Yellowtail kingfish ( Seriola lalandi ) is a species of significant value in aquaculture, with a broad distribution across subtropical and temperate seas. Although global production has doubled in 7 years, reaching approximately 9000 tons per year in 2021, its cultivation remains limited compared to other mainstream species. The commercial aquaculture of this species faces several key challenges in achieving improved production and sustainability: nutrition requirements, disease management, and the optimization of reproductive technologies. Current diets for yellowtail kingfish require further improvement to enhance both growth performance and sustainability. Diseases continue to be a major constraint, with at least 41 specific diseases reported for yellowtail kingfish and 31 affecting other Seriola species, emphasizing the necessity of targeted diagnostic tools and treatment strategies. Recent genomic advances have shed light on the biology and taxonomy of yellowtail kingfish, revealing genetically distinct populations across the South Pacific, Indian, and South Atlantic Oceans. However, the taxonomic status within the Pacific region remains unclear, requiring further research. Addressing these gaps is vital for developing robust breeding programs and improving genetic resilience. To support the sustainable expansion of yellowtail kingfish aquaculture, key areas for future research include increasing larval and juvenile survival rates, minimizing malformations, and tailoring farming models to diverse environmental conditions. Focusing on these priorities will ensure better productivity and disease resistance, ultimately promoting the global competitiveness of yellowtail kingfish as an aquaculture species.

Aquaculture mollusc production is predominantly from Asia, with more than 80% of the total biomass produced in China. Vietnam’s annual mollusc production is growing rapidly but is comparatively small given its coastal resources. A significant challenge for future mollusc production, and oysters in particular, is the supply of high-quality spat. Most mollusc spat in Vietnam comes from local wild sources or is imported from China. Particularly in the case of oysters, where wild collection is low and importation of oyster spat into Vietnam from other jurisdictions is not controlled, supply is unreliable and presents a biosecurity risk to the industry. Controlling the life cycle in hatcheries can increase the sustainability and reliability of spat supply with the advantages of genetic enhancement in the long term. Beyond well-established selection methods based on phenotypic data for pedigreed families, the rapid development of genomic technology has enabled innovation in hatchery production based on genetic programs. This technology allows greater insight into oyster genetics in intensive aquaculture production systems. Recent reviews of selection programs demonstrate that inbreeding control via mate selection is an effective strategy for oyster species. Genetic response through combinations of individual and family-based selection can enhance morphometric traits by 10% per generation and disease resistance by 15% per generation in many aquaculture species. Genomic techniques provide information for selecting candidates at an earlier stage and improve prediction accuracy. In this paper, we review the literature on popular genomic tools and breeding techniques used for molluscs, focusing on the Portuguese oyster, Crassostrea angulata. This is to better comprehend how modern quantitative and molecular genetic technologies are being applied in mollusc breeding programs. It considers opportunities for and the feasibility of using genomic-based selection as well as the challenges that are faced in breeding programs transitioning to these new methods.

Pedigrees are essential components in selective breeding programs to manage genetic diversity and obtain accurate genetic parameter estimates to ensure long-term response to selection in captive populations. High throughput and cost-effective sequencing technologies has offered opportunities of using single nucleotide polymorphisms (SNPs) to resolve penaeid shrimp pedigrees from mass spawning cohorts and communal rearing. Effects of SNPs for sibship assignment were investigated on 546 shrimp using two software programs, Colony and Sequoia. Assignment rates and accuracies using SNP subsets with six different minor allele frequencies (MAFs), four sets of SNPs, and five genotyping error rates were compared to the microsatellite-based pedigree established in a previous study. High MAFs and numbers of SNPs contributed to significant increases in assignment rates and accuracies, whereas genotyping error rates showed negligible impacts on assignment results. Sibship assignments achieved rates and accuracies of 98% and 83%, respectively, with a minimum number of 91 SNPs (average MAF ≥ 0.14), and the two different programs exhibited similar resulting patterns for different SNP subsets. High consistencies between SNP-based and microsatellite-based pedigrees showed that accurate pedigrees could be achieved by using SNPs and thus contribute to the long-term response to selection in farmed banana shrimp.

