Sakamoto; Nobuaki Okamoto


Aquaculture | 2010

Identification of the sex-linked locus in yellowtail, Seriola quinqueradiata

Kanako Fuji; Kazunori Yoshida; Keita Hattori; Akiyuki Ozaki; Kazuo Araki; Masanori Okauchi; Satoshi Kubota; Nobuaki Okamoto; Takashi Sakamoto


Aquaculture | 2010

Linkage analysis of resistance to Streptococcus iniae infection in Japanese flounder (Paralichthys olivaceus)

Akiyuki Ozaki; Hiroyuki Okamoto; Toshiyuki Yamada; Tomomasa Matuyama; Takamitsu Sakai; Kanako Fuji; Takashi Sakamoto; Nobuaki Okamoto; Kazunori Yoshida; Keita Hatori; Kazuo Araki; Masanori Okauchi


Archive | 2012

Progress of DNA Marker‑Assisted Breeding in Maricultured Finfish

Akiyuki Ozaki; Kazuo Araki; Hiroyuki Okamoto; Masanori Okauchi; Keiichi Mushiake; Kazunori Yoshida; Tatsuo Tsuzaki; Kanako Fuji; Takashi Sakamoto; Nobuaki Okamoto

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Takashi Sakamoto

Tokyo University of Marine Science and Technology

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Nobuaki Okamoto

Tokyo University of Marine Science and Technology

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