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Authorship：Lead author   Language：Japanese   Publishing type：Research paper (scientific journal)  

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Authorship：Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)  

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DOI： 10.3389/fgene.2021.739781

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DOI： 10.1111/jai.14184

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Authorship：Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)  

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Authorship：Lead author   Language：English  

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s10228-019-00730-9

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Other Link： http://link.springer.com/article/10.1007/s10228-019-00730-9/fulltext.html

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

Identification of the population structure of harvested species is the first step in the management of wild fisheries. Although the marbled rockfish Sebastiscus marmoratus is a commercially important species in Japan, information on the population structure of this species is limited. We analyzed 646 individuals of S. marmoratus from 13 sampling locations in the coastal waters of western Japan using seven microsatellite markers with the aim to examine the genetic population structure and establish baseline data on the genetic diversity and effective population size (N-e) of this species. Our results indicate that western Japan populations are characterized by a large N-e and that genetic diversity is higher than has been previously reported. We performed several population genetics analyses but these failed to provide evidence of appreciable genetic population structure, although low but significant genetic differentiation was found in 2.6% of the population pairs. This study provides baseline information on the genetic diversity and population structure of S. marmoratus in the coastal waters of western Japan.

DOI： 10.1007/s12562-019-01359-3

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We previously reported a body color deformity in juvenile red sea bream, which shows transparency in the juvenile stage because of delayed chromatophore development compared with normal individuals, and this finding suggested a genetic cause based on parentage assessments. To conduct marker-assisted selection to eliminate broodstock inheriting the causative gene, developing DNA markers associated with the phenotype was needed. We first conducted SNP mining based on AFLP analysis using bulked-DNA from normal and transparent individuals. One SNP was identified from a transparent-specific AFLP fragment, which significantly associated with transparent individuals. Two alleles (A/G) were observed in this locus, and the genotype G/G was dominantly observed in the transparent groups (97.1%) collected from several production lots produced from different broodstock populations. A few normal individuals inherited the G/G genotype (5.0%), but the A/A and A/G genotypes were dominantly observed in the normal groups. The homologs region of the SNP was searched using a medaka genome database, and intron 12 of the Nell2a gene (located on chromosome 6 of the medaka genome) was highly matched. We also mapped the red sea bream Nell2a gene on the previously developed linkage maps, and this gene was mapped on a male linkage group, LG4-M. The newly found SNP was useful in eliminating broodstock possessing the causative gene of the body color transparency observed in juvenile stage of red sea bream.

DOI： 10.1007/s10126-018-9810-z

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Nihon Suisan Gakkai  

Inheritance and seasonal variation of the thickness of the nacreous elemental lamina (TNEL) of shells of Akoya pearl oysters Pinctada fucata were investigated. Nine full-sib families were produced from two parental populations selected on the basis of three colors (red, green, and other) of shell nacre in May 2012. TNEL was estimated by measuring the maximum peak of the spectrophotometric reflectance wavelength for selected parents vand offspring (at ages 14 and 16 months) at a hatchery. We analyzed the data to compare the mean TNEL values among families and the relationship between mid-parental values and mean values of the offspring. Also, seasonal fluctuations in TNEL and the relationship between TNEL and shell size and weight were observed in 2 families and in an additional 4 families (produced in March 2013) during a two-and-a-half-year period from 2013 to 2016. The results suggested that TNEL was significantly different between families. The TNEL of the parents had a strong positive correlation with the TNEL of the offspring. TNEL decreased as the shell grew and a negative relationship was observed between shell size or weight and TNEL in individuals during periodical long-term observation.

DOI： 10.2331/suisan.17-00036

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Nihon Suisan Gakkai  

To breed physically strong strains of Akoya pearl oyster Pinctada fucata martensii, a selection experiment was conducted for one generation from a local population. Parents were selected by serum carbohydrate (SC) content for high (H) and low (L) content groups. The first generation (H-G1 and L-G1) produced from these groups showed a significant difference in SC content at the age range of 12-18 months, reflecting the parent phenotype. H-G1 also showed superior trends to L-G1 in serum protein content, carbohydrate content of adductor muscle, and delta-a value of adductor muscle color (a diagnostic indicator of the Akoya oyster disease). Pearl production experiments using H-G1 indicated that the quality of obtained pearls, evaluated by size, weight and nacre thickness, was comparable to those harvested from two other commercially available strains bred several generations from Japanese or Chinese populations. These results present a possible practical method for selective breeding of Akoya pearl oyster based on SC content, to produce new strains suitable for pearl production.

DOI： 10.2331/suisan.17-00077

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class II beta, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class II beta. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class II beta gene and could be useful for MAS of red sea bream.

DOI： 10.1007/s10126-017-9779-z

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC FISH PATHOL DEPT FISHERIES-FAC AGR  

In this study, we evaluated the red sea bream iridoviral disease-resistant (RSIVD-resistant) trait of broodstock of red sea bream used in a commercial production based on DNA parentage analysis. We compared family structures of two groups from the same production lot and cultured at two different farms: a population without any outbreak of diseases (farm A) and a high mortality population after an RSIVD outbreak (farm B). The survival percentage of the fish at the farm A and farm B were 86.4% and 20.5%, respectively. Pedigree tracing was conducted on 200 individuals from each farm using eight microsatellite DNA markers among 22 potential breeders (20 dams and 2 sires), and parental pairs at farm A and B were successfully assigned with 93.0 and 90.5%, respectively. After allocating parentage information to each specimen collected from both farms, the estimated survival percentages of each family were calculated. The estimated survival of offspring from a male was 82.3%, and this survival was higher than that from the other male (estimated survival was 2.5%). Also, offspring from a female showed a high survival. These results suggest that some broodstock have resistant traits against RSIVD and shows the potential for developing an RSIVD-resistant strain of red sea bream.

File： RSIVD.pdf

DOI： 10.3147/jsfp.52.23

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC FISHERIES SCIENCE  

We investigated the thickness of the nacreous elemental lamina (TNEL) and the quality of cultured pearls using two lineages, thick or thin TNEL, of sacrificed pearl oysters Pinctada fucata used as grafts (donors) in the same hosts. The purpose of this study was to understand the influence of the TNEL of donors on both the TNEL and the quality of Akoya oyster pearls. Donors with thick or thin TNEL were hatched in May 2012. Two mantle grafts derived from each donor having thick or thin TNEL were implanted into the same pearl hosts, at two experimental divisions in two locations in Uwajima City during April 2014. The pearls in the oysters were cultivated until January 2015. The results showed that the TNEL of pearls developed from donors with thick TNEL were significantly thicker than the pearls developed from donors with thin TNEL, at both experimental divisions. The TNEL of the pearls had a strong positive correlation with the TNEL of the donors. The TNEL of the pearls influenced pearl interference color, suggesting that the TNEL of the pearls could influence pearl value.