Blue swimmer crab species are widely distributed in Indian and west Pacific Oceans including the coastline around Australia and have been identified as potential candidates for stock enhancement. A recent taxonomic review revealed the presence of two blue swimmer crab species in Australia, namely Portunus armatus which is found around most of the Australian coastline, and Portunus pelagicus which is found in the northern coast where it is sympatric with P. armatus. It is important to understand population structure and genetic diversity of Portunus spp. to efficiently manage stocks. In the present study we investigated species classification and population structure of Portunus spp. in Australia using full and partial genomic information, namely mitochondrial COX1 gene sequences derived from whole genome sequencing and single nucleotide polymorphic (SNP) markers developed from partial genome sequencing. Blue swimmer crab samples were collected from the western (n = 52), northern (n = 17) and eastern (n = 110) coasts of Australia. Genetic diversity and population genetic structure were assessed for within and between region variation. Our genomic results indicated the presence of two blue swimmer crab species in Australia. One, namely, P. pelagicus was found only in Northern Territory (Darwin), and other, namely P. armatus was found around Australia. There was evidence of natural hybridisation between two species in Northern Territory (Darwin) where they were sympatric. P. armatus populations from the western, northern and eastern regions were genetically different although there were no significant genetic differences observed between the Queensland and New South Wales populations nor between the two neighbouring populations in Western Australia. Results found in the present study supports the view that the P. armatus populations in western, northern and eastern regions of Australia should be treated as at least three different stocks. A lack of genetic structuring along the eastern coast suggests blue swimmer crabs can be considered as a single stock along the sampled range at least in relation to fisheries enhancement, release programs and broodstock management.

The black sea cucumber Holothuria leucospilota is a commercially exploited species in the Western and Central Pacific region including Australia and Vietnam, where it has been overfished. There is interest to develop captive breeding, sea ranching and restocking programs for H. leucospilota. However, the wide distribution of this species could lead to genetic structure among site, which needs to be considered for responsible genetic management for example, restocking. This is the first study to investigate population genetics in H. leucospilota, between Australia and Vietnam, using single nucleotide polymorphisms (SNPs). The results indicated that there was high gene flow (Nm > 4) and genetic similarities among three Vietnamese populations, which inferred a high panmictic stock structure in Vietnam. Less gene flow (Nm > 1) was indicated between Vietnam and Mooloolaba (Eastern Australia) populations, and there was a significant genetic differentiation among any Vietnamese populations and Mooloolaba population (FST from 0.034 to 0.043; P < 0.05). Surprisingly, there was a major genetic difference (FST > 0.2) and a restricted gene flow (Nm <1) between Darwin (Northern Australia) population and other sea cucumber populations studied (Vietnam and Eastern Australia), which revealed a genetic break/divergence in Darwin. Based on these findings, we can propose that the Vietnamese sea cucumber stocks be considered as a single genetic stock with concordant implications for genetic management. We consider whether the genetic differences in the Darwin stock arise from bottlenecking and are not reflective of adaptive differences. In summary, the results from this study provide basic genetic information on H. leucospilota populations, that would help to design restocking management plans, genetic conservation initiatives and sea ranching programs for H. leucospilota.

Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin, and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South-Central Coast of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. Pulsed-field gel electrophoresis identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and single-nucleotide polymorphism (SNP) genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0-2 SNPs). There was no association between geographic origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 217 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55-7.96 Mbp in size, have an average G+C content of 68.2%, and encode 7,602-7,958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into N. seriolae epidemiology and pathogenicity and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.

Background Viral diseases are a major problem in shrimp aquaculture facilities as these diseases reduce growth rates, which inevitably lead to production and profit losses. Hepatopancreatic parvoviruses (HPV) are common diseases in shrimp that appear to be associated with high or low levels of replication in specific genetic lineages. Selective breeding may result in resistance to HPV and improved body traits such as body weight, meat yield and shrimp colour, facilitating shrimp farming. HPV virus titre is commonly determined by quantitative PCR (qPCR), which is a time-consuming method requiring laboratory equipment unsuitable for field implementation. The aim of this study was to develop a simple, robust, rapid and reliable method to detect HPV in low-resource environments. Methods We developed a rapid shrimp HPV test that uses (1) a simple three-step sample preparation protocol, followed by (2) isothermal recombinase polymerase amplification (RPA) and lateral flow strip detection (LFD). Analytical sensitivity testing was performed in a background banana shrimp sample matrix, and retrospective testing of Fenneropenaeus merguiensis hepatopancreas tissues (n = 33) with known qPCR viral titres was used to determine diagnostic sensitivity and specificity. Results The rapid shrimp HPV test could detect as little as 35 genome-equivalent copies per reaction in homogenized F. merguiensis banana shrimp. Retrospective testing of stored tissues (n = 33) indicated 100% diagnostic sensitivity (95% confidence interval, CI: 86–100%) and 100% specificity (95% CI: 66–100%) for detection of HPV. Conclusion The rapid shrimp HPV test could be completed in only 40 minutes, and required only homogenization pestles, some pipettors, and a small heating block for single temperature incubation at 39°C. Critically, our procedure eliminated the time-consuming purification of nucleic acids from samples and when combined with RPA-LFD offers a user-friendly HPV detection format that can potentially be performed on-site. Our approach represents a major step forward in the development of a simple and sensitive end-point method for quick determination of unfavourable HPV virus numbers in shrimp, and has great potential to advance on-site management of shrimps in aquaculture.

