Analysis of genetic variation and inbreeding among three lines of hatchery-reared Crassostrea virginica broodstock

Varney, Robin L.; Wilbur, Ami E.

doi:10.1016/j.aquaculture.2020.735452

Cited by 19 publications

(14 citation statements)

References 56 publications

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“…Although the direct comparison of heritability estimates from different studies is difficult (e.g., due to intrinsic differences between populations), estimates for growth rate in oysters tend to be moderate (e.g., 0.31 and 0.55— Evans and Langdon (2006) and De Melo et al (2016) , respectively). As a result, fast-growing lines of oysters have been developed for some of the main commercial species, such as the Pacific ( C. gigas ) ( Zhang et al, 2019 ), Portuguese ( C. angulata ) ( Vu et al, 2020 ), Eastern ( C. virginica ) ( Varney and Wilbur, 2020 ) and Sydney rock ( Saccostrea glomerata ) ( Fitzer et al, 2019 ) oyster. Initial attempts to genetically improve the European flat oyster O. edulis resulted in an average 23% increase in growth rate compared to an unselected (control) line ( Newkirk and Haley, 1982 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…The latter practice provides a valuable opportunity to explore the effects of oyster genetic identity and diversity in the form of different seed sources with unique population histories (e.g. commercial hatchery lines versus wild progenitor cohorts; [64,65]). While small-scale manipulations indicate that oyster seed source variation underlies differences in population characteristics and performance [66][67][68], whether these effects scale up to the reef level and impact community dynamics requires examination.…”

Section: Methods (A) Study Systemmentioning

confidence: 99%

Host genetic identity determines parasite community structure across time and space in oyster restoration

et al. 2023

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Intraspecific variation in host susceptibility to individual parasite species is common, yet how these effects scale to mediate the structure of diverse parasite communities in nature is less well understood. To address this knowledge gap, we tested how host genetic identity affects parasite communities on restored reefs seeded with juvenile oysters from different sources—a regional commercial hatchery or one of two wild progenitor lines. We assessed prevalence and intensity of three micro- and two macroparasite species for 4 years following restoration. Despite the spatial proximity of restored reefs, oyster source identity strongly predicted parasite community prevalence across all years, with sources varying in their relative susceptibility to different parasites. Oyster seed source also predicted reef-level parasite intensities across space and through time. Our results highlight that host intraspecific variation can shape parasite community structure in natural systems, and reinforce the importance of considering source identity and diversity in restoration design.

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“…0.26 and 0.31 – De Melo et al (2016) and Evans and Langdon (2006), respectively). As a result, fast-growing lines of oysters have been developed for some of the main commercial species, such as the Pacific ( C. gigas ) (Zhang et al 2019), Portuguese ( C. angulata ) (Vu et al 2020), American ( C. virginica ) (Varney and Wilbur 2020) and Sydney rock ( Saccostrea glomerata ) (Fitzer et al 2019) oyster. Initial attempts to genetically improve the European flat oyster O. edulis resulted in a 23% increase in growth rate compared to an unselected (control) line (Newkirk and Haley 1982).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

Peñaloza

Barría

Papadopoulou

et al. 2022

Preprint

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The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed in 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 anthropogenic activities 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 moderate-low, 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 genetic 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 (down to 100 SNPs) 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 relationship should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

show abstract

Analysis of genetic variation and inbreeding among three lines of hatchery-reared Crassostrea virginica broodstock

Cited by 19 publications

References 56 publications

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

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

Host genetic identity determines parasite community structure across time and space in oyster restoration

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

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