Genetics and Genomics of Infectious Diseases in Key Aquaculture Species.

Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

Isolation and Evaluation of the Probiotic Activity of Lactic Acid Bacteria Isolated from Pickled Brassica juncea (L.) Czern. et Coss.

The naturally occurring lactic acid bacteria can be isolated from various sources. Pickled Brassica juncea (L.) Czern. et Coss. was used to isolate lactic acid bacteria (LAB). This study was conducted to compare the probiotic properties of probiotics isolated from pickled Vietnamese cabbage with some commercial strains of probiotics available on the Vietnamese market. The results showed that two strains (Lactobacillus fermentum and Lactiplantibacillus plantarum) isolated from pickled Vietnamese cabbage and three commercial strains of probiotics (Bacillus subtilis, Bacillus clausii, Lactobacillus acidophilus) all showed probiotic properties. Probiotic properties were evaluated through the ability to survive in low pH, pepsin, pancreatin, and bile salt media, the hydrophobicity of the bacteria, the antibiotic resistance, and the resistance to pathogenic bacteria. The isolated strain Lactiplantibacillus plantarum had fewer probiotic properties than Bacillus subtilis but more than the two commercial strains Bacillus clausii and Lactobacillus acidophilus, and the isolated Lactobacillus fermentum showed the fewest probiotic properties of the five strains.

Genomic Selection in Aquaculture Species.

To date, genomic prediction has been conducted in about 20 aquaculture species, with a preference for intra-family genomic selection (GS). For every trait under GS, the increase in accuracy obtained by genomic estimated breeding values instead of classical pedigree-based estimation of breeding values is very important in aquaculture species ranging from 15% to 89% for growth traits, and from 0% to 567% for disease resistance. Although the implementation of GS in aquaculture is of little additional investment in breeding programs already implementing sib testing on pedigree, the deployment of GS remains sparse, but could be boosted by adaptation of cost-effective imputation from low-density panels. Moreover, GS could help to anticipate the effect of climate change by improving sustainability-related traits such as production yield (e.g., carcass or fillet yields), feed efficiency or disease resistance, and by improving resistance to environmental variation (tolerance to temperature or salinity variation). This chapter synthesized the literature in applications of GS in finfish, crustaceans and molluscs aquaculture in the present and future breeding programs.

Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms.

Assessments of genomic prediction accuracies using artificial intelligent (AI) algorithms (i.e., machine and deep learning methods) are currently not available or very limited in aquaculture species. The principal aim of this study was to examine the predictive performance of these new methods for disease resistance to Edwardsiella ictaluri in a population of striped catfish Pangasianodon hypophthalmus and to make comparisons with four common methods, i.e., pedigree-based best linear unbiased prediction (PBLUP), genomic-based best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP) and a nonlinear Bayesian approach (notably BayesR). Our analyses using machine learning (i.e., ML-KAML) and deep learning (i.e., DL-MLP and DL-CNN) together with the four common methods (PBLUP, GBLUP, ssGBLUP, and BayesR) were conducted for two main disease resistance traits (i.e., survival status coded as 0 and 1 and survival time, i.e., days that the animals were still alive after the challenge test) in a pedigree consisting of 560 individual animals (490 offspring and 70 parents) genotyped for 14,154 single nucleotide polymorphism (SNPs). The results using 6,470 SNPs after quality control showed that machine learning methods outperformed PBLUP, GBLUP, and ssGBLUP, with the increases in the prediction accuracies for both traits by 9.1-15.4%. However, the prediction accuracies obtained from machine learning methods were comparable to those estimated using BayesR. Imputation of missing genotypes using AlphaFamImpute increased the prediction accuracies by 5.3-19.2% in all the methods and data used. On the other hand, there were insignificant decreases (0.3-5.6%) in the prediction accuracies for both survival status and survival time when multivariate models were used in comparison to univariate analyses. Interestingly, the genomic prediction accuracies based on only highly significant SNPs (P < 0.00001, 318-400 SNPs for survival status and 1,362-1,589 SNPs for survival time) were somewhat lower (0.3-15.6%) than those obtained from the whole set of 6,470 SNPs. In most of our analyses, the accuracies of genomic prediction were somewhat higher for survival time than survival status (0/1 data). It is concluded that although there are prospects for the application of genomic selection to increase disease resistance to E. ictaluri in striped catfish breeding programs, further evaluation of these methods should be made in independent families/populations when more data are accumulated in future generations to avoid possible biases in the genetic parameters estimates and prediction accuracies for the disease-resistant traits studied in this population of striped catfish P. hypophthalmus.

Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus.

Common full-sib families (c 2 ) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c 2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%-130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.

Transcriptomic responses of saline-adapted Nile tilapia (Oreochromis niloticus) to rearing in both saline and freshwater.

The Nile tilapia, Oreochromis niloticus, is an important species for global aquaculture. Recently, a single genetic line of Nile tilapia was developed using estimated breeding values (EBVs) for body weight under moderately saline water that showed significant improvement in growth performance. To explore the molecular mechanisms underlying this enhanced growth capacity, RNA-Seq was used to profile differences in gene expression in the liver and pituitary gland of high- and low-growth performance families of male Nile tilapia progeny, reared in either saline or freshwater environments. Comparisons of tissues from high- and low-EBV families, and also between fish reared in either saline or freshwater, revealed 142 and 2208 differentially expressed genes (DEGs), respectively. DEGs identified between the EBV groups comprised a number of genes involved in the regulation of growth and reproduction. We found an overexpression of hormone genes involved in growth-inhibition in the pituitary of Low-EBV tilapia including 2 somatostatin genes (GHIH), corticoliberin (CRH) and tachykinin-3-like protein. Furthermore, several genes associated with the cAMP pathway were underexpressed in low-EBV tilapia pituitary together with several early response genes. This study provides insight into the transcriptomic factors associated with growth performance in saline-adapted Nile tilapia reared in environments with high and low salinity levels and provides valuable knowledge for the future development of selection strategies to improve growth performance in this species.

Effects of genotype × environment interaction on the estimation of genetic parameters and gains in Nile tilapia.

Nile tilapia (Oreochromis niloticus) is the major fish species produced in Brazil, a country with a vast territory and great climate diversity. This study assessed the effects of the genotype × environment interaction on heritability estimates and selection responses in Nile tilapia (Tilamax strain) cultivated in earthen ponds and net cages. The weight at harvest, trunk length, and head percentage of 4400 individuals were determined. Trait heritabilities were higher in pond fish (0.27-0.52) than in caged fish (0.09-0.33). Genetic correlations between farming systems were lower than 0.5 for the three traits. The rank position of the top 10 families differed according to the environment, as did the response to direct and indirect selection. The results revealed significant genotype × environment effects on the heritability of Nile tilapia farmed under different systems.

Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis.

Conventional genetic improvement of disease resistance in aquatic animal species involves challenge tests or using qPCR to quantify viral load that is costly, time-consuming and causing biosecurity concerns. Recent developments in high throughput next generation genome sequencing platforms such as genotyping by sequencing (GBS) have opened new possibilities for improving disease traits based on DNA information. The principal aim of this study was thus to examine potential application of genomic selection to improve resistance to hepatopancreatic parvovirus (HPV) in banana shrimp Fenneropenaeus merguiensis. Specifically, we used a total of 9472 single nucleotide polymorphisms (SNPs) developed de novo from GBS platforms to assess accuracy of genomic prediction for HPV resistance and growth, carcass and quality-related traits in this white shrimp species. Our multi-locus mixed model analysis showed moderate heritabilities for HPV resistance (h2 = 0.46) and other traits studied (0.10 to 0.55). Genetic correlations of HPV titre with growth and carcass traits, estimated using SNPs markers, were negative (i.e., favourable), suggesting that selection for improved growth and carcass traits may have increased HPV resistance (i.e., reduced HPV titre). More importantly, our gBLUP model demonstrated that the accuracy of gBLUP prediction was moderate for HPV disease resistance (0.46). The genomic prediction accuracy was somewhat greater for growth and carcass related traits especially for body weight (0.76) and meat or tail weight (0.77). On the other hand, the prediction accuracy was from 0.25 to 0.41 for quality traits (raw and cooked colour and flesh streaks). Collectively, it is concluded that there are prospects to apply genomic selection in the genetic improvement for increased disease resistance, carcass and quality-related traits in this population of banana shrimp F. merguiensis.

Resistance to Streptococcus iniae and its genetic associations with traits of economic importance in Asian seabass (Lates calcarifer).