DOI： 10.2331/suisan.16-00090

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

In this study, we identify clones of S-type rotifers Brachionus koreanus based on haplotypes of mitochondrial gene cytochrome c oxidase subunit I (mtCOI) and microsatellite DNA genotypes. We then study how clonal diversity affects the population growth of rotifers in a mass culture at a hatchery using a lot of B. koreanus rotifers for analysis. Microsatellite DNA markers were also developed to identify clones of B. koreanus. Clones of B. koreanus were identified based on haplotypes of mtCOI, microsatellite genotypes, as well as a combination of these haplotypes and genotypes. Three haplotypes of mtCOI, three clones based on microsatellites, and six clones based on a combination of mtCOI haplotypes and microsatellite genotypes were identified. The population growth rate of mass-cultured rotifers was monitored for a month, and the correlation between population growth rate and these clonal diversities was analyzed. Observed was a significant positive correlation between the population growth rate and haplotype diversity (r = 0.695, P = 0.004), however no correlations were found between the population growth rate and clonal diversity based on either microsatellite genotypes (r = 0.320, P = 0.245) or a combination of mtCOI haplotype and microsatellite genotypes (r = 0.435, P = 0.105). Some clones shared mtCOI haplotypes and microsatellite genotypes suggesting sexual reproduction occurred in the hatchery stock of B. koreanus.
Statement of relevance: This study showed the correlation between population growth rate and clonal diversities based on mtCOI haplotypes and microsatellite DNA genotypes in Brachionus koreanus. There was a significant correlation between the population growth rate and haplotype diversity and suggested genetic factor is one of the possible causes affecting population growth rate. Our results will be useful in mass-production and maintenance of Brachionus koreanus at hatcheries. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.aquaculture.2016.09.020

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

DOI： 10.1111/jai.13056

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

The genetic diversity and structure of nine domesticated strains of red sea bream used in a private hatchery were studied and compared to a wild population. A total of 313 individuals were genotyped at eight microsatellite loci. Average number of alleles per locus ranged from 5.5 to 9.4 in domesticated strains, but that of the wild population was 28.4. Heterozygosity of domesticated strains (ranged 0.697-0.804) was also lower compared to the wild population (0.952). Estimated Ne also decreased in all domesticated strains (ranged 10.3-126.0) compared to the wild population (1422.5). The UPGMA tree and 3-D FCA showed that there were two main clusters containing domesticated strains, and the wild population was at the middle of both of the domesticated clusters. The STRUCTURE analysis also supported the phylogenetic analysis, and revealed three sub-clusters in the domesticated strains. Pairwise F-ST revealed that all domesticated strains were statistically different from the wild population, and also the differentiation between domesticated strains was all statistically significant. Information on genetic diversity and structure of domesticated strains of red sea bream obtained in this study will be useful for future broodstock management and selective breeding programmes.

DOI： 10.1111/are.12498

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PENSOFT PUBL  

A long-spined sea urchin Diadema-sp reported from Japanese waters was genetically distinct from all known Diadema species, but it remained undescribed. Extensive field surveys in Japan with molecular identification performed in the present study determined five phenotypes (I to V) in Diadema-sp according to the presence and/or shape of a white streak and blue iridophore lines in the naked space of the interambulacral area. All phenotypes were distinct from Diadema setosum (Leske, 1778) and Diadema savignyi (Audouin, 1829), of which a major type (I) corresponded to Diadema clarki Ikeda, 1939 that was questioned and synonymized with D. setosum by Mortensen (1940). The holotype of D. clarki has not been found, but three unlabeled dried tests of Diadema were found among Ikeda's original collection held in the Kitakyushu Museum of Natural History and Human History, Fukuoka, Japan. A short mtDNA COI fragment (ca. 350bp) was amplified from one of the tests, and the nucleotide sequence determined (275bp) was nearly identical with that of Diadema-sp. Arrangements of the primary tubercles on the coronal plates in Diadema-sp and the museum specimen also conformed with D. clarki, indicating that Diadema-sp is identical to D. clarki and a valid species. Narrow latitudinal distribution (31 degrees N to 35 degrees N) of D. clarki in Japan was observed, where it co-existed with abundant D. setosum and rare D. savignyi. No D. clarki was found in the southern islands in Japan, such as Satsunan Islands to Ryukyu Islands and Ogasawara Island, where D. setosum and D. savignyi were commonly observed.

DOI： 10.3897/zookeys.585.8161

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC FISHERIES SCIENCE  

Genetic variability estimated by using 4 loci of microsatellite DNA markers was evaluated in 8 families produced in the breeding program for Akoya pearl oyster Pinctada fucata martensii in Japan. The extent of the influence of genetic variability was revealed in many of the traits of each family with regard to growth, mortality, and pearls produced. A significant or high correlation was observed between the extent of genetic variability of each family and growth, mortality during the nursery stage of mother pearl oyster, and efficiency of pearl production. Quality of pearls was not related to the extent of genetic diversity. The results suggest that the extent of genetic variability is important for breeding within Akoyagai pearl oyster culture.

DOI： 10.2331/suisan.15-00072

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Language：Japanese   Publisher：日本水産増殖学会  

DOI： 10.11233/aquaculturesci.63.399

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

Red sea bream is one of the most important aquaculture fish species in Japan. To improve the productivity of this fish during seed production, improved growth traits and reduced size variation are needed. In this study, we assessed parental contribution of fast- and slow-growing individuals observed in two different rearing phases in a mass production lot: (1) 50 dph reared in a tank and (2) 200 dph reared in a net cage. We also assessed GH gene (pmaGH) polymorphisms based on a previously developed minisatellite DNA marker. Specific broodstock individuals were significantly associated with fast- or slow-growing individuals at 50 dph and 200 dph. Significant differences in pmaGH minisatellite allele frequencies were observed between fast- and slow-growing groups at 50 dph in the frequency of two alleles (pmaGH-740 and pmaGH-900, respectively). Combining the results of DNA parentage analysis and pmaGH minisatellite allele analysis, one dam and two sires, possessing pmaGH-740, were significantly associated with the slow-growing groups. These results suggest that the minisatellite marker of pmaGH could be a useful tool for growth selection of this fish species.

DOI： 10.1016/j.aqrep.2015.10.001

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

DOI： 10.1111/jai.12800

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Language：English   Publisher：水産育種研究会  

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Language：Japanese   Publisher：日本水産増殖学会  

The stock enhancement programs of kuruma prawn <I>Marsupenaeus japonicus</I> started in Kagawa Prefecture in 1967. The catch of this species increased from 1980s to early 1990s, but gradually decreased after 1997. Therefore, it is necessary to estimate the stocking effectiveness of hatchery-reared (HR) kuruma prawn. In this study, we traced released HR prawns of stock enhancement programs using DNA-markers. 1.82 to 1.02 million HR prawns with approximately 50 mm were released in the east and central coast of Kagawa Prefecture, Bisan-seto and Harima-nada, in 2009 and 2010, respectively. The released HR prawns were discriminated based on the parent-child relationship with mitochondrial DNA and three microsatellites DNA markers. The released prawns were mainly recaptured in the waters off of the release areas. A portion of released population of prawns migrated to the western Kii Channel, whereas a number of were recaptured just north of Harima-nada. The recapture rate (economic efficiency of stocking) of released prawns in 2009 and 2010 in the first year after release was 0.54% (0.16) and 4.67% (1.51), respectively. These results indicated that stock enhancement programs increased catch of kuruma prawn, although differences in the recapture rates between the two years were high.

