Development of specific chemiluminescent immunoassays for three subtypes of vitellogenin in grey mullet (Mugil cephalus).

Chemiluminescent immunoassays (CLIAs) were developed for each of three subtypes of vitellogenin (VtgAa, VtgAb and VtgC) in grey mullet, primarily for use in monitoring estrogenic pollution of the environment. The working range of VtgAa-CLIA and VtgAb-CLIA was from 0.975 to 1,000 ng/ml, while that of VtgC-CLIA was from 0.487 to 1,000 ng/ml. Each CLIA appeared to be specific to the targeted Vtg subtype. Intra- and inter-assay coefficients of variation in the developed CLIAs were lower than 10%. In male serum, VtgAa, VtgAb and VtgC were detected in ranges from 0.01 to 0.38, 0.02 to 1.01, and 0.01 to 3.12 µg/ml, respectively, during various sampling periods. In vitellogenic females (October), serum VtgAb levels (1,192.05 ±â€¯237.81 µg/ml) were significantly higher than levels of the other two Vtg subtypes (120.82 ±â€¯30.42 and 119.23 ±â€¯16.95 µg/ml for VtgAa and VtgC, respectively). When immature mullet were fed diets containing 17α-ethinylestradiol (EE2) at three different doses (0.4, 40 and 4,000 ng/g body weight), all Vtg subtypes were induced by 40 ng/g and 4,000 ng/g EE2. The VtgC (610.30 ±â€¯150.18 µg/ml) was most highly expressed among the three Vtgs in fish fed 40 ng/g EE2, while VtgAb (33.25 ±â€¯13.58 mg/ml) was highest in expression in fish fed 4,000 ng/g EE2. The present study provided practical subtype-specific Vtg assays for the first time in grey mullet, providing the necessary means to evaluate estrogenic activities in aquatic environments.

Identification of Sex-associated SNPs of Greater Amberjack (Seriola dumerili).

The sex determination systems of fish are highly diverse compared with those of mammals. Thus, performing investigations using nonmodel fish species helps to understand the highly diverse sex determination systems of fish. Because greater amberjack (Seriola dumerili) is one of the most important edible fish globally and knowledge of its sex determination system is economically important in the field of aquaculture, we are interested in the mechanisms of sex determination of Seriola species. In this study, we identified sex-associated SNPs of greater amberjack using SNP information of 10 males and 10 females by an association test. We determined that the sex-associated SNPs were on chromosome 12 and mainly covered with two scaffolds (about 7.1 Mbp). Genotypes of sex-associated SNPs indicated that females are the heterogametic sex (ZZ/ZW). Furthermore, we compared the genomic structure of greater amberjack with those of Japanese amberjack (Seriola quinqueradiata), California yellowtail (Seriola dorsalis), and medaka (Oryzias latipes). Whole-genome alignments and synteny analysis indicated that the sex determination system of greater amberjack is markedly different from that of medaka and implied that the sex determination system is conserved in the Seriola species.

Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements.

To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome. Between yellowtail and Japanese medaka (Oryzias latipes), almost all regions of the chromosomes were conserved and some blocks comprising several markers were translocated. Using the genome information of the spotted gar (Lepisosteus oculatus) as a reference, we further documented syntenic relationships and chromosomal rearrangements that occurred during evolution in four other acanthopterygian species (Japanese medaka, zebrafish, spotted green pufferfish and three-spined stickleback). The evolutionary chromosome translocation frequency was 1.5-2-times higher in yellowtail than in medaka, pufferfish, and stickleback.

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

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.

Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish.

BACKGROUND: Physical and linkage maps are important aids for the assembly of genome sequences, comparative analyses of synteny, and to search for candidate genes by quantitative trait locus analysis. Yellowtail, Seriola quinqueradiata, is an economically important species in Japanese aquaculture, and genetic information will be useful for DNA-assisted breeding. We report the construction of a second generation radiation hybrid map, its synteny analysis, and a second generation linkage map containing SNPs (single nucleotide polymorphisms) in yellowtail. RESULTS: Approximately 1.4 million reads were obtained from transcriptome sequence analysis derived from 11 tissues of one individual. To identify SNPs, cDNA libraries were generated from a pool of 500 whole juveniles, and the gills and kidneys of 100 adults. 9,356 putative SNPs were detected in 6,025 contigs, with a minor allele frequency ≥ 25%. The linkage and radiation hybrid maps were constructed based on these contig sequences. 2,081 markers, including 601 SNPs markers, were mapped onto the linkage map, and 1,532 markers were mapped in the radiation hybrid map. CONCLUSIONS: The second generation linkage and physical maps were constructed using 6,025 contigs having SNP markers. These maps will aid the de novo assembly of sequencing reads, linkage studies and the identification of candidate genes related to important traits. The comparison of marker contigs in the radiation hybrid map indicated that yellowtail is evolutionarily closer to medaka than to green-spotted pufferfish, three-spined stickleback or zebrafish. The synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.

Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

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

BACKGROUND: Yellowtail (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. RESULTS: Clonal 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. CONCLUSIONS: We 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.

Quantitative trait loci (QTL) associated with resistance to a monogenean parasite (Benedenia seriolae) in yellowtail (Seriola quinqueradiata) through genome wide analysis.

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.

Effects of ethynylestradiol on vitellogenin synthesis and sex differentiation in juvenile grey mullet (Mugil cephalus) persist after long-term exposure to a clean environment.