Streptococcus iniae is one of the most serious aquatic pathogens, causing significant economic losses in marine and freshwater species, including Asian seabass (Lates calcarifer). Controlling this gram-positive bacterial pathogen has been an issue in aquaculture systems, due to the combined effects of aquaculture intensification and climatic impacts. To date, there have not been any genetic parameter estimates for S. iniae resistance in Asian seabass. The main aim of this study was to examine genetic variation in S. iniae resistance and its genetic correlations with growth and cannibalism in Asian seabass families produced from a breeding programme for high growth in 2016 and 2017. The study included a total of 5,835 individual fish that were offspring of 41 sires and 60 dams (31 half-sib and 34 full-sib families). The experimental fish were challenged by intraperitoneal injection with a volume containing 105  CFU (colony-forming unit)/fish. Resistance to S. iniae was measured as survival rate at 6 hr, 3, 5, 7, 10 and 15 days post-challenge test. There were significant variations in S. iniae resistance among families at different observation periods (ranging from 24.4% to 80%). Restricted maximum-likelihood method and mixed model analysis were applied to estimate heritability for S. iniae resistance. The heritability for S. iniae resistance ranged from 7% to 18% across different statistical models used. The common full-sib effects accounted for 0.1%-2% of the total variation in resistance to S. iniae. Genetic correlations of the S. iniae resistance at 6 hr and 3 days with later post-challenge test periods were low to moderate. However, these estimates for S. iniae resistance between successive measurement times (5, 7, 10 and 15 days) were high and close to 1. The genetic correlations of resistance with body weights at 180, 270 and 360 days post-hatch were not significant as well with cannibalism. It is concluded that there is substantial additive genetic variation in resistance to S. iniae, suggesting there is potential for genetic improvement of Asian seabass for resistance to S. iniae through selective breeding.

Breeding for improved resistance to Edwardsiella ictaluri in striped catfish (Pangasianodon hypophthalmus): Quantitative genetic parameters.

Bacillary necrosis of Pangasius (BNP), caused by Edwardsiella ictaluri, is one of the most devastating diseases in striped catfish farming. To date, quantitative genetic inheritance of BNP resistance is not known in striped catfish Pangasianodon hypophthalmus. The main aim of this study was to estimate genetic parameters for BNP resistance in a breeding population of striped catfish undergoing four generations of selection for high growth. Specifically, the study examined whether BNP resistance is heritable to enable family selection and whether genetic improvement for enhanced BNP resistance may have detrimental effects on growth and survival rate. To test these hypotheses, 720 full- and half-sib families were challenged with E. ictaluri pathogen using injection and cohabitation methods over four years, from 2010 to 2012 and 2015. In total, the data included 398,234 animals in the pedigree, from which 18,849 animals had disease challenge test records and 39,103 siblings had growth performance. Both univariate and bivariate sire-dam linear and threshold mixed models were used to estimate (co)variance components for BNP resistance, survivals and growth traits. The estimates of heritability for the BNP resistance recorded as death or survival were low regardless of models used (0.10-0.16), whereas survival time (days post-challenge test) showed moderate heritability (0.35). The survival rate during hapa rearing had medium heritability (0.33-0.52). The genetic correlations of BNP resistance with body weight and survival were all positive (0.03-0.53), suggesting that selection of increased BNP resistance may have positive impacts on growth and survival traits, and these traits could be easily improved simultaneously in the selective breeding programme for striped catfish.

Selection for improved white spot syndrome virus resistance increased larval survival and growth rate of Pacific Whiteleg shrimp, Liptopenaeus vannamei.