DOI： 10.11233/aquaculturesci.62.393

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Language：Japanese   Publisher：日本水産増殖学会  

To understand genetic factors affecting observed deformities in the head regions of artificially raised red sea bream, we evaluated morphological features of deformed fish at 60 days post-hatching. The incidence of deformities in the head region was 3.4%, and included cases featuring twisted lower jaws, lack of an upper jaw fragment, pugheadness and shortened lower jaws. The highest incidence of deformity was a shortened lower jaw, and as a direct consequence, we focused upon individuals exhibiting a shortened lower jaw for further genetic analysis. Genetic assessment based on microsatellite DNA markers was conducted in order to evaluate the genetic cause of the shortened lower jaw deformity. There were no obvious differences in heterozygosity or allele frequencies between individuals exhibiting normal and shortened lower jaws. DNA parentage analysis indicated that normal individuals were generated from 9 dams and 16 sires, and 43 parental pairs were observed. Shortened lower jaw individuals were generated from 9 dams and 15 sires, and 40 parental pairs were observed. No broodstock generated a significant numbers of individuals with a shortened lower jaw. Our results suggest that the shortened lower jaw individuals assessed in this study had arisen via environmental factors rather than genetic factors.

DOI： 10.11233/aquaculturesci.62.155

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Skeletal malformations are a serious problem in seed production of Japanese flounder Paralichthys olivaceus, and genetic effect is sometimes suggested as one of the causative factors. In this study, we examined a skeletal deformity named incomplete ossification, and studied its morphological character and parentage assessment of the deformity by microsatellite DNA markers in the hatchery produced offspring at a commercial farm. Naturally spawned fertilized eggs from flounder broodstocks (eight dams and 19 sires) were introduced into 50 kl tanks and reared with normal procedures. We conducted two lots of seed production with lot 2 started one-week later under the same rearing conditions as lot 1. Deformed and normal individuals were collected at 35 days post-hatch and used for further analysis. Body shape of deformed individuals was narrower than that of normal individuals. Moreover, alcian blue-alizarin red staining revealed that vertebrae and the cranium were partly ossified and the appendicular skeleton and fin rays were not ossified even if those parts were completely ossified in normal individuals. DNA parentage analysis revealed that one darn and sire in lot 1 and a dam and two sires in lot 2 were significantly related to the deformed individuals. The dam and sire significantly related to the deformed individuals were the same in the two lots, even though parentages related to normal individuals were different in the two lots. Our results suggest that this type of deformity of Japanese flounder is caused by incomplete ossification and probably affected by genetic factors. Therefore, pedigree selection will be useful for prevention of this deformity. (C) 2013 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.aquaculture.2013.06.006

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Kelp grouper (Epinephelus bruneus) is an important aquaculture species in Japan, Korea and China. Mariculture production of the species has increased due to its high demand and market price. However, some problems affect kelp grouper aquaculture such as the low growth rate, high mortality due to diseases and low ability to survive the larval stage. To analyze economically important traits, genetic linkage maps are an effective tool. We constructed sex-specific linkage maps of kelp grouper using 222 microsatellite markers. The male map consisted of 23 linkage groups with 161 markers and the female map consisted of 25 linkage groups with 173 markers. The total lengths of the male and female maps were 650.5 cM and 944.4 cM, respectively, and the average intervals were 5.0 cM and 6.7 cM, respectively. The average ratio of recombination between males and females was 1:1.5. Moreover, syntenic sequence comparisons provided basic information of several potential candidate genes affecting organism physiological and biochemical reactions. Based on the linkage map, further quantitative trait loci (QTL) or candidate gene(s) detection can be anticipated to contribute to assist breeding programs of kelp grouper. In addition, by providing basic genome information of kelp grouper, the map provides a first step towards comparative QTL as well as comparative genome analyses with other groupers in the future. (C) 2013 Published by Elsevier B.V.

DOI： 10.1016/j.aquaculture.2013.07.041

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The population genetic structure of the messmate pipefish, Corythoichthys haematopterus, in the northwest Pacific was investigated based on the partial mitochondrial DNA cytochrome b (589 bp) and 16S rRNA (528 bp) region sequences of 108 individuals collected from six sites along the coast of the Japanese archipelago and one site on Mactan Island, the Philippines. A total of 60 and 28 haplotypes were obtained from the cytochrome b and 16S rRNA regions, respectively. Two genetically distinct lineages were detected: lineage A and B, which are separated by mean pairwise genetic distances of 23.3 and 14.1% in the partial cytochrome b and 16S rRNA genes, respectively. Such a huge genetic divergence between lineages, which is comparable to or even higher than the interspecific level, and the difference in their geographical distributions and habitat preferences suggests that they are distinct species, although there is no marked difference in their morphology. Haplotype network and gene and nucleotide diversity statistics indicate that the two lineages have different biogeographic histories: lineage A experienced rapid population expansion after a population bottleneck whereas lineage B has a long evolutionary history in a large stable population. In contrast, the levels of genetic variation among populations are relatively low in both lineages, probably because of frequent gene flow among populations resulting from the dispersal of pelagic larvae by the Kuroshio Current. These results indicate that past climatic events and contemporary oceanographic features have played a major role in establishing the population genetic structure of C. haematopterus. © 2013 Sogabe and Takagi.

DOI： 10.1186/2193-1801-2-408

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：応用生態工学会  

Population genetic structure of a common freshwater goby Rhinogobius fluviatilis in the Yoshino River and its tributaries was surveyed using three microsatellite loci to examine effects of dams. Allelic richness of the Akui and Sadamitsu River populations below the dams were high (15. 7, 15. 9) and that of the above the dams populations were low (10. 9 ∼13. 0). Heterozygosity was same level diversity between above and below dam populations (0. 870∼0. 890) except for Takeno river population (0. 788). Considerable genetic differences were observed between populations above and below the dams. Migratory history was also examined using otolith Sr/Ca ratio. The otolith Sr/Ca ratio analysis confirmed that the populations above the dams were landlocked by the dams. It was also suggested that some individuals below the dams do not undertake amphidromous migration.

DOI： 10.3825/ece.16.13

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Language：Japanese   Publisher：日本生物地理学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

To elucidate possible causes of skeletal malformations in larval Japanese flounder, we reared larvae fed rotifers enriched with three types of preserved (fresh, refrigerated, and frozen). The incidence of malformations at 50 days post hatch ranged from 14.5 to 38.5 % within the three experimental groups, and elongation of the lower jaw (LJ) was the most frequently observed malformation, ranging from 68 to 89 % of total malformations. We also investigated larval parentages using microsatellite markers. Parentage analysis of the fresh group showed that one sire and a pair generated significant numbers of LJ-elongated individuals. In the refrigerated group, one dam and two sires generated significant numbers of LJ-elongated individuals. In the frozen group, no broodstocks or pairs generated significant numbers of LJ-elongated individuals. Our results suggest that LJ elongation in Japanese flounder likely results from the application of different types of preserved during rotifer feeding stage. However, there is also some level of genetic influence associated with this deformity.

DOI： 10.1007/s12562-012-0494-4

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Artificially raised red sea breams with abnormal body shapes were morphologically characterized, and genetic investigations were conducted using microsatellite DNA markers. Normal and deformed individuals were collected at 68 days post-hatch. Deformed individuals were truncated because their dorsal regions were swelled and had scoliosis. A complex spinal column deformity consisting of a consecutive repetition of lordosis, kyphosis, and scoliosis from the head to the caudal fin was described by soft X-ray analysis. Four microsatellite markers, Pma- 2*, -3*, -4*, and -5*, were used for parentage analysis, and two dams and sires generated significant numbers of deformed individuals. Genetic investigations were also conducted and genotype frequency revealed that 90% of deformed individuals had an allele-113 on Pma-4*, even though 60% of normal individuals also had the allele. Our results suggest that genetic factors may be one of the causes of the deformed individuals identified as juveniles of a hatchery population of red sea bream.

