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This study describes the development and application of a 20 K single nucleotide polymorphism (SNP) array in fugu (Takifugu rubripes). The main goal of this newly developed SNP array is to enhance selective breeding practice via the incorporation of genomic information. Fugu is one of the economic aquaculture species and mainly threatened by parasite disease. The performance of the array was evaluated in a farmed pufferfish population challenged with Cryptocaryon irritans and benchmarked against whole-genome sequencing of a subset of the animals. The array showed very high call rates, consistency between technical replicates, and concordance with genome-resequencing data. Heritability estimates using pedigree and SNP datasets demonstrated a significant genetic component of resistance to C. irritans , with heritability estimates ranging from 0.53 to 0.67, and prediction accuracies were significantly improved with the use of genomic data. Genome-wide association study identified two putative quantitative trait loci (QTLs) on chromosomes 3 and 17. Our findings suggest resistance to C. irritans can be rapidly increased in fugu populations by selective breeding, further expedited via the application of genetic markers. Therefore, they represent a valuable resource for selective breeding programmes aimed at enhancing disease resistance in fugu aquaculture. • The first SNP array was developed and applied in fugu genomic breeding. • Heritability of resistance to C. irritans was very high. • Two putative QTLs associated with resistance to C. irritans were detected. [ABSTRACT FROM AUTHOR]

In recent years, intensive recirculating aquaculture systems (RAS) as an eco-responsible and more efficient aquiculture model have been emerged into practice, and have been taking place of the traditional flow-through systems (FTS). The aim of this study was to estimate genetic parameters for body weight (BW), total length (TL) and survival (SUR) reared in the both environments (i.e. RAS and FTS) in olive flounder, and investigate genotype by environment (G × E) interactions for these traits between RAS and FTS. The heritability estimates for BW and TL were moderate (0.15–0.22) in both environments. For SUR, the heritability was 0.13 ± 0.05 and 0.19 ± 0.06 for RAS and FTS respectively. The genetic correlations of BW (0.65 ± 0.13), TL (0.33 ± 0.12), and survival (0.40 ± 0.10) were relatively low between the two rearing environments. The differences in the heritabilities and the low genetic correlations between the two environments suggested that the magnitude of G × E interactions was very high, which showed evidence that there was severe re-ranking of family performance. We concluded that G × E interactions for olive flounder between the two rearing environments were of vital importance. These results will be beneficial for developing breeding programs in olive flounder because the accuracy of selection and genetic gain for growth and survival may differ between rearing environments. Hence, it is necessary to select environment-specific strains in olive flounder. This paper offers guidelines to select breeding strategy in olive flounder when fish are reared in different aquaculture systems. • Heritabilities of body weight, total length and survival were estimated in two different rearing systems in olive flounder. • There were significant genotype by environment interactions for growth and survival traits between different rearing systems. • This is the first report about genotype by environment interactions for growth and survival traits in olive flounder. • According to our work, it is necessary to establish environment-specific breeding programs in olive flounder. [ABSTRACT FROM AUTHOR]

Abstract Recently, Vibrio harveyi has emerged as an important pathogenic disease with a high mortality rate (50%–70%) in Chinese tongue sole. The aim of this study was to estimate genetic parameters for resistance to V. harveyi in Chinese tongue sole and to evaluate the genetic correlation between resistance and growth traits (i.e. body weight and total length) (involving 50 full-sib families and 8547 individuals). Longitudinal linear models and cross-sectional threshold models were fitted by using different trait definitions (binary and categorical). After a 14-day test, the overall challenge test survival was 57.86% (ranging from 9.30% to 94.30% in families). The heritabilities of survival were ranging from 0.11 to 0.28, estimates obtained by linear models were higher than threshold models. The genetic correlations between resistance (binary and categorical traits) and two growth traits were moderately positive (0.27–0.51). Very high Pearson and Spearman correlations (0.99 to 1) of full-sib family EBVs between different models were all close to unity which might reveal the similar predictive ability of the four models. The favourable heritabilities and moderate positive genetic correlations indicate that joint genetic improvement of vibriosis resistance and growth performance would be feasible. Statement of relevance This paper offers guidelines to disease-resistance selective breeding strategies in Chinese tongue sole. Highlights • Genetic variation for disease resistance traits were evaluated by challenge test with Vibrio harveyi in Chinese tongue sole. • Two types of models (cross-sectional and longitudinal models) were used for genetic analyses based on different trait definitions (i.e., binary test survival and categorical test day survival). • Low to moderate heritabilities for V. harveyi resistance traits were estimated, indicating that resistance could be genetically improved by selective breeding. • Genetic correlations between disease resistance traits and growth traits were moderately positive (ranging from 0.27 to 0.51) and significantly different from zero. • Estimated breeding values (EBVs) of the four models showed high and positive correlations (0.99–1), which meant that these models demonstrated similar utility for predicting breeding value. [ABSTRACT FROM AUTHOR]