Outbreaks of contagious diseases, including White spot syndrome virus (WSSV), occur more frequently due to environment changes and as commercial shrimp production becomes intensified. The over-arching aim of this study was to examine new traits to improve disease resistance of Whiteleg shrimp, Liptopenaeus vannamei, to WSSV. Specifically, we made a compressive evaluation of the breeding population to determine a suitable selection criterion for improved WSSV resistance. To achieve this objective, we analysed five traits (viral titre, WSSV resistance, larval survival, body weight and standard length) recorded for 120,000 individual shrimps that were offspring of 228 sires and 300 dams produced over two generations of selection in 2017 and 2018. Our restricted maximum likelihood mixed model analysis showed that there is additive genetic variation in viral copy number (or viral titre, viral load) with the heritability that equals 0.18 ±â€¯0.02. Viral titre displayed a moderate and negative genetic correlation with WSSV resistance (rg = -0.55). These results suggest that viral titre can be used as a selection criterion to improve WSSV resistance, but selection for decreased viral titre (i.e., increased resistance) may not capture all genetic expression in WSSV resistance. In addition to the estimation of population genetic parameters, we evaluated direct response to selection for increased WSSV resistance, which was measured as differences in estimated breeding values between the high and low resistant lines. The direct genetic gain achieved for WSSV resistance averaged 12.9% after one generation of selection in this Whiteleg shrimp population. The selection program also resulted in positive impacts on growth and larval survival by 7% and 17%, respectively. There is abundant genetic variation in WSSV resistance (h2 = 0.19-0.27), suggesting that the tested Whiteleg shrimp population will continue to respond to future selection. Collectively, the results obtained in our study provide important information to assist the design and implementation of genetic improvement programs for disease traits in aquaculture species, including L. vannamei.

Genetic Variation in Disease Resistance Against White Spot Syndrome Virus (WSSV) in Liptopenaeus vannamei.

White Spot Syndrome Virus (WSSV) is the most damaging pathogen in terms of production and economic losses for the shrimp sector world-wide. Estimation of heritability for WSSV resistance was made in this study to obtain necessary parameter inputs for broadening the breeding objectives of an ongoing selective breeding programme for Whiteleg shrimp (Liptopenaeus vannamei) that has focussed exclusively on improving growth performance since 2014. The present study involved a disease challenge test experiment using a total of 15,000 shrimps from 150 full- and half-sib families (100 individuals per family). Survival rates were recorded at six different experimental periods: 1-3 days (S1), 1-5 days (S2), 1-7 days (S3), 1-9 days (S4), 1-12 days (S5), and 1-15 days (S6) and were used as measures of WSSV resistance. There was significant variation in WSSV resistance among families studied. Quantitative-real time PCR (qPCR) analysis showed that the amount of viral titer (viral load) was significantly lower in high than low resistance families. Analyses of heritability were carried out using linear mixed model (LMM) and threshold logistic generalized model (TLGM). Both linear and threshold models used showed that the heritability (h2) for WSSV resistance was moderate in the early infection phases (S1-S4), whilst a low h2 value was observed for survival after 12 and 15 days of the challenge test (S5 and S6). The transformed heritabilities for WSSV resistance ranged from 1 to 31% which were somewhat lower than those estimated on the liability scale. Genetic correlations between survival rates measured over six different days post-infection were high and positive (0.82-0.99). The phenotypic correlations ranged from 0.31 ± 0.01 to 0.97 ± 0.01. The genetic correlations between body weights and WSSV resistance were negative. Our results on the heritability and genetic correlations show that improvement of WSSV resistance can be achieved through selective breeding in this population of Whiteleg shrimp.

Quantitative genetic changes in reproductive performance of giant freshwater prawn after 10 years of selection for increased growth rate.

Effect of long-term selection for improved growth on reproductive performance of giant freshwater prawn (GFP) Macrobrachium rosenbergii has not been reported in the literature. The present study aimed to measure correlated responses in reproductive traits and to estimate genetic parameters for these characters in a GFP population selected for high growth over ten generations from 2007 to 2016. A total of 959 breeding females (offspring of 515 sires and 810 dams) had measurements for seven reproductive traits (weight before spawn WBS; weight after spawn WAS; Fecundity FEC or number of larvae per female at hatching; first age to reach post-larvae PLAGE; zoea (e) weight ZOEAWT; larval survival during hatchery phase SURV1 and survival from PL to tagging SURV2. The restricted maximum likelihood (REML) and mixed model analysis were used to estimate genetic parameters and evaluate selection responses for the seven traits studied. Our REML analysis showed that heritability for these traits ranged from 0.04 to 0.42 (SE: 0.19-0.28). Female body weight either before or after spawning had strong positive phenotypic correlations with fecundity (0.52-0.98). By contrast, the phenotypic correlations of WBS/WAS with larval and fry survivals were not significant (-0.08-0.05). Genetic correlations among fecundity-related traits studied were not different from zero due to their high standard errors. Correlated responses in reproductive traits were measured by comparing least squares means of the selection line and control group. Females of the selected line for high growth had significantly greater weight before or after spawning than that of the control group. There were, however, no statistical differences between the two lines in the other traits. It is concluded that selection for high growth did not have detrimental impact on reproductive performance of breeding females in the present population of GFP.