DOI： 10.2331/suisan.78.62

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Artificially raised Japanese flounder exhibiting short body length were morphologically characterized and genetic investigations were conducted using microsatellite DNA. Individuals exhibiting short and normal body lengths were collected 60 days after hatching. Flounder with short bodies were morphologically analyzed by soft X-ray and divided into three groups, A, B and C, based upon body shapes and the positions of fused vertebrae. All short bodied individuals exhibited highly fused vertebrae. Main vertebrae fusion points were determined as follows: type A: all positions upon the vertebrae, type B: vertebra numbers 1 to 4 and 17 to 30, and type C: vertebra numbers 1 to 4 and 19 to 36. The frequency of these short body individuals observed in this study was 1.7%. Four microsatellite markers [Pol-1*, -3 *, -4*, -5*) were deployed for parentage analysis and 99.3% of specimens were successfully assigned. One each of dam and sire were significantly associated with type B short body individuals. Furthermore, we identified that the same sire was also significantly associated with type C short body individuals. These results suggest that genetic factors are probably one of the underlying factors of short body individuals identified in juvenile Japanese flounder.

DOI： 10.2331/suisan.78.429

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Influence of the dams in the Kamo and Nakayama River systems in the Ehime Prefecture on the common freshwater gobies Rhinogobius flumineus (non-diadromous species), R. sp. CB, R. fluviatilis and R. kurodai (amphidromous species) were surveyed using three microsatellite loci. Genetic variability was high in R. sp. CB (0. 900-0. 919) and low in R. flumineus (0.191-0. 278). Considerable genetic differences were observed among the species. The effects of a dam with a reservoir were examined for R. flumineus and R. sp. CB. In R. flumineus (non-diadromous species), genetic differences were not observed between populations above and below the Nakayama-gawa Dam (Nakayama R.). In R. sp. CB (amphidromous species), migratory history was also examined using otolith Sr/Ca ratio. The otolith Sr/Ca ratio analysis confirmed that the population above the Kurose Dam (Kamo R.) was landlocked by the dam. However, genetic heterogeneity was not observed between populations above and below the Kurose Dam.

DOI： 10.3825/ece.15.161

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Language：Japanese   Publisher：日本生物地理学会  

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Language：Japanese   Publisher：水産増殖談話会  

躯幹部の湾曲を伴うヒラメ形態異常（湾曲個体）の発生要因を調べるために、形態学的な観察とマイクロサテライトDNAによる遺伝指標の比較および親子鑑定を実施した。27個体の親魚を用いて種苗生産を行い、58日齢の正常個体40個体と湾曲個体53個体を得た。形態学的な観察から、湾曲個体においては神経棘と血管棘の異常形成が確認された。ヘテロ接合体率やアリル頻度といった遺伝指標は、正常個体と湾曲個体で大きな違いは確認されなかった。親子鑑定の結果から、正常個体は7個体のメス親魚と10個体のオス親魚からなる20組合せが、湾曲個体では5個体のメス親魚と9個体のオス親魚からなる17組合せが確認された。また、湾曲個体を多く生んでいる親魚は確認されなかった。以上の結果から、本湾曲個体は遺伝的な要因よりも、何らかの後天的な要因が強く影響しているものと推測される。

DOI： 10.11233/aquaculturesci.59.585

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

We isolated 12 candidate microsatellite loci from a small insert genomic DNA library of the Red-spotted grouper, Epinephelus akaara. Evaluation of full-sib progeny and unrelated individuals revealed that two of the 12 loci had distorted segregation states based on lack of adherence to Mendelian laws and Hardy-Weinberg equilibrium. We assessed polymorphism in the 10 loci using 20 unrelated individuals from a single population. The number of alleles per locus ranged from 2 to 19, allelic richness ranged from 2 to 17.6, and the observed heterozygosity ranged from 0.35 to 1.00 with no evidence of linkage disequilibrium.

DOI： 10.1007/s12686-011-9416-5

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Language：Japanese   Publisher：水産増殖談話会  

愛媛県宇和海に自生しているアコヤガイ野生集団と、天然採苗および人工採苗集団について、遺伝的多様性および集団間の異質性をアイソザイム分析により調査した。検出された19遺伝子座中15遺伝子座で多型が見られ、集団を通じて高い遺伝的変異性を保有していた。野生集団と天然採苗集団間の遺伝的分化の程度は低かったが（平均遺伝的距離D＝0.002-0.009）、人工採苗集団は他との間、および集団内で大きく分化していた（D＝0.014-0.024、および0.050）。人工採苗集団は異質性検定、分子階層分散分析によっても他との間、および集団内に異質性が検出された。符号検定では、天然採苗集団と人工採苗集団の一部にヘテロ接合体率の低下が検出された。本研究の結果より、天然アコヤガイに対する養殖種苗の遺伝的影響を積極的に支持する証拠は見いだされなかったが、遺伝的多様性が低く、異質性が高い人工採苗集団が天然海域の遺伝子組成に与える影響が懸念された。

DOI： 10.11233/aquaculturesci.59.411

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC FISHERIES SCIENCE  

Transparent individuals have been identified in juveniles of a hatchery population of red sea bream. This study characterized the numbers of melanophores, xantphores, and erythrophores, in normal and transparent individuals. The transparent individuals were partly transparent at the 40 day-post-hatch stage and the numbers of all chromatophores were significantly lower. In 100 day-post-hatch juveniles, the transparent individuals exhibited slight differences to normal individuals. However, the numbers of xantphores and erythrophores remained significantly lower. The parentage of normal and transparent individuals was identified by five microsatellite loci. Analysis indicated that normal individuals were generated from 6 female and 8 male parents, and 15 parental pairs were identified. However, all transparent individuals were generated from 1 female with 5 male parents. Our results suggest that the transparent individuals identified in larvae of the hatchery population of red sea bream had arisen via genetic effects.

DOI： 10.2331/suisan.77.630

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

We examined habitat factors related to the distribution and abundance of the spinous loach Cobitis shikokuensis, an endangered benthic fish, in the Shigenobu River system, southwestern Japan. In the study river, the spinous loach was distributed widely along the main stem, from headwater to near the mouth, whereas it was rarely found in tributary streams. Classification tree analysis showed that the presence/absence of spinous loach was explained by a combination of percent pebble and length of river fragment between artificial barriers. Spinous loach incidence was high in sites with abundant pebble (> 27.7%), but low in sites with short river fragment (a parts per thousand currency sign0.97 km) even if pebbles were abundant. A regression tree model for loach density retained only percent pebble as a single best predictor, with sites with higher percent pebble (> 40.4%) having higher density. These results suggest that substrate condition is an important factor determining the distribution and abundance of spinous loach and also that habitat fragmentation by artificial barriers has great potential to threaten the spinous loach population in this river. Considering the highly fragmented situation of the study river and prevention of upstream migration by barriers, we conclude that maintenance of suitable habitats in upper reaches has high priority for conservation of the spinous loach.