Despite Japanese flounder ( Paralichthys olivaceus ) is of importance in aquaculture of Northeast Asia, selective breeding programs for growth performance traits remain limited. The aim of this study was to estimate parameters of growth performance traits in this species. The heritabilities, genetic and phenotypic correlations, and breeding values were estimated for body weight (BW), total length (TL), condition factor (K), and average daily gain (ADG). The genetic analyses were performed on a total number of 186 full-sib families (108 sires and 146dams, 16,807 individuals with integrated pedigree information) from 4 year-classes based on three mixed animal models with tank and year-class as fixed effects, mean family trait values at tagging as a covariate, and additive genetic effect as a random effect using the restricted maximum likelihood method. For all growth traits the maternal and sir-dam interaction effects in proportion to phenotypic variance were very low (0.00–0.05). The heritability estimates for growth traits ranged from 0.12 to 0.39, which is in a low to moderate level. These results indicated that there is a considerable additive genetic variation in growth traits, and the ongoing selective breeding project will produce considerable genetic improvement in growth traits of Japanese flounder. The genetic and phenotypic correlations among BW, TL and ADG were high and positive (0.87–0.94, P < .001). However, the correlations between K and other three traits were low to moderate (−0.10–0.58, P < .001). These data indicate that these traits (except K) could be selected and enhanced simultaneously and also imply that direct selection of TL, which is an easily measurable trait, will be more favorable than selection on BW and ADG. The estimated breeding values of parents and individuals and the average family breeding values for 4 traits were obtained. In summary, all the findings in this study will be of significance to optimize the flounder selective breeding program. Statement of relevance This paper offers guidelines to select breeding strategy in Japanese flounder. [ABSTRACT FROM AUTHOR]

Tongue sole is an economically important marine flatfish with significant sexual growth dimorphism that female with superior growth performance, and phenotypic female proportion (FP) is rather low (10%–30%) under rearing conditions. Knowledge of whether genetic variation exists for FP is needed for determining the feasibility of including this desirable trait into breeding goal in tongue sole. The aims of this study were to estimate the heritability of FP and genetic correlations between FP and growth traits (body weight, BW; total length, TL) by using a population of 16,240 individuals from 157 full-sib families (involving four year-classes (YCs), three consecutive pedigreed generations). At juvenile stage, fish from each family were random sampled to measure BW and TL, and then sexed by examining gonad tissues under microscope. The overall FP was 43.8% across all year-classes, and family FP ranges from 25.4% to 69.9%. Across YCs, there was a low but significant genetic variation for FP with heritability estimates of 0.02 ± 0.00 (observed scale) and 0.03 ± 0.01 (underlying scale). Within YC, heritability estimates varied from 0.00 ± 0.00 to 0.08 ± 0.01 on observed scale, and from 0.00 ± 0.00 to 0.04 ± 0.01 on underlying scale. Genetic correlations between FP and BW, and between FP and TL were both of moderately positive magnitude, which were 0.46 ± 0.09 and 0.39 ± 0.10 respectively, and significantly different from zero (P < 0.05). These results confirm the existence of genetic variation for FP and demonstrate the feasibility of joint improvement of FP and growth traits through selective breeding. • The analytic results indicate the existence of genetic variation of female proportion in tongue sole. • Low but significant heritability estimates were obtained based on two models. • Genetic correlations between female proportion and growth traits were of moderately positive magnitude. [ABSTRACT FROM AUTHOR]

Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine flatfish which is now severely threatened by various bacterial pathogens (especially at juvenile stage) in China. As we all known, it is of great importance to increase the natural disease resistance of farmed fish. So, the aim of this study was to verify the exitance of genetic variance of natural disease resistance and to detect the selection response by using juvenile natural survival data (involving four year-classes and three generations with 221 full-sib families, 195,589 individuals). Survival was defined as binary trait (dead/alive) fitted in two cross-sectional models (i.e. cross-sectional linear sire-dam model (CLM) and cross-sectional threshold (logit) sire-dam model (CTM)). Heritabilities of survival were estimated with each generation dataset and with complete dataset. Heritability estimates varied among generations regardless of model used, i.e., 0.01–0.17 and 0.03–0.25 for CLM and CTM respectively. On the observed (CLM) and underlying (CTM) scale with complete dataset, the heritabilities were 0.09 ± 0.04 and 0.13 ± 0.06 respectively. Both models performed nearly identical and very high selection accuracy (> 0.99), the accuracy of selection obtained from CLM (0.993) was slightly higher than CTM (0.991). By cross-validation, the prediction accuracy of CLM is 21% higher than CTM, which was 0.885 and 0.730 for CLM and CTM respectively. The average of predicted genetic gain for each generation was 14.89%, and the average of realized genetic gain was 8.10% per generation for juvenile survival. These results confirmed the existence of genetic variation for juvenile natural survival and highlighted the enormous potential for improving natural survival by selective breeding in tongue sole. • Survival at juvenile stage was improved substantially based on full-sib family EBVs. • The heritabilities of juvenile survival on observed and underlying scale were 0.09 ± 0.04 and 0.13 ± 0.06 respectively. • The predicted and realized genetic gain was 14.89% and 8.10% per generation respectively for tongue sole juvenile survival. [ABSTRACT FROM AUTHOR]