An 8-Year Breeding Program for Asian Seabass Lates calcarifer: Genetic Evaluation, Experiences, and Challenges.

Selective breeding for marine finfish is challenging due to difficulties in reproduction, larval rearing, and on-growth in captive environments. The farming of Asian seabass (Lates calcarifer) has all these problems and our knowledge of the quantitative genetic information (heritability and correlations) of traits necessary for commercial exploitation is poor. The present study was conducted to address this knowledge gap and to provide information that can be applied to sea bass and other aquaculture species. We carried out a comprehensive genetic evaluation for three traits (body weight, total length, and survival) collected from a breeding population for Asian seabass over an eight-year period from 2010 to 2017. Statistical analysis was carried out on 4,567 adult fish at 105, 180, 270, 360, 450, and 570 days post-hatch (dph). The heritabilities (h2) estimated for body weight and length using linear mixed model were moderate to high (0.12 to 0.78 and 0.41 to 0.85, respectively) and they differed between the measurement periods. Survival during grow-out phase was analyzed using threshold logistic and probit models. The heritability estimates for survival rate on the underlying liability scale ( hL2 ) varied from 0.05 to 0.21. When the observed heritability obtained from the linear mixed model was back-transformed to the liability scale, they were similar but not significant. In addition, we examined effects of genotype by environment (G × E) interaction on body traits. The genetic correlation for body weight between tank and sea cage cultures were high (0.91-0.94) in the first and second rearing periods (180 and 270 dph) but the correlation was decreased to 0.59 ± 0.33 at 360 dph. This suggests that the genotype by environment interaction is important for body traits in this population. Furthermore, the genetic correlations of body weights between different measurement periods were moderate but different from one. This suggests that body weights measured at different time points may be different traits and selection for improved early weight may not capture all genetic expressions in subsequent rearing periods in Asian seabass. Selection of the nucleus in sea cages may produce genotypes that do not perform equally well in tanks, although this deserves further studies to determine a suitable selection environment and optimize the breeding program. This paper discusses challenges encountered during implementation of the selection program for L. calcarifer.

Genetic analysis of a red tilapia (Oreochromis spp.) population undergoing three generations of selection for increased body weight at harvest.

Quantitative genetic analysis was performed on 10,919 data records collected over three generations from the selection programme for increased body weight at harvest in red tilapia (Oreochromis spp.). They were offspring of 224 sires and 226 dams (50 sires and 60 dams per generation, on average). Linear mixed models were used to analyse body traits (weight, length, width and depth), whereas threshold generalised models assuming probit distribution were employed to examine genetic inheritance of survival rate, sexual maturity and body colour. The estimates of heritability for traits studied (body weight, standard length, body width, body depth, body colour, early sexual maturation and survival) across statistical models were moderate to high (0.13-0.45). Genetic correlations among body traits and survival were high and positive (0.68-0.96). Body length and width exhibited negative genetic correlations with body colour (- 0.47 to - 0.25). Sexual maturity was genetically correlated positively with measurements of body traits (weight and length). Direct and correlated genetic responses to selection were measured as estimated breeding values in each generation and expressed in genetic standard deviation units (σG). The cumulative improvement achieved for harvest body weight was 1.72 σG after three generations or 12.5% per generation when the gain was expressed as a percentage of the base population. Selection for improved body weight also resulted in correlated increase in other body traits (length, width and depth) and survival rate (ranging from 0.25 to 0.81 genetic standard deviation units). Avoidance of black spot parent matings also improved the overall red colour of the selected population. It is concluded that the selective breeding programme for red tilapia has succeeded in achieving significant genetic improvement for a range of commercially important traits in this species, and the large genetic variation in body colour and survival also shows that there are prospects for future improvement of these traits in this population of red tilapia.

Regional genetic diversity for NNV grouper viruses across the Indo-Asian region - implications for selecting virus resistance in farmed groupers.