Eastern king prawn (Penaeus plebejus) is endemic to eastern Australia and is of high commercial and recreational value. As part of a recreational fisheries enhancement initiative, hatchery reared juveniles from Queensland were released into two, more Southern New South Wales (NSW) estuaries between 2014 and 2015. Responsible stock enhancement programs rely on knowledge of the population structure of the released species. Previously, in consideration of fisheries data, it was assumed the king prawn populations in Australia are one single breeding stock. In the present study, our first aim was to test this posit of no genetic differentiation using mtDNA control region (mtCR) sequences from the wild samples collected from four estuaries ranging from Queensland/NSW border (source of the stocked animals) to Southern NSW. The second objective was to test for signals of hatchery-released animals in the two stocked estuaries. All four surveyed populations had an extremely high level of haplotype diversity (average h = 99.8%) and low level of haplotype sharing between populations. Estimates of PhiPT values were <0.01 or close to zero and AMOVA test did not indicate any significant differences among populations. Further, phylogenetic analysis and principal coordinate analysis did not support division of samples by population. Collectively these results suggest that eastern king prawn populations along the NSW coast can be considered as a single stock and stocking from the Queensland samples will not necessarily impact the genetic composition of the overall stock. After stocking of two estuaries, sharing of haplotypes was moderate to very high in the stocked sites (>80% in some collections) but negligible in the two unstocked estuaries (≤2%, which is assumed to be background coancestry unrelated to the hatchery). Moreover, some haplotypes present in the hatchery broodstock were detected in stocked sites, but not in unstocked sites. The highest stocking signal was detected in the estuary which becomes isolated from the sea by sand barrier suggesting such "lakes" maybe more favourable for stocking than estuaries directly open to the sea. Findings in the current study should assist in designing and implementation of future prawn stocking programs.

In a selective breeding program for the Portuguese oyster, Crassostrea angulata, oysters are cultured in several environments including the broodstock for breeding (Cat Ba) and production (Van Don) locations. This raises the potential that a genotype by environment interaction may occur and oyster genotypes may re-rank across environments. Whole weight and uniformity in weight at the time of harvest are two of the most important economic traits for oyster production in northern Vietnam. Limited information, particularly with respect to uniformity, exists for C. angulata. Our primary aim was to quantify the genetic variance in harvest whole weight and its uniformity and the genetic correlation between them using a double hierarchical generalized linear model. We investigated the degree of genotype by environment interaction on the uniformity of harvest whole weight in the two environments. Since the weights had a skewed distribution, we also investigated the affect of log-transformation on the estimates of the genetic variance in harvest whole weight, its uniformity, the genetic correlation between them and on the genotype by environment interactions. Results showed that heritability estimates for uniformity of harvest whole weight were low for Cat Ba (0.07) and Van Don (0.06) environments using standardized data, while these estimates were lower using log transformation for both environments. There was no re-ranking of oysters with regard to harvest whole weight and uniformity across environments; the genetic correlations were effectively one, with and without log transformation. Therefore, there is no scope to improve uniformity in the Portuguese oyster population while increasing whole weight at harvest.

Genetic improvement for quality traits, especially color and meat yield, has been limited in aquaculture because the assessment of these traits requires that the animals be slaughtered first. Genotyping technologies do, however, provide an opportunity to improve the selection efficiency for these traits. The main purpose of this study is to assess the potential for using genomic information to improve meat yield (soft tissue weight and condition index), body shape (cup and fan ratios), color (shell and mantle), and whole weight traits at harvest in the Portuguese oyster, Crassostrea angulata. The study consisted of 647 oysters: 188 oysters from 57 full-sib families from the first generation and 459 oysters from 33 full-sib families from the second generation. The number per family ranged from two to eight oysters for the first and 12–15 oysters for the second generation. After quality control, a set of 13,048 markers were analyzed to estimate the genetic parameters (heritability and genetic correlation) and predictive accuracy of the genomic selection for these traits. The multi-locus mixed model analysis indicated high estimates of heritability for meat yield traits: 0.43 for soft tissue weight and 0.77 for condition index. The estimated genomic heritabilities were 0.45 for whole weight, 0.24 for cup ratio, and 0.33 for fan ratio and ranged from 0.14 to 0.54 for color traits. The genetic correlations among whole weight, meat yield, and body shape traits were favorably positive, suggesting that the selection for whole weight would have beneficial effects on meat yield and body shape traits. Of paramount importance is the fact that the genomic prediction showed moderate to high accuracy for the traits studied (0.38–0.92). Therefore, there are good prospects to improve whole weight, meat yield, body shape, and color traits using genomic information. A multi-trait selection program using the genomic information can boost the genetic gain and minimize inbreeding in the long-term for this population.

