Tochigi Prefectural Fisheries Experimental Station

Uranouchi Inlet, situated on the Pacific coast of southwestern Japan, has been a highly enclosed inlet known for yellowtail farming since 1959. Since the 1980s, harmful algal blooms (HABs) have repeatedly occurred, resulting in mass mortality of fish and shellfish. In the sediment at the inlet, the resulting cysts of the HAB species may be preserved, which reflects the history of HAB events. However, the vertical distributions of HAB species in sediment have not been elucidated. In this study, core sediment samples were analyzed by metabarcoding. The dating of each sample was cited from previous study dating the same samples. The findings revealed the presence of eleven HAB species, with notable shifts from approximately 1977–1988. The timing of the shifts corresponded to that of the development of aquaculture and the resulting eutrophication. Vertical core metabarcoding provides footprints of how HAB species composition may be influenced by anthropogenic environmental changes.

The commercial value of snow crabs and red snow crabs is low immediately after molting due to low meat quantities and soft shells. As time passes, the meat content and shell hardness increase, making them more valuable. In Japanese market, male snow crabs are arbitrary divided into soft and hard shells. Previous studies also categorized crabs soft-shell and hard-shell arbitrarily and compared the quality between the two groups. A durometer and a penetrometer have been used to determine the shell hardness in the stock management of the snow crab and the red snow crab, but they destroy the crab shells. In the present study, we developed a new non-destructive technique using a portable near-infrared spectrometer to evaluate the dry matter content of pereiopods, which were correlated with the shell hardness. The cheliped was found to be sufficient for measurement in both species, providing a wider range of values and higher precision than the first walking leg. This non-destructive technique would be valuable for assessing both commercial value and the approximate time since the terminal molt of snow crabs and red snow crabs.

ABSTRACT Insufficient sulfur (S) can reduce rice yield under certain soil conditions. The availability of S in paddy soils is determined by the concentrations of inorganic S and some heavy metals that react with sulfide ions to form sparingly soluble sulfides. In order to evaluate the S fertility of paddy soils, a predictive model was formulated to simulate the formation of sulfides and the effect of heavy metal content on the concentration of sulfate ions (SO4 2-) in the soil solution under reducing conditions. The basic computational algorithm of the model was an iterative method incorporating the equilibria of major aqueous species, sparingly soluble salts, and soil adsorption. A field survey was also conducted to evaluate S availability in actual rice paddy soils. SO4 2- and heavy metal contents were measured in 250 paddy fields located in central Japan. The model calculation using the field survey results showed that as the redox potential (Eh) decreases from −80 to −170 mV, sulfide-forming metals (Ni, Cu, Zn, Cd, and Pb) take precedence over iron (Fe) in sulfide formation. The major sulfides present were chalcocite (Cu2S), greenockite (CdS), sphalerite (ZnS), galena (PbS), chalcopyrite (CuFeS) and α-NiS, Due to their predominance in paddy soil, zinc (Zn) and copper (Cu) have a strong influence on the reduction of SO4 2- concentration. The formation of metal sulfides increases the Eh value corresponding to the critical SO4 2- concentration and decreases the S availability under the individual Eh condition. The model calculation also showed that an increase in sulfide-forming metal content leads to S deficiency, even if the SO4 2- content is not exceeded. Model calculations for each geographical division against the field survey results suggest that S deficiency is more likely to occur in lowland paddy fields formed by river sediments than in Andisols on terraces.

We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP. Meanwhile, DK had the highest prediction accuracy for NIRS-based C18:1 and MUFA, but the difference in accuracies between DK and KAML was slight. For all traits, accuracies of RF and CNN were lower than those of GBLUP. The KAML extends GBLUP methods, of which marker effects are weighted, and involves only additive genetic effects; whereas machine learning methods capture non-additive genetic effects. Thus, KAML is the most suitable method for breeding of fatty acid composition in Japanese Black cattle.