We investigated the continuing effects of exposure to ethynylestradiol (EE(2)) in juvenile grey mullet after transfer to a clean environment. Eleven-month-old juvenile fish containing immature phenotype gonad were fed dry diets; the low and high EE(2)-treated groups were fed diets with 0.04 and 4 µg EE(2)/g body weight for 4 weeks, respectively. After treatment, they were transferred to clean seawater, and reared with an EE(2) free diet for 350 days. Vitellogenin (VTG) was not detected in the serum of the control group throughout the experimental period. However, in both treatment groups, abnormal values of serum VTG were detected until approximately 100 days after transfer to a clean environment. In the control group, sex differentiation was not confirmed until 206 days after transfer to a clean environment. However, some of the fish in the 0.04 µg EE(2)-treated group had ovarian cavity and oocytes at 26 days. In most of the fish in the 4 µg EE(2)-treated group, the ovarian cavity had already appeared at the end of EE(2) treatment (0 day), and oocytes were observed at 26 days, suggesting that EE(2) accelerates ovarian differentiation. These results suggest that previous exposure to EE(2) has long-term effects on VTG synthesis and gonadal development.

The effects of 17beta-estradiol on various reproductive parameters in the hermaphrodite fish Kryptolebias marmoratus.

The effect of a single injection of 17beta-estradiol (E2) was evaluated in the hermaphrodite fish Kryptolebias marmoratus. The fish [average body weight (BW), 0.15+/-0.01 g] were injected with either two concentrations of E2 (1 and 100 microg/g BW) once intraperitoneally. They were sampled at intervals of 7, 15, and 30 days after a single E2 injection. Gonadosomatic index (GSI), hepatosomatic index (HSI), the frequency of gonadal development, number of ovulated eggs, and plasma steroids levels were measured. The transcript abundances of vitellogenin (VTG) and estrogen receptors (ERalpha and beta) mRNA in the liver were also analyzed using quantitative real time polymerase chain reaction (real time PCR). GSI and the frequency of mature oocytes in the 100-microg E2-exposed group decreased compared to that of the control group during the experiment, and the number of ovulated eggs in the 100-microg E2-exposed group was lower when compared to the other groups. However, plasma E2 and 11-ketotestosterone (11-KT) levels were not significantly different between the experimental groups. On the other hand, plasma testosterone level and VTG mRNA abundance in the 100-microg E2-exposed group were significantly lower than the control group after 30 days. These results indicate that E2 stimulation at high concentration interferes with reproductive phenomena through delayed response. In addition, HSI in the 100-microg E2-exposed group and ERalpha mRNA abundance in the 1-microg E2-exposed group were significantly higher than the control group at 7 days after E2 injection, although there was no significant difference in HSI and ERalpha mRNA between all groups at 30 days. These results indicate temporal responses in reproductive parameters following high-dose E2 exposure in the hermaphrodite fish K. marmoratus.

Survey of contamination of estrogenic chemicals in Japanese and Korean coastal waters using the wild grey mullet (Mugil cephalus).

We monitored the contamination by environmental estrogens (EEs) of coastal areas in Korea and Japan using the wild grey mullet. The grey mullet were collected from Ansan, Jeju, Yeosu, Tongyeong, and Busan in Korea and Nagasaki, Omuta, and Fukuoka in Japan. Contamination by EEs was determined by measuring vitellogenin (VTG) levels in serum and identifying gonadal abnormalities histologically (i.e., testis-ova). In four sites in Korea (Ansan, Yeosu, Tongyeong, and Busan) and two sites in Japan (Nagasaki and Fukuoka), serum VTG in immature and male grey mullet was detected at levels greater than 1.0 microg/ml, which is considered to be an abnormal level. Although, testis-ova were observed in some individuals collected in Ansan, Tongyeong, and Busan in Korea and Omuta in Japan, there was no correlation between individuals with testis-ova and individuals with abnormal levels of VTG. Furthermore, in Japan, serum VTG levels of fish collected from Nagasaki and Fukuoka were also greater than 1.0 microg/ml. Although individuals with testis-ova were found in Omuta, these fish expressed normal levels of serum VTG. Our results suggest that the grey mullets living in these coastal areas are influenced by EEs in the environment. Furthermore, it appears that the production of VTG and the occurrence of testis-ova are caused by different mechanisms.

Estrogen-responsive element (ERE)-like motifs affect the 3-methylcholanthrene induction of eel CYP1A gene.

Some forms of cytochrome P450 (CYP) genes are known to be induced by xenobiotics such as dioxins. Induction of the CYP1A gene is mediated by an aryl hydrocarbon receptor (AHR) which binds to a specific nucleotide sequence called a dioxin-responsive element (DRE) located in the 5' enhancer region of the gene. Functional analysis of the regulatory region of the eel CYP1A gene had shown that a 654-bp region near the basal promoter, containing no DREs but three motifs that resemble estrogen-responsive element (ERE) halfsites, contributes substantially to the induced expression. Considering the importance of non-DRE elements in CYP1A gene induction, we investigated the role of ERE-like motifs using a point mutation technique. The regulatory region of the eel CYP1A gene was identified by creating mutations in all three ERE half-sites simultaneously or individually. The regulatory region constructs were cloned upstream of the luciferase gene in an expression vector which was microinjected into medaka ova. Expression of luciferase as a foreign gene in medaka fry exposed to 3-methylcholanthrene (3-MC)-treated feed was measured by competitive PCR analysis. Mutation in all the three ERE half-sites reduced expression to 10%. Mutation in ERE(-2) or ERE(-3) reduced the expression to 50%, whereas mutation in ERE(-1) did not affect the induction. The two functional half-sites of the eel CYP1A gene are palindromic to each other and appear to constitute the full-ERE.