As an important farmed flatfish species, Chinese tongue sole (Cynoglossus semilaevis) is heavily threatened by vibriosis in recent years. Genetic selection for disease resistance is a sustainable and effective approach to reduce frequent outbreaks. To verify whether the resistance of vibriosis (caused by co-infections of different Vibrio spp. in natural outbreak) can be included in breeding programs, in this study, genetic analysis of resistance to vibriosis based on natural outbreak survival data was carried out by using four statistical models (three cross-sectional models and one longitudinal model). The magnitude of the genetic variation in the resistance of vibriosis was estimated through a 56-day natural outbreak test of 15,912 individuals from 78 full-sib families (the offspring of 77 sires and 78 dams). Variance components and heritabilities were estimated at two cut-off points respectively, i.e. day 35 with 49.2% cumulative mortality and day 56 with 71.6% finial cumulative mortality. Heritabilities of resistance to vibriosis were low to moderate, where values at day 56 (0.04–0.21) were significantly different from zero, while values at day 35 (0.03–0.10) were not significantly different from zero in each corresponding model. The Spearman rank correlations between family EBVs for different models were high (> 0.98), indicating a nearly identical ranking of families. Compare to three simpler cross-section models, the longitudinal model taken the time until death into account demonstrated the highest accuracy of family selection. These results confirmed the existence of genetic variation for resistance to vibriosis and provided novel insights into the selective breeding for disease resistance to vibriosis by using natural outbreak survival data in tongue sole. • Significant variation of vibriosis natural outbreak survival was observed among families of Chinese tongue sole. • Low to moderate heritabilities for vibriosis resistance traits were estimated. • The results provided novel insights for genetic improvement of vibriosis resistance by selective breeding in tongue sole. [ABSTRACT FROM AUTHOR]

Edwardsiella tarda is one of the most prevalent and economically important diseases worldwide in aquaculture, including olive flounder (Paralichthys olivaceus). Genetic improvement for resistance to E. tarda is an alternative strategy for the prevention of disease outbreaks. The objective of this work was to evaluate the genetic parameters of disease resistance by challenge test data. Mortality was recorded daily for 16 days (day1 to 16). At day 4 and 16, the cumulative mortality was 52%, and 87%, respectively. Resistance was defined as binary test survival (BTS), day of death (DD), and binary test day survival (BTDS). For DD, only day 16 was set as the cut-off day, while for the other two traits, each test day was set as a cut-off day. These traits were fitted in four statistical models for estimating variance components and calculating genetic parameters. Namely, 1) cross-sectional linear model for BTS (CLM) and DD (LM), 2) threshold (logit) model (CTM) for BTS, and 3) linear (logit) repeatability model (LRM) for BTDS. In LM, the heritability of resistance was 0.23 ± 0.06. In other three models, heritabilities were estimated at each cut-off point (test day) respectively, and heritabilites fluctuated daily. At day 4 (with approximately 50% overall mortality), the heritability was 0.17 ± 0.11 for CLM, 0.20 ± 0.14 for CTM and 0.09 ± 0.08 for LRM. Heritabilities obtained based on LM (at day16) and other three model estimated at day 4 are considered to be accurate. The selection accuracies of LM and LRM are nearly identical (0.735 and 0.755 respectively) and are 9.5% to13.9% higher than values of CLM and CTM (0.663 and 0.671 respectively). The rank correlations between EBVs obtained from CLM, CTM and LRM were very high (ranging from 0.97–1.00), indicating a near identical ranking of families. However, the correlations between EBVs from LM and from other three models were substantially lower (ranging from 0.79–0.82), which imply a substantial reranking of families. Low to moderate heritabilities indicated that resistance against E. tarda can be genetically improved, and selection by using models (i.e. LM and LRM) which take time to death into account is more accurate than cross-sectional models. • Heritabilities for resistance to E. tarda were estimated by using four different models with three types of definitions. • Heritabilities were estimated on each test day and the values changed over time. • Low to moderate heritabilities indicate potential prospects for genetic improvement. • Models which taking time of death into account can improve the accuracy of selection by 9.5%–13.9%. [ABSTRACT FROM AUTHOR]