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.

In recent decades, developing countries with traditionally strong links with aquaculture have adopted genetic improvement programs for newly domesticated and captively bred aquaculture species. Accurate genealogical and pedigree information is an essential tool for efficient and successful genetic improvement programs and traditionally this type of information was obtained by separate rearing of families and physical tagging of the animals. More recently, molecular based pedigrees (e.g. using SNPs) is becoming a potential option, which also may permit the communal rearing of families at a stage earlier than usual, prior to physical tagging. Here we consider the utility of molecular based pedigrees in a multi-generation breeding and selection program for the Portuguese oyster (Crassostrea angulata) and assess parameters for parentage assignment.Using 18,849 SNP markers obtained from 489 sequenced oysters including parents and their progeny, our results indicated that approximately 400 SNPs with minor allele frequency ≥ 0.3 were capable of assigning offspring to their 33 parents (18 sires and 15 dams).

Nocardia seriolae has caused significant fish losses in Asia and the Americas in recent decades, including in Vietnam, which has witnessed devastating economic and social impacts due to this bacterial pathogen. Surveillance strategies are urgently needed to mitigate N. seriolae dissemination in Vietnamese aquaculture and mariculture industries. Whole-genome sequencing (WGS) offers the highest level of resolution to discriminate closely related strains and to determine their putative origin and transmission routes. However, WGS is impractical for epidemiological investigations and pathogen surveillance due to its time-consuming and costly nature, putting this technology out-of-reach for many industry end-users. To overcome this issue, we targeted two previously characterised, phylogenetically informative single-nucleotide polymorphisms (SNPs) in N. seriolae that accurately distinguish: i) Vietnamese from non-Vietnamese strains, and ii) the two Vietnamese subclades. Using the mismatch amplification mutation assay (MAMA) format, we developed assays that genotype strains based on differences in amplicon melting temperature (melt-MAMA) and size (agarose-MAMA). Our MAMA assays accurately genotyped strains both from culture and fish tissues at low cost, using either real-time (~AUD$1/per sample) or conventional (~AUD$0.50/per sample) PCR instrumentation. Our novel assays provide a rapid, reproducible, and cost-effective tool for routine genotyping of this pathogen, allowing faster identification and treatment of nocardiosis-effected permit fish within Vietnamese aquaculture/mariculture facilities, an essential step in mitigating N. seriolae -associated losses.

Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species.

Stock enhancement involves the augmentation of wild populations with hatchery-reared recruits. Stock enhancement generally also includes a postrelease monitoring program which tracks stocked individuals within the fishery, and this relies on having a means to identify the likely origin of recaptured fish (e. g., physical, otolith, or genetic tags). This study reports the application of sibship analysis to retrospectively infer the origin of mulloway ( Argyrosomus japonicus ) within stocked estuaries when other means of identification were not available. Eight cohorts of mulloway were stocked into two estuaries across a seven-year period, but only some of the fish released during the program were physically marked with chemical otolith stains. Fish were sampled from stocked estuaries (mostly through an angler-based sampling program) and genotyped for six microsatellite loci, alongside 129 fish sampled from nonstocked estuaries. The presence of multiple sibs within the mixed populations in stocked estuaries was used to infer the origin of captured fish against a background of sibship for known-origin individuals (verified by otolith marks) and sibship levels within unstocked estuaries. The analysis suggested hatchery-reared fish could have contributed 9% of individuals sampled from the augmented populations (7% when corrected for background sibship). The proportion of fish inferred to be of hatchery origin decreased with size (likely due to mortality and migration), and the expected contribution rates for hatchery-reared fish differed among cohorts. The results highlight that sibship analysis may be useful for retrospective genetic evaluation of stocked estuaries.