DOI： 10.1007/s10228-011-0208-4

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Ecology and Civil Engineering Society  

Population genetic structure and migratory history of the common freshwater goby Rhinogobius sp. LD in the Shigenobu River system were surveyed by using three microsatellite loci and otolith Sr /Ca ratio, to examine effects of two types of dams, a single dam with a reservoir (Ishite-gawa Dam) and multiple erosion-control dams without reservoir. Genetic variabilities were high in the Shigenobu River populations and the estimated hetero zygosity ranged from 0.843 to 0.889. Considerable genetic differences were observed between populations above Ishite-gawa Dam (two sites) and populations of the other nine sites (above multiple erosion-control dams), within which the genetic heterogeneity was not observed. These results suggested that the populations above Ishite-gawa Dam were landlocked and differentiated genetically by the dam, whereas the goby populations were not isolated by multiple erosion-control dams. This was supported by the otolith Sr /Ca analysis, which indicated that the goby individuals sampled from the sites above the Ishitegawa Dam had not experienced saltwater whereas those above multiple erosion-control dams had experienced. In addition, Sr /Ca analysis suggested that a population just below the Ishitegawa Dam consisted of both landlocked (drifted from the reservoir) and sea-migratory individuals.

DOI： 10.3825/ece.14.35

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Language：Japanese   Publisher：水産増殖談話会  

種苗生産場で生じたヒラメの逆位個体について、マイクロサテライトDNAマーカーを用いた遺伝的多様度の解析およびDNA親子鑑定により、発生要因の推定を行った。種苗生産には17個体の親魚を用い、96日齢時に正常個体52個体と逆位個体49個体を得た。ヘテロ接合体（観察値、期待値、観察値／期待値）およびアリル頻度において、正常個体群と逆位個体群で違いは見られなかった。マイクロサテライトマーカー座の多型により全ての親子関係を判別できた。親子鑑定の結果から、正常個体は7個体のメス親魚と5個体のオス親魚からなる14組から生じていることが分かり、また逆位個体は7個体のメス親魚と7個体のオス親魚からなる18組から生じていることが分かった。１個体のメス親魚は他の親魚よりも高い割合で逆位個体を産んでいることがわかった。以上の結果から、本異常の発生要因は後天的な影響が強いものの、一部のメス親魚は遺伝的もしくは他の母性要因により逆位個体を産生していることが示唆された。

DOI： 10.11233/aquaculturesci.58.441

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Language：Japanese   Publisher：The Ichthyological Society of Japan  

Variations in genetic and morphological characteristics were investigated in two populations of the exotic pond loach, Paramisgurnus dabryanus, which has invaded rice fields in Kuma-kougen Town, Ehime Prefecture. A sequence analysis of the mitochondrial DNA control region of 46 individuals collectedf rom two sampling sites (Higashi-myoujin and Koudono, separation distance1.6 km) revealed two divergent clades (average nucleotide divergence: 15%)representing separate introductions: Group 1 (four haplotypes), related to P. dabryanus, and Group 2 (two haplotypes), related to Misgurnus anguillicaudatus, as a result of mitochondrial DNA introgression. In 29 of the 46 specimens, which included individuals of both genetic clades, four of 13 morphological characteristics(relative to body size) (head length, pre-pectoral length, dorsal fin base length and caudal peduncle depth) differed significantly (ANOVA, df 28, P 0.01-0.05)between populations, but not between genetic clades. Haplotype constitutions differed significantly between sampling sites (exact test, P 0.001), diversities being greater in Koudono which is located downstream of Higashi-myoujin. The existence of genetically divergent clades among the specimens suggested that the early introductions of this species to Japan originated from several localities.

DOI： 10.11369/jji.57.125

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Language：Japanese  

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Language：Japanese   Publisher：水産増殖談話会  

Color variations were identified in a hatchery population of Japanese flounder: body color was yellowish compared to normal individuals. This study characterized red, green, blue, and luminance body color components in normal and yellowish individuals. Further studies estimated microsatellite DNA marker-based relationships using sibship reconstruction approaches. Color components of red and green in yellowish individuals were significantly higher than that of normal individuals. However, the blue component of yellowish individuals was significantly lower than that of normal individuals. Four microsatellite loci were used for sibship reconstruction. Results indicated that most yellowish individuals were generated predominantly by two half-sibs. Sibship reconstruction suggested that the yellowish individuals identified in a hatchery population of Japanese flounder may have arisen via genetic effects. Assessing the parentage of abnormal fish used in seed production, and the removal of parents generating abnormal fish, would represent a new strategy for retrospective selective breeding.

DOI： 10.11233/aquaculturesci.58.345

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Language：Japanese   Publisher：The Ichthyological Society of Japan  

The genetic structure of natural populations of Misgurnus anguillicaudatus in Ehime Prefecture and the impact of introduced specimens were investigated by partial mitochondrial DNA sequence analysis. A total of 452 specimens from 59 samples were analyzed, comprising 49 populations from eight Prefectures (including 38 from Ehime Prefecture), six populations from Korea, and four samples of food material and fish bait obtained in Ehime Prefecture. Fifty-one haplotypes were identified, falling into two large clades (B-1 and B-2; average nucleotide divergence: 4.2 0.6%), which formed a sister lineage of Paramisgurnus dabrianus (bootstrap value: 100%). Among clade B-1 members, the haplotypes from 25 populations representing 15 water systems in Ehime Prefecture revealed genetic divergence correlated with their geographic distribution (nucleotide divergence distance: 0.3-4.0%). The maximum parsimony network of these haplotypes suggested one major haplotype (89% of the clade's individuals in Ehime Prefecture) with genetically close satellites present in specific rivers or locations. Some divergent haplotypes, somewhat similar to haplotypes from other Prefectures or from Korea, may have resulted from artificial introductions into Ehime. In clade B- 2, five of the 17 haplotypes were distributed in only four river systems in Ehime Prefecture, without any apparent relation to geographic features, and showed genetic identity or closeness to haplotypes of imported and commercial (food material, fish bait) lines. These results are strongly indicative of recent artificial introductions of alien individuals into natural waters in Ehime Prefecture, resulting in serious genetic disturbances.* Corresponding author: Tarumi Branch, South Ehime Fisheries Research Center, Ehime University, Tarumi, Matsuyama, Ehime 790-8566, Japan (e-mail: takagi@agr.ehime-u.ac.jp)

DOI： 10.11369/jji.57.13

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Publisher：日本水産増殖学会  

Genetic variability and disturbance of the Japanese common loach <I>Misgurnus anguilicaudatus</I> were surveyed by using 11 samples from 9 wild populations and two artificial stocks, based on 3 microsatellite loci. Investigation of these marker loci of the loach sample showed the difference of genetic variability from each other. The estimated heterozygosity ranged from 0.435 to 0.834. Ratio of observed and estimated heterozygosity was very low in Hokota reservoir samples, fishing item shop and food market. Genetic divergence among the loach samples was observed in the genotype and allele frequencies at the marker loci. Considerable genetic difference was observed between Hokota reservoir samples and the other wild samples. Meanwhile, Genetic distance among Hokota reservoir samples, fishing item shop and food market was very low. The results suggested that the present distribution of the loach in Ehime Prefecture was received several degree of invasion originated from artificial stocks. The microsatellite markers showed a potential as indicators to evaluate genetic variability and to trace genetic changes in Japanese common loach.

DOI： 10.11233/aquaculturesci.58.113

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

This study was performed to obtain information on the occurrence of multiple paternities in three species of viviparous Japanese surfperch using allelic markers of microsatellite DNA loci. Direct evidence for multiple fertilizations was established by reconstructing paternal genotypes from the progeny of gravid females. Multiple paternities were ascertained in five of 10 broods of Ditrema temmincki and in three of nine broods of Neoditrema ransonneti, but not in Ditrema viride. The number of patrilines detected in the progeny of D. temmincki and N. ransonneti females were two or three, respectively, as determined by the GERUD v2.0 algorithm for reconstructing parental genotypes from half-sib progeny arrays.