Japanese flounder (Paralichthys olivaceus) is an important marine fish species of both fisheries and aquaculture in Northeast Asia. The commercial interest for all-female progenies due to several sex-related traits has prompted basic research on the mechanisms of sex determination in this species. By conducting a linkage analysis of the sex-determining locus, we initially identified 12 microsatellite markers linked to sex in 11 scaffolds, whose localization was restricted to a specific region of linkage group 9. Sequence analysis of this region identified 181 genes based on the UniProt database annotations. Among them, the amh gene was considered a potential candidate for sex determination because this gene is known to have taken over the role of sex determination in many teleosts. An in-depth sequence analysis of both the coding and non-coding regions of amh in XX and XY individuals detected nine SNPs linked with maleness. However, because these substitutions were synonymous, the upstream and downstream regions of amh were also investigated and a male-specific variant with deletions in the promoter region was detected. This truncated Y-specific amh variant was named amhy, and the amh shared by both sexes was named amhx. The association analysis using both females and males of the genotypic sex inferred by the presence/absence of amhy found complete association with phenotypic sex and genotype. Gene expression analysis in larvae derived from a single-pair progeny by quantitative real-time PCR detected amhy transcripts in the larval trunks between 20 and 100 days after hatching only in XY larvae. Localization of amhy by in situ hybridization was detected in presumptive Sertoli cells of XY gonads. Expression of amhx was almost undetectable in both XX and XY genotypes. Loss of Amh function by CRISPR-Cas9 induced male-to-female sex reversal, indicating that this gene was necessary for the masculinization of XY individuals. In conclusion, the complete linkage of amhy with males, its early expression in XY gonads before testicular differentiation, and the induction of sex reversal by loss-of-function mutation support the view that amhy is the sex-determining gene in this species.

We detected three chicken astrovirus strains in 4-day-old broiler chickens with high mortality and visceral gout and one strain from 150-day-old hens without clinical symptoms in Saga prefecture, Japan. Phylogenetic analysis based on ORF2 amino acid sequences revealed that the strains from the visceral gout cases belonged to subgroup Bi, and the strain from hens without clinical symptoms belonged to subgroup Aiii. Our study showed that CAstV had infiltrated into Saga prefecture, Japan. This is the first report of CAstV in Japan.

イチゴ萎黄病（Fusarium oxysporum f. sp. fragariae）は，イチゴ栽培における難防除病害で，イチゴ萎黄病に対する抵抗性はイチゴ育種における重要形質の一つである．本研究では，抵抗性品種の育成の効率化を図るため，イチゴ萎黄病抵抗性に関する遺伝領域の解析を行った．罹病性品種「とちおとめ」と抵抗性品種「アスカウェイブ」を交雑したF1集団のランナー苗と培養苗を作出し，それぞれ異なる条件で接種試験を行った結果，F1集団の発病度の分布から「アスカウェイブ」の抵抗性は，一つの主働遺伝子と複数の量的形質遺伝子が関与していることが推察された．また，「とちおとめ」と「アスカウェイブ」の連鎖地図を用いてQTL解析を行った結果，「アスカウェイブ」の連鎖地図上に，主働遺伝子に連鎖すると考えられる1領域を含む複数のQTLが検出された．

Two new species of Halacarsantia are described, as the first record of this genus from Japan. Halacarsantia ovata sp. nov. differs from its congeners in having coxal plates hidden in dorsal view on pereonites 1, 2 and 4-7, dorsal-laterally situated eyes on head, without conspicuous bulging processes, pleopod 1 bearing 2 long ventral and 6 short apical setae, and sympod of pleopod 2 about three times as long as broad. Halacarsantia setosa is distinguishable from its congeners in having many dorsal robust setae on head, pereonites and pleotelson.

Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis were employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density single-nucleotide polymorphism (SNP) genetic linkage map. Using the genome sequence data, and two F2 populations, the SNPs linked to double flower loci (djo and dsu) were discovered. DNA markers linked to djo and dsu were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for dsu, since frameshift was specifically observed in the double flower accession with dsu.