The Portuguese oyster Crassostrea angulata is one of the economically important mollusc species but to date there has been no genetic improvement program conducted for this species. The principal aim of this study was to assess genetic gains achieved from a selection program for improved whole weight at harvest over three generations from 2015 to 2017. A total of 30,212 oysters had performance data recorded; they were the offspring of 323 sires and 461 dams. Linear mixed models were used to estimate genetic parameters of the traits studied. Selection for improved harvest whole weight achieved significant direct response by 17.4% after three generations. There were also positively correlated changes in soft tissue weight and shell shape traits (3.67% and 3.98%, respectively). The genetic gains in harvest whole weight and favourably correlated changes in meat yield and shell shape traits were consistent with the positive genetic correlations of whole weight with these traits (0.08-0.50). There is abundant genetic variation in the selection criterion (heritability for whole weight = 0.24), suggesting that the present population of Portuguese oysters will continue showing responses to future selection. The estimates of heritability for meat yield and shell shape traits were low (0.10-0.16). Hence, a multi-trait selection program can be used to enhance overall productivity and economic return for oyster producers.

Delineating stocks and quantifying population structure are critical for the management of exploited populations, but the stock structure of many species remains unclear. In New South Wales (NSW), Australia, a marine stock enhancement program for dusky flathead (Platycephalus fuscus) is developing, and knowledge of stock structure is required to inform enhancement strategies, as well as to support broader fisheries management. A combination of mitochondrial and microsatellite markers was used in this study to evaluate structuring among fish from eight estuaries, spanning the majority of the NSW coast. Pairwise comparisons of mitochondrial haplotypes revealed that seven of the eight estuaries were genetically homogeneous (St Georges Basin was distinct). Moreover, analysis of molecular variance showed that 97% of sequence diversity occurred within estuaries. The results from microsatellite markers were almost identical to those for mitochondrial DNA, with St George’s Basin having the only distinct genotype, and within estuary variation accounting for 99% of the genotype variation. Isolation by distance analysis showed that <5% of genetic variation was due to distance. These results indicate that dusky flathead forms a single stock across NSW, where mixing most likely occurs during early life phases and through limited adult migration. The outlying estuary, St Georges Basin, likely suffers from limited connectivity due to a constricted entrance, and it is possible that stocking may improve local genetic diversity.

This paper shows the results of the efficiency of a circulating fluidized bed biofiltration system using polyethelene as a filtering material.Changes in water quality parameters and the growth rates of shrimp (broodstock and commercial production) were used to assess the efficiency of water treatment system.The concentration of NH4 + in waste water from the broodstock tanks decreased 61% after three months of treatment.The final concentration of NH4 + after treatment was 0.07 mg/ml which meet the Vietnamese regulations for discard of aquaculture waste into coastal waters.Biological oxygen demand decreased 48%.The corresponding figures for treating waste water from commercial shrimp tanks were decreases of NH4 + by up to 61% with outlet concentration 0.07 mg/ml accepted to discard according to Vietnamese Standard and biological oxygen demand by 55%.Outlet water providing from broodstock and commercial shrimp tanks were treated with COD concentration decreased from 3.12 down to 2.62 mg/ml and 4.62 down to 2.68 mg/ml, or 16% and 41.9% of COD removal, respectively.

Production of the Portuguese oyster, Crassostrea angulata, is increasing rapidly in Vietnam, and consumer preferences for oyster appearance and meat quality have become more economically important. However, no studies have been conducted to estimate genetic parameters for meat colour, edible traits and the occurrence of disfiguring parasite infestation in any oyster species. In this study, we report genetic parameters for parasite disease traits, objective measurements of shell and mantle colours (L*, a* and b* colour) and edible traits (water holding capacity, taste and tenderness) for a selectively bred Portuguese oyster breeding population. We applied a restricted maximum likelihood method to estimate genetic parameters for the traits studied. Heritability estimates for the colour measurements of shell and mantle were low to high (h(2) = 0.13-0.57), whereas those obtained for the parasite diseases on shells and tissues were close to zero (h(2) = 0.011). Interestingly, there was genetic variation in edible traits (h(2) = 0.04-0.17). The genetic correlations among whole weight and parasitic shell and tissue disease traits was significant but unfavourable, whereas the genetic correlations between whole weight and water holding capacity was considerable and favourable (r(g) = 0.87 +/- 0.05). These suggest that a multi-trait restricted selection index should be used to improve productivity and economic returns for the oyster aquaculture sector.

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 (h(2) = 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.