A genome-wide association study for host resistance to Ostreid Herpesvirus in Pacific oysters (<i>Crassostrea gigas</i>)

Gutiérrez, Alejandro P.; Bean, Tim P.; Hooper, Chantelle; Stenton, Craig A.; Sanders, Matthew; Paley, Richard; Rastas, Pasi; Bryrom, Michaela; Matika, Oswald; Houston, Ross D.

doi:10.1101/223032

Cited by 18 publications

(52 citation statements)

References 41 publications

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“…The approximately 20 000 mapped SNPs correspond to 1880 scaffolds and 133 contigs, according to the latest oyster genome assembly (GCA_000297895.1; Zhang et al ). We observed that approximately 38% (719 out 1880) of the scaffolds with informative markers showed evidence of errors in the assembly, owing to assignment to at least two distinct LGs in our map, following a similar pattern to that described in our previous linkage map (Hedgecock et al ; Gutierrez et al ).…”

Section: Resultssupporting

confidence: 83%

“…The linkage map construction resulted in approximately 20 000 SNPs distributed across 10 linkage groups in similar positions to those previously described in a different population (Gutierrez et al ). As with previous linkage maps, the mapping of SNPs located within single reference genome contigs to multiple linkage groups highlighted putative reference genome assembly errors (Zhang et al ; Hedgecock et al ).…”

Section: Discussionmentioning

confidence: 63%

“…In particular, a previous study found that LGs V–VII and IX (which correspond to LGs 6–8 and 10 on our map) contain genomic regions associated with summer mortality resistance (Sauvage et al ). Additionally, we recently reported that regions on multiple LGs are probably involved in the resistance to OsHV‐1 in a Pacific oyster population from Guernsey (Gutierrez et al ). When taken together, these studies suggest that host resistance to OsHV‐1 in Pacific oyster is consistently a polygenic trait.…”

Section: Discussionmentioning

confidence: 99%

“…This causes periodic mass mortality in farms worldwide and has been mainly attributed to a specific variant of the ostreid herpesvirus (OsHV‐1; Segarra et al ), amongst other factors (Malham et al ; Petton et al ; de Lorgeril et al ). Selective breeding to improve resistance to OsHV‐1 may have potential as a prevention strategy, and there is significant additive genetic variation in survival during OsHV‐1 infection, with estimated heritability values ranging from 0.12 to 0.63 (Dégremont et al ; Azéma et al ; Camara et al ; Gutierrez et al ). However, QTL and GWAS approaches to investigating the genetic architecture of host resistance to the virus have suggested that the trait may be polygenic (Sauvage et al ; Gutierrez et al ).…”

Section: Introductionmentioning

confidence: 99%

“…Selective breeding to improve resistance to OsHV‐1 may have potential as a prevention strategy, and there is significant additive genetic variation in survival during OsHV‐1 infection, with estimated heritability values ranging from 0.12 to 0.63 (Dégremont et al ; Azéma et al ; Camara et al ; Gutierrez et al ). However, QTL and GWAS approaches to investigating the genetic architecture of host resistance to the virus have suggested that the trait may be polygenic (Sauvage et al ; Gutierrez et al ). For that reason, marker‐assisted selection for OsHV‐1 resistance is unlikely to be effective, and the trait is a good candidate for genomic selection.…”

Section: Introductionmentioning

confidence: 99%

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Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

et al. 2020

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Summary In genomic selection (GS), genome‐wide SNP markers are used to generate genomic estimated breeding values for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the ‘summer mortality syndrome’. This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the ostreid herpesvirus (OsHV‐1). In the current study, we evaluated the potential of genomic selection for host resistance to OsHV‐1 in Pacific oysters, and compared it with pedigree‐based approaches. An OsHV‐1 disease challenge was performed using an immersion‐based virus exposure treatment for oysters for 7 days. A total of 768 samples were genotyped using the medium‐density SNP array for oysters. A GWAS was performed for the survival trait using a GBLUP approach in blupf90 software. Heritability ranged from 0.25 ± 0.05 to 0.37 ± 0.05 (mean ± SE) based on pedigree and genomic information respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below approximately 500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programmes, and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate genomic estimated breeding values, thus potentially making the implementation of GS more cost effective.

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Section: Resultssupporting

confidence: 83%

Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

et al. 2020

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Genomic selection in salmonids: new discoveries and future perspectives

et al. 2021

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Over the past 20 years, the introduction of new molecular techniques has given a new impetus to genetic and genomic studies of fishes. The main traits selected in the aquaculture sector conform to the polygenic model, and, thus far, effective breeding programmes based on genome-wide association studies (GWAS) and marker-assisted selection (MAS) have been applied to simple traits (e.g. disease resistance and sexual maturation of salmonids) and known Quantitative Trait Loci (QTLs). Genomic selection uses the genomic relationships between candidate loci and SNPs distributed over the entire genome and in tight linkage disequilibrium (LD) with genes that encode the traits. SNP (low and high density) arrays are used for genotyping thousands of genetic markers (single nucleotide polymorphisms, SNPs). The genomic expected breeding value (GEBV) of selection candidates is usually calculated by means of the GBLUP or ssGBLUP (single step) methods. In recent years, in several aquaculture breeding programmes, the genomic selection method has been applied to different fish and crustacean species. While routine implementation of genomic selection is now largely carried out in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), it is expected that, in the near future, this method will progressively spread to other fish species. However, genomic selection is an expensive method, so it will be relevant mostly for traits of high economic value. In several studies (using different salmonid species), the accuracy of the GEBVs varied from 0.10 to 0.80 for different traits (e.g. growth rate and disease resistance) compared to traditional breeding methods based on geneology. Genomic selection applied to aquaculture species has the potential to improve selection programmes substantially and to change ongoing fish breeding systems. In the long term, the ability to use low-pass genome sequencing methods, low-cost genotyping and novel phenotyping techniques will allow genomic selection to be applied to thousands of animals directly at the farm level.

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Susceptibility variation to the main pathogens of Crassostrea gigas at the larval, spat and juvenile stages using unselected and selected oysters to OsHV-1 and/or V. aestuarianus

Dégremont

Morga

Maurouard

et al. 2021

Journal of Invertebrate Pathology

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French commercial hatcheries are massively producing Crassostrea gigas selected for their higher resistance to OsHV-1, and soon should also implement selection for increasing resistance to Vibrio aestuarianus. The first objective of this study was to optimize the breeding programs for dual resistance to OsHV-1 and V. aestuarianus to determine the