Grouper aquaculture around Asia is impacted by the nervous necrosis virus (NNV) and, in response, host resistance to this infection is being considered as a trait for selection. However efficient selection may be confounded if there are different genetic strains of NNV within and between regions and over years. This study uses statistical approaches and assessment of "characteristic attributes" (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Rather clear evidence was found for regional strains of NNV. Interestingly, most of the geographic defining "characteristic attributes" were in codon position three, and not translated into differences for the protein capsid (i.e. they were synonymous variations), suggesting that while NNV strains were geographically isolated and had diverged in different regions for RNA sequences, selection had largely conserved the protein sequences among regions. The apparent selection constraint on the capsid protein may mitigate the risk that despite geographic subdivision, NNV strain variability will confound genetic selection for host resistance. The existence of regional Asian NNV strains may suggest that hatcheries are at risk from NNV not only from imported material but also from endemic reservoirs.

Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific, but with recent divergence.

Captive breeding programs and aquaculture production have commenced worldwide for the globally distributed yellowtail kingfish (Seriola lalandi), and captive bred fingerlings are being shipped from the Southern Hemisphere to be farmed in the Northern Hemisphere. It was recently proposed that Pacific S. lalandi comprise at least three distinct species that diverged more than 2 million years ago. Here, we tested the hypothesis of different "species" in the Pacific using novel genomic data (namely single nucleotide polymorphisms and diversity array technology markers), as well as mtDNA and DNA microsatellite variation. These new data support the hypothesis of population subdivision between the Northeast Pacific, Northwest Pacific and South Pacific, and genetic divergence indicates restriction to the gene flow between hemispheres. However, our estimates of maximum mtDNA and nuclear DNA divergences of 2.43% and 0.67%, respectively, were within the ranges more commonly observed for populations within species than species within genera. Accordingly our data support the more traditional view that S. lalandi in the Pacific comprises three distinct populations rather than the subdivisions into several species.

Genetic variation and correlated changes in reproductive performance of a red tilapia line selected for improved growth over three generations.

The present study examines genetic variation and correlated changes in reproductive performance traits in a red tilapia (Oreochromis spp.) population selected over three generations for improved growth. A total of 328 breeding females (offspring of 111 sires and 118 dams) had measurements of body weight prior to spawning (WBS), number of fry at hatching (NFH), total fry weight (TFW) and number of dead fry (NDF) or mortality of fry including unhatched eggs at hatching (MFH). Restricted maximum likelihood (REML) analysis in a multi-trait model showed that there are heritable genetic components for all traits studied. The heritability for WBS was very high (0.80). The estimates for traits related to fecundity (NFH, TFW) and survival (NDF) were low and they were associated with high standard errors. Genetic correlations of WBS with other reproductive performance traits (NFH, TFW and NDF) were generally positive. However, NFH was negatively correlated genetically with TFW. As expected, body measurements during growth stage exhibited strong positive genetic correlations with WBS. The genetic correlations between body traits and reproductive performance (NFH, TFW, NDF) were not significant. Correlated responses in reproductive traits were measured as changes in least squares means between generations or spawning years. Except for WBS that increased with the selection programs, the phenotypic changes in other reproductive traits observed were not statistically significant (P>0.05). It is concluded that the selection program for red tilapia has resulted in very little changes in reproductive performance of the animals after three generations. However, periodic monitoring of genetic changes in fecundity and fitness related traits such as NDF or MFH should be made in selective breeding programs for red tilapia.

Effects of selection for fast growth on survival rate during grow-out phase in giant freshwater prawn (Macrobrachium rosenbergii).

BACKGROUND: Correlated genetic response in survival to selection for high growth has not been reported in giant freshwater prawn (GFP) (Macrobrachium rosenbergii). The main aim of this study was to measure genetic changes and estimate heritability for this character (survival rate) and its genetic associations with body traits in a GFP population selected over eight generations from 2008 to 2015. Statistical analyses were conducted on 106,696 data records, using threshold logistic mixed model. RESULTS: The estimated heritability for survival was 0.14 ± 0.04 and significant. Genetic associations of survival with body traits (weight, length and width) were weak, with the estimates of genetic correlations between the traits close to zero. Realised genetic changes in survival, calculated as the difference in estimated breeding values between the selection line and control group within the same generation, was in positive direction but the estimates were not significantly different from zero regardless of the expression unit used either in actual unit of measurement or genetic standard deviation unit. On the other hand, communal testing of stocks in the latest generation, namely G7 (2015), showed that the selection line had 18% higher survival rate than progeny of the wild prawns originated from Mekong river. This result suggests that inadvertent changes in survival occurred during domestication-selection. CONCLUSIONS: It is concluded that selection for high growth had no significant effect on survival in the present population of M. rosenbergii.