Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis).

The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

The increased prevalence of Vibrio species and the first reporting of Vibrio jasicida and Vibrio rotiferianus at UK shellfish sites.

Warming sea-surface temperature has led to an increase in the prevalence of Vibrio species in marine environments. This can be observed particularly in temperate regions where conditions for their growth has become more favourable. The increased prevalence of pathogenic Vibrio species has resulted in a worldwide surge of Vibriosis infections in human and aquatic animals. This study uses sea-surface temperature data around the English and Welsh coastlines to identify locations where conditions for the presence and growth of Vibrio species is favourable. Shellfish samples collected from three locations that were experiencing an increase in sea-surface temperature were found to be positive for the presence of Vibrio species. We identified important aquaculture pathogens Vibrio rotiferianus and Vibrio jasicida from these sites that have not been reported in UK waters. We also isolated human pathogenic Vibrio species including V. parahaemolyticus from these sites. This paper reports the first isolation of V. rotiferianus and V. jasicida from UK shellfish and highlights a growing diversity of Vibrio species inhabiting British waters.

Ephemeral detection of Bonamia exitiosa (Haplosporida) in adult and larval European flat oysters Ostrea edulis in the Solent, United Kingdom.

The haplosporidian parasite Bonamia exitiosa was detected using PCR in four adult and six larval brood samples of the European flat oyster Ostrea edulis from the Solent, UK. This represents the second reported detection of this parasite along the south coast of England. Adult oysters were collected and preserved from seabed populations or restoration broodstock cages between 2015 and 2018. The larvae within brooding adults sampled during 2017 and 2018 were also preserved. Molecular analysis of all samples was performed in 2019. The DNA of B. exitiosa was confirmed to be present within the gill tissue of one oyster within the Portsmouth wild fishery seabed population (n = 48), sampled in November 2015; the congeneric parasite Bonamia ostreae was not detected in this individual. This is the earliest record of B. exitiosa in the Solent. Concurrent presence of both B. ostreae and B. exitiosa, determined by DNA presence, was confirmed in the gill and heart tissue of three mature individuals from broodstock cages sampled in October 2017 (n = 99), two from a location on the River Hamble and one from the Camber Dock in Portsmouth Harbour. B. exitiosa was not detected in the November 2018 broodstock populations. A total of six larval broods were positive for B. exitiosa, with five also positive for B. ostreae. None of the brooding adults were positive for B. exitiosa suggesting that horizontal transmission from the surrounding environment to the brooding larvae is occurring. Further sampling of broodstock populations conducted by the Fish Health Inspectorate at the Centre for Environment, Fisheries and Aquaculture Science in June 2019 did not detect infection of O. edulis by B. exitiosa. These findings together suggest that the pathogen has not currently established in the area.

Active management is required to turn the tide for depleted Ostrea edulis stocks from the effects of overfishing, disease and invasive species.

The decline of the European oyster Ostrea edulis across its biogeographic range has been driven largely by over-fishing and anthropogenic habitat destruction, often to the point of functional extinction. However, other negatively interacting factors attributing to this catastrophic decline include disease, invasive species and pollution. In addition, a relatively complex life history characterized by sporadic spawning renders O. edulis biologically vulnerable to overexploitation. As a viviparous species, successful reproduction in O. edulis populations is density dependent to a greater degree than broadcast spawning oviparous species such as the Pacific oyster Crassostrea (Magallana) gigas. Here, we report on the benthic assemblage of O. edulis and the invasive gastropod Crepidula fornicata across three actively managed South coast harbors in one of the few remaining O. edulis fisheries in the UK. Long-term data reveals that numbers of O. edulis sampled within Chichester Harbour have decreased by 96%, in contrast numbers of C. fornicata sampled have increased by 441% over a 19-year period. The recent survey data also recorded extremely low densities of O. edulis, and extremely high densities of C. fornicata, within Portsmouth and Langstone Harbours. The native oyster's failure to recover, despite fishery closures, suggests competitive exclusion by C. fornicata is preventing recovery of O. edulis, which is thought to be due to a lack of habitat heterogeneity or suitable settlement substrate. Large scale population data reveals that mean O. edulis shell length and width has decreased significantly across all years and site groups from 2015 to 2017, with a narrowing demographic structure. An absence of juveniles and lack of multiple cohorts in the remaining population suggests that the limited fishing effort exceeds biological output and recruitment is poor. In the Langstone & Chichester 2017 sample 98% of the population is assigned to a single cohort (modal mean 71.20 ± 8.78 mm, maximum length). There is evidence of small scale (<5 km) geographic population structure between connected harbors; the 2015 Portsmouth and Chichester fishery populations exhibited disparity in the most frequent size class with 36% within 81-90 mm and 33.86% within 61-70 mm, respectively, the data also indicates a narrowing demographic over a short period of time. The prevalence of the disease Bonamiosis was monitored and supports this microgeographic population structure. Infection rates of O. edulis by Bonamia ostreae was 0% in Portsmouth Harbor (n = 48), 4.1% in Langstone (n = 145) and 21.3% in Chichester (n = 48) populations. These data collectively indicate that O. edulis is on the brink of an ecological collapse within the Solent harbors. Without effective intervention to mitigate the benthic dominance by C. fornicata in the form of biologically relevant fishery policy and the management of suitable recruitment substrate these native oyster populations could be lost.