DOI： 10.1111/j.1444-2906.2008.01615.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL PUBLISHING  

Thirteen microsatellite loci were isolated from a size-selected genomic library of the surfperch (Ditrema temmincki Bleeker). All loci displayed a high degree of length polymorphism, as observed in the total number of alleles per locus (two to 23) and a high degree of estimated heterozygosity ranging from 0.080 to 0.893. The primers developed for D. temmincki were also tested for their ability to amplify homologous sequences in D. viride and Neoditrema ransonetii. Distinct differences were observed among three species of surfperches, in both genetic variability and the frequency distribution of the alleles.

DOI： 10.1111/j.1755-0998.2008.02145.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ZOOLOGICAL SOC JAPAN  

Genetic diversity and genetic divergence were investigated in the landlocked goby Rhinogobius sp. YB by analysis of seven microsatellite DNA loci and the mtDNA control region sequence, and were compared with those of the closely related amphidromous species Rhinogobius sp. DA. Samples of Rhinogobius sp. YB and Rhinogobius sp. DA were collected from seven and four rivers, respectively. All pairwise F-st tests based on microsatellite DNA showed significant genetic differences, except for one pair of populations of Rhinogobius sp. DA (P<0.00064, alpha=78). The average Nei's genetic distance was 0.616 in Rhinogobius sp. YB and 0.394 in Rhinogobius sp. DA. Forty-two haplotypes were detected in both species, and almost all Rhinogobius sp. YB populations included different haplotypes. The means of allelic richness, Ho, and He in Rhinogobius sp. YB (2.057, 0.149, and 0.156, respectively) were significantly lower than in Rhinogobius sp. DA (4.868, 0.366, and 0.403, respectively; P<0.05). The high genetic divergence and low genetic diversity in Rhinogobius sp. YB may have resulted from repeated colonizations of rivers by different founders. Efforts to conserve genetic resources should take these evolutionarily significant units (ESU) of Rhinogobius sp. YB into account. The genetic markers used in this study provide simple and highly informative indicators for Rhinogobius sp. YB population management.

DOI： 10.2108/zsj.25.391

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Language：Japanese   Publisher：日本水産増殖学会  

Genetic variability and divergence of the largemouth bass, <I>Micropterus salmoides</I>invaded Ehime Prefecture, Japan, were surveyed by using 10 samples from seven reservoirs, based on 5 microsatellite loci. Investigation of these marker loci of the largemouth bass sample showed the difference of genetic variability from each other. The estimated heterozygosity ranged from 0.231 to 0.487. Genetic divergence among the largemouth bass samples was observed in the genotype and allele frequencies at the marker loci. Considerable genetic difference was observed within Nomura samples between 2003 and 2004, 2005 year stocks in the population pairwise FST. Relationship between geographic and genetic similarities was not observed among some samples. The results suggested that the present distribution of largemouth bass in Ehime Prefecture originated from several degree of artificial introduction. Occurrence of recent introduction of largemouth bass among the inland waters of Ehime Prefecture was also suggested. The microsatellite markers showed a potential as indicators to evaluate genetic variability and to trace genetic changes in largemouth bass.

DOI： 10.11233/aquaculturesci1953.55.237

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Language：English   Publisher：Japanese Society for Aquaculture Science  

Genetic variability of wild and cultured black tiger shrimp populations in Thailand was studied by the microsatellite DNA technique. In wild populations from the Gulf of Thailand, South Thailand, and South Myanmar, high genetic variability was detected. Mendelian inheritances were evaluated in juveniles from 4 farms. In three of the farms, more than 4 genotypes were identified, indicating that the farms did not use single parental line. Genetic approaches are required to achieve stable production rates in black tiger shrimp cultures.

DOI： 10.11233/aquaculturesci1953.55.131

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL PUBLISHING  

The Japanese population of the cyprinid minnow Aphyocypris chinensis is nearing extinction in the wild. The genetic diversity of three microsatellite loci in five captive populations was investigated, and an effective breeding strategy to reduce inbreeding from pairwise relatedness (R-xy) between each captive line is discussed. The average number of alleles ranged 2.33-4.67 and the average heterozygosity ranged 0.283-0.602. The pairwise relatedness observed in most combinations showed a significant decrease between the populations. It is suggested that exchange of individuals between different breeding lines should effectively stop inbreeding. Studies show that the effective population size (N-e) estimated from the number of parental individuals was 8.54 in one captive population, which is insufficient to maintain genetic diversity. It is recommended that more parental individuals should be used, and to exchange fish in a rotating mating mode between institutions participating in captive breeding of A. chinensis.

DOI： 10.1111/j.1444-2906.2007.01313.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

The genetic diversity and population structure of Rhinogobius sp. BB, the fluvial landlocked endangered goby, were investigated and were compared with those of the closely related amphidromous Rhinogobius sp. MO at 11 microsatellite loci. Specimens of Rhinogobius sp. BB were collected from the Genka and Takae-A rivers, and those of Rhinogobius sp. MO were collected from the Genka and Suginda rivers in Okinawa Island. At 11 microsatellite loci, the two populations of Rhinogobius sp. BB showed lower variation than the two Rhinogobius sp. MO populations: the average number of alleles was 3.6 and 2.0 vs. 8.6 and 7.6, respectively; and the observed heterozygosity was 0.263 and 0.281 vs. 0.440 and 0.545, respectively. Pairwise F-st tests showed significant differences (P < 0.001) among the populations: F-st was 0.525 between the two Rhinogobius sp. BB populations, 0.079 between the two Rhinogobius sp. MO populations, and varied from 0.456 to 0.462 for comparisons among Rhinogobius sp. BB and MO. Nei's genetic distance between the two Rhinogobius sp. BB populations is extremely large (0.604) compared with that between the two Rhinogobius sp. MO populations (0.126). The two populations of Rhinogobius sp. BB are genetically divergent, and they have extremely low genetic diversity. Therefore, the conservation of Rhinogobius sp. BB in Okinawa Island requires the assessment of each river's population.

DOI： 10.1007/s10228-005-0284-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL PUBLISHING LTD  

The Rhinogobius species complex (Pisces: Gobiidae) includes great variation in colour, morphology and ecological form. In particular, R. sp. OR (Orange type) exhibits some of the greatest colour variation among the species complex, although the genetic relationships among the variations in this fish remain unclear. Thirteen microsatellite loci were identified from R. sp. OR, and all loci were polymorphic with two to 17 alleles per locus. Observed heterozygosity ranged from 0.1 to 0.9, while the expected heterozygosity ranged from 0.19 to 0.96. Multiplex polymerase chain reaction reaction (PCR) were optimized. All loci except Rhi-5 conform to Hardy-Weinberg equilibrium (P > 0.05).

