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Blooms of the harmful algal plankton Chattonella spp. cause severe economic damage to aquaculture. This study aimed to investigate the potential for selective breeding of resistance trait to Chattonella red tides in Japanese yellowtail Seriola quinqueradiata. Two experimental populations were prepared using different production procedures, one was produced by full factorial mating and common rearing tanks, and another was produced by pair mating and family separated rearing tanks. Fingerlings were exposed to mass cultured Chattonella antiqua and their mortality time was recorded as the phenotype of Chattonella resistance. There were significant differences in survival rate among full‐sib families (range 0–50%). Heritability estimates of mortality time were moderate and similar in both populations as 0.329 ± 0.104 and 0.314 ± 0.118 respectively. The environmental variance caused by difference in rearing tanks was relatively small compared with the genetic variance, and had minimal influence on genetic parameter estimation. In contrast, body weight was highly influenced by the environmental variance of rearing tanks, thus heritability estimates varied between populations, 0.275 ± 0.102 and 0.153 ± 0.083 respectively. The genetic correlation between mortality time and body weight was not significant. This is the first report that reveals the contribution of a genetic difference to Chattonella resistance and indicates the potential for selective breeding of Chattonella resistance in Japanese yellowtail. [ABSTRACT FROM AUTHOR]

The aim of this study is to assess the feasibility of the genetic improvement of traits related to resistance to the monogenean ectoparasite Benedenia seriolae in Japanese yellowtail Seriola quinqueradiata. Resistance to benedeniosis (incidence of infection by Benedenia parasites) of individual sample fish was evaluated over two generations in long term field trials, as repeated counts of the number of parasites attached to their skin surface. The broodstock was evaluated by repeated counts 12 times, and 13 resistant and 5 susceptive individuals were selected as the parents among 779 candidates. Fourteen families were produced by mating the selected parents and 598 progenies were evaluated by repeated counts 4 times. A total of 7550 phenotypic records for the 1377 individuals were applied to the repeated measures animal model. Estimates of heritability and repeatability for resistance were as h 2 = 0.28 ± 0.03 and R = 0.37 ± 0.01, respectively. The differences of resistance among the families were significant and reflected the performances of the selected parents. Whereas severities of benedeniosis varied among the evaluation periods, the individual and family performances of resistance were consistent throughout the study. Both genetically and phenotypically, there were no significant correlations between resistance and body size traits. This report indicates that selective breeding is a promising approach to control benedeniosis in Japanese yellowtail aquaculture. • The number of parasites attached to fish was repeatedly counted in long term tests. • Individual / family level resistance was consistent throughout trials. • Family mean of parasite counts reflected resistance performances of parental stock. • Heritability and repeatability for resistance were moderate. • Body size did not correlate with resistance both genetically and phenotypically. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: The sex-determining system of yellowtail (Japanese amberjack), Seriola quinqueradiata, is not known. In this study, we identified the sex-linked locus in yellowtail and we characterized the sex-determining system by genetic linkage analysis conducted on 19 female and 19 male progenies from a single family. The associations between phenotypic sex and genotypic data of 71 microsatellite markers selected from yellowtail genetic linkage map were tested. The putative sex-determining locus is located between locus Sequ21 and locus Sequ17 in LG12, and the sex-linked alleles were inherited from the female parent. This result suggests that yellowtail has a ZZ–ZW sex-determining system, and that it would be possible to use these sex-linked markers to discriminate the sexes. [ABSTRACT FROM AUTHOR]

Benedenia disease is a parasitic disease occurring in cultured marine fish which is caused by the ectoparasite, Benedenia seriolae. This parasitic disease causes serious damage to yellowtail culture due to secondary infections, however prevention methods for the ectoparasite have limited efficacy. Thus, we attempted to initiate a marker-assisted selection (MAS) program to produce a yellowtail strain that has resistance to Benedenia disease. In this study, we conducted a genome scan for quantitative trait loci (QTL) that affect Benedenia disease resistance in five full-sib families using 7910 SNP markers. Sex-specific linkage maps was constructed for the five families and the total number of markers on each map was ranged from 1115 to 1427. We found four significant and five suggestive QTLs affecting Benedenia disease resistance. The phenotypic variation explained (PVE) by each QTL ranged from 8.2% to 29.6%. The QTL with a PVE of 29.6% on LG Squ6 in the family Rr1 was considered to be the major QTL. Novel Benedenia disease resistance QTLs detected in this study enhance our understanding of the genes and genomic regions related to Benedenia disease resistance in yellowtail and can serve as a basis for MAS breeding. • Benedenia disease is one of problems in yellowtail aquaculture production. • A genome scan for QTLs was conducted in five full-sib families. • New QTLs related to Benedenia disease resistance was detected in yellowtail. [ABSTRACT FROM AUTHOR]

Recent improvements in next-generation sequencing technology have made it possible to do whole genome sequencing, on even non-model eukaryote species with no available reference genomes. However, de novo assembly of diploid genomes is still a big challenge because of allelic variation. The aim of this study was to determine the feasibility of utilizing the genome of haploid fish larvae for de novo assembly of whole-genome sequences. We compared the efficiency of assembly using the haploid genome of yellowtail ( Seriola quinqueradiata ) with that using the diploid genome obtained from the dam. De novo assembly from the haploid and the diploid sequence reads (100 million reads per each datasets) generated by the Ion Proton sequencer (200 bp) was done under two different assembly algorithms, namely overlap-layout-consensus (OLC) and de Bruijn graph (DBG). This revealed that the assembly of the haploid genome significantly reduced (approximately 22% for OLC, 9% for DBG) the total number of contigs (with longer average and N50 contig lengths) when compared to the diploid genome assembly. The haploid assembly also improved the quality of the scaffolds by reducing the number of regions with unassigned nucleotides (Ns) (total length of Ns; 45,331,916 bp for haploids and 67,724,360 bp for diploids) in OLC-based assemblies. It appears clear that the haploid genome assembly is better because the allelic variation in the diploid genome disrupts the extension of contigs during the assembly process. Our results indicate that utilizing the genome of haploid larvae leads to a significant improvement in the de novo assembly process, thus providing a novel strategy for the construction of reference genomes from non-model diploid organisms such as fish. [ABSTRACT FROM AUTHOR]