DOI： 10.1111/j.1471-8286.2004.00677.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC FISHERIES SCIENCE  

The existence and distribution patterns of microsatellites in the tiger puffer genome were evaluated utilizing DNA databank entries. Microsatellite regions amounted to only 0.96% of the 22.5 million bp included in the tiger puffer database. Di-nucleotide repeats were most common (90.1 % of all microsatellites). Twelve microsatellite loci were isolated from the entries. Analysis of genetic polymorphism at these loci in the wild tiger puffer (n = 50) revealed a high degree of length polymorphisms, in which the number of alleles per locus ranged from 11 to 34. The expected heterozygosity was between 0.869 and 0.953. Mendelian inheritance was demonstrated in all but two loci (which seemed to include null alleles) by analysis of genotype ratios in the offspring of a single captive. Probability of identity of all loci ranged from 0.007 to 0.028. Band sharing index was low (0.119) in wild tiger puffer and high in the offspring of the captive (0.525). These results indicate the usefulness of the microsatellite markers identified for future population analyzes in tiger puffer.

DOI： 10.1111/j.0919-9268.2003.00732.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC FISHERIES SCIENCE  

DOI： 10.1111/j.0919-9268.2003.00761.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER-VERLAG TOKYO  

Aphyocypris chinensis has drastically decreased in Japan and has been designated as an endangered species. Using allozyme analysis, we tested the genetic diversity of A. chinensis strains maintained by five institutions in Japan for conservation purposes. Twelve loci encoding eight enzymes were scored. Alleles per locus ranged from 1 to 1.250, proportion of polyallelic loci was 0 to 0.250, and heterozygosity varied between 0 and 0.128. Genetic variations were found in the strains of three institutions, although no genetic variation was observed in the strains of the other two. Genetic diversity of a strain kept by the Hinamoroko Foster-parent Club was the highest, and even exceeded that of other freshwater fishes.

DOI： 10.1007/s102280300013

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Language：Japanese   Publisher：水産育種研究会  

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Language：Japanese   Publisher：水産大学校  

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Language：Japanese   Publisher：水産育種研究会  

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Language：Chinese   Publisher：JAPANESE SOC FISHERIES SCIENCE  

DOI： 10.2331/suisan.67.610

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Language：Japanese   Publisher：水産育種研究会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Hatchery broodstocks used for genetic conservation or aquaculture may represent their ancestral gene pools rather poorly. This is especially likely when the fish that found a broodstock are close relatives of each other. We re-analysed microsatellite data from a breeding experiment on red sea bream to demonstrate how lost genetic variation might be recovered when gene frequencies have been distorted by consanguineous founders in a hatchery. A minimal-kinship criterion based on a relatedness estimator was used to select subsets of breeders which represented the maximum number of founder lineages (i.e., carried the fewest identical copies of ancestral genes). UPGMA clustering of Nei's genetic distances grouped these selected subsets with the parental gene pool, rather than with the entire, highly 'drifted' offspring generation. The selected subsets also captured much of the expected heterozygosity and allelic diversity of the parental gene pool. Independent pedigree data on the same fish showed that the selected subsets had more contributing parents and more founder equivalents than random subsets of the same size. The estimated mean coancestry was lower in the selected subsets, meaning that inbreeding in subsequent generations would be lower if they were used as breeders. The procedure appears suitable for reducing the genetic distortion due to consanguineous and over-represented founders of a hatchery gene pool.

DOI： 10.1023/A:1013772205330

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Language：Japanese   Publisher：水産育種研究会  

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Six (CA)n and one (CT)n(CA)n microsatellite loci were isolated from a size-selected genomic library of ayu Plecoglossus altivelis altivelis. Primers for PCR amplification were designed for the microsatellite loci and the loci characterized by screening polymorphisms in the amphidromous form of ayu. All loci displayed a high degree of length polymorphism, as observed in the total number of alleles per locus (2-21), and a high degree of heterozygosity ranging from 0.414-1.000. Distinct differences were observed between amphidromous and landlocked populations of ayu, in the frequency distributions of the alleles. The primers developed for ayu Plecoglossus a. altivelis were also tested for their ability to amplify homologous sequences in endangered subspecies of Ryukyu-ayu, Plecoglossus altivelis ryukyuensis. Genetic variability was obviously low in both average number of alleles per locus and average heterozygosities. These microsatellite loci show great potential as indicators for genetic variability and divergence among populations of ayu species.

DOI： 10.2331/fishsci.65.507

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Microsatellite loci were isolated from a size-selected genomic library of Pacific northern tuna Thunnus thynnus orientalis, and PCR primer sets to amplify four loci were designed. Investigation on genetic polymorphism at these loci in the Pacific northern bluefin tuna sample (n=35-40) revealed high degree of length polymorphisms in all loci, in which number of alleles per locus ranged from 8 to 23 and observed heterozygosity from 0.533 to 1. These primer sets were applied to Atlantic northern bluefin tuna T. t. thynnus, albacore T. alalunga, bigeye tuna T. obesus and yellowfin tuna T. albacares, detecting polymorphism in all loci comparable with those of Pacific northern bluefin tuna. Significant differences in the allele frequency were observed between Pacific and Atlantic northern bluefin tuna samples. These primer sets developed for Pacific northern bluefin tuna appeared to be useful for amplifying homologous microsatellite loci in the other Thunnus tuna species, and may have great potential as indicators for genetic variability within and between samples of tuna species of the genus Thunnus.

DOI： 10.2331/fishsci.65.571

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Language：Japanese   Publisher：水産増殖談話会  

DOI： 10.11233/aquaculturesci1953.47.257

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Stock enhancement programs that use a small number of breeders for the production of hatchery-reared juveniles to be released to the environment, may have negative effects on the genetic diversity of wild populations due to a reduced genetic variability of the released stock. This study compared the genetic diversity of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement with that of their broodstock. Its pedigree was also traced, using four to five microsatellite DNA markers, to quantify the actual number of reproducing parents. Then, the effective number of contributing parents (N-e) and the inbreeding coefficient were estimated. It was found that the genetic diversity of the hatchery-reared stock in terms of the mean observed heterozygosity (H-o = 0.856), was not significant different (P > 0.05) than that of the broodstock (H-o = 0.841). However, significant differences (P < 0.05) were found in the number of alleles per locus and in the frequencies among some major alleles of the two stocks. The pedigree of more than 73% of the progeny was effectively determined and at least 91 breeders tout of 250) actually reproduced. The estimated N-e was N-e = 63.7, consequently the estimated inbreeding coefficient was less than 0.8%. The results provide no evidence to consider a loss of genetic variation of the hatchery-reared stock, and a discussion on the possible effects of its release is presented. (C) 1999 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0044-8486(98)00469-4

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Language：Japanese   Publishing type：Doctoral thesis   Publisher：水産大学校  

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Other Link： http://ypir.lib.yamaguchi-u.ac.jp/fu/metadata/474

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Blackwell Publishing  

Three microsatellite loci, Cca-17*, Cca-21*, and Cca-30*, were isolated from a partial genome library of common carp Cyprinus carpio. Primers for PCR amplification of template DNA were designed based on the unique sequences flanking each motif. The total number of alleles detected from nishikigoi and wild type common carp population were five, six and nine at loci Cca-17*, Cca-21*, and Cca-30*, respectively. Inheritance was shown to be Mendelian by analysis of genotype ratio in Fl off-spring of six families of nishikigoi. Allele *69 at locus Cca-21* and allele *266 at locus Cca-30* were detected only in wild type common carp with frequencies of 0.304 and 0.458, respectively, while allele *288 was observed only in the nishikigoi with the frequencies ranged from 0.600-0.610.

DOI： 10.2331/fishsci.65.235

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Blackwell Publishing  

DOI： 10.2331/fishsci.65.486

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC SCI FISHERIES SCI  

DOI： 10.2331/fishsci.64.836

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Language：Japanese   Publisher：水産育種研究会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC SCI FISHERIES TOKYO UNIV FISHERIES  

Restriction fragment length polymorphism (RFLP) analysis of the mitochondrial DNA (mtDNA) D-loop region was used to compare the genetic diversity of 5 strains of red sea bream Pagrus major. Composite haplotypes, representing the information from 6 restriction endonucleases, were generated for samples of 35-40 fish from each strain. The components of haplotypes in the cultured strains differed considerably from those of the natural population. This is remarkable from the point of view of haplotype specialization. The results of a chi-square randomization test, in which differences between the strains were very significant, also showed that the specializations of haplotype were accelerated. Haplotypes occurred at a rate of 0.11 to 0.29 in the cultured strains, and 0.33 in the natural population. Haplotypic diversities were 0.34 to 0.84 in the cultured strains, and 0.86 in the natural population. The UPGMA clustering, based on pure mean nucleotide sequence divergence, differed entirely from the UPGMA clustering based on the allozyme genetic distance. For this reason, it is thought that RFLP analysis of the mtDNA D-loop region could sensitively detect the bottleneck effect caused by a decrease in the effective number of parents. The pure mean nucleotide sequence divergences between the cultured strains were wider (17 times) and higher (29 times) than the values between the natural population. Thus, RFLP analysis of the mtDNA D-loop region was thought to be a good method for monitoring the genetic changes that occur during selective breeding.

DOI： 10.2331/fishsci.63.344

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

Five (GT./CA)(n) microsatellite loci were isolated from a size-selected genomic library of red sea bream (Paqrus major). Primers for PCR amplification were constructed for the microsatellite loci and the loci characterized by screening polymorphisms in three wild populations of the red sea bream. All loci displayed a high degree of length polymorphism, as observed in the total number of alleles per locus (16-32), and a high degree of heterozygosity ranging from 0.675-0.907. Distinct differences were observed among three wild populations of red sea bream collected from coastal waters of Japan, both in the average number of alleles per locus and the frequency distributions of the alleles.
The primers developed for red sea bream were also tested for their ability to amplify homologous sequences from 5 closely related species of Sparidae.
These microsatellite loci show great potential as indicators for genetic variability and divergence among subpopulations of Pagrus major, and to a lesser degree with some of the related species tested.

DOI： 10.2331/fishsci.63.199

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC SCI FISHERIES TOKYO UNIV FISHERIES  

DOI： 10.2331/fishsci.63.149

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Language：English  

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Language：Japanese   Publisher：水産育種研究会  

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Language：Japanese   Publisher：動物遺伝研究会  

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Language：English  

DOI： 10.11233/aquaculturesci1953.44.299

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Other Link： http://agriknowledge.affrc.go.jp/RN/2010571422

Language：Japanese   Publisher：高知大学黒潮圏研究所  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

Four clonal lines of ayu, Plecoglossus altivelis, were produced from mitotic-gynogenetic diploids, mixed before hatching and reared communally. After 9 months, the clonal fish were sacrificed for measurement of body size, morphometric relationships, and meristic counts. DNA fingerprinting was used to confirm the clonal nature of the fish and to identify the clonal line of origin for each fish. Significant differences were observed among clonal lines for almost all body size, morphometric and meristic measures. Such differences are suggested to represent genotypic difference among clonal lines given the common environmental conditions provided to all the experimental groups, assuming that the genotype-environment interaction was negligible. By applying the human twin model, genetic and environmental variances in the clonal population was estimated after the clonal lines were separated by DNA fingerprinting. Heritability estimates for data collected at 9 months were relatively high for body size and varied from low to high in meristic and morphometric traits. These results suggest the possible usage of clonal lines as a control fish for estimation of heritability of traits important to aquaculture.

DOI： 10.1016/0044-8486(95)01204-4

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Language：Japanese   Publisher：水産増殖談話会  

DOI： 10.11233/aquaculturesci1953.43.491

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC SCI FISHERIES TOKYO UNIV FISHERIES  

DNA fingerprint (DNA-FP) was applied for confirmation and identification of clones induced by the suppression of the first cleavage in ayu, Plecoglossus altivelis. The samples used were 2 homozygous clonal lines, 3 successive homozygous combinations and compared radioisotope (RI) and non-radioisotope (Non-RI) labelled probes to get clear DNA-FP.
The clear DNA fingerprints were obtained by using YNZ 22, 33.15 and 33.6 probes with Nae III, Msp I and HinfI restriction enzymes. In these DNA-FPs, the bands were separated distinctly throughout the membrane in both higher and lower molecular weight regions. The DNA-FP bands obtained with the Non-RI labelled 33.15 probes were as intense and clearly separated as those obtained with the RI method. All the fragments were shared among individuals within the same clonal line, but the pattern of bands detected was significantly different between clonal lines.
It was confirmed that DNA-FP is effective for the identification of clonal lines. DNA-FP pattern by Non-RI labelled probe would be suitable for wide applications in studies on inbreeding and identification of individuals and families.

DOI： 10.2331/fishsci.61.909

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Language：Japanese   Publisher：水産育種研究会  

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Language：English   Publisher：JAPAN SOC SCI FISHERIES TOKYO UNIV FISHERIES  

DOI： 10.2331/fishsci.61.884

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Language：Japanese   Publisher：水産増殖談話会  

DOI： 10.11233/aquaculturesci1953.43.97

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Language：Japanese   Publisher：水産育種研究会  

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Language：Japanese   Publisher：水産育種研究会  

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Language：Japanese   Publisher：Japanese Society for Aquaculture Science  

Distribution of kamakiri a river sculpin, <I>Cottus kazika</I> was surveyed in the lower reaches of 80 rivers of Kochi Prefecture in Japan during September to November 1991 by underwater observation. The kamakiri was found in the lower reaches of rivers located in the east and west of Kochi Prefecture. The fish was little observed in the lower reaches of rivers located in middle part of Kochi Prefecture. It is suspected that the fish has been extincted in these rivers where the water was polluted by waste water from factories and houses.

DOI： 10.11233/aquaculturesci1953.40.329

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC SCI FISHERIES TOKYO UNIV FISHERIES  

We observed the behaviours of released juvenile red sea bream Pagrus major, stocked in a small fishing port. Three types of individuals showing distinct behaviours were distinguished: 1) territorial individuals, 2) territorylike individuals, 3) individuals keeping no restricted cruising area. A portunid crab Thalamita sima and/or gobiid fishes were observed to dig the sandy substratum to make their shelters at the center of the defended area of the territorial individuals. This behaviour might make deep burrowing benthos to which P. major cannot generally gain access readily available to the territorial ones. The territorial individuals tended to defend smaller area, attack more frequently and show smaller number of feeding bout than the territorylike ones. Concerning the territorylike individuals, as the density became lower, the defended area of each individual became larger, but the number of both attacks and feedings smaller.

DOI： 10.2331/suisan.57.1

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Language：Japanese   Publisher：湊文社  

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Language：Japanese   Publisher：福山大学  

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Language：English   Publisher：Zoological Society of Japan  

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Other Link： http://id.nii.ac.jp/1141/00038365/

Language：Japanese   Publisher：The malacological society of Japan  

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Presentation type：Oral presentation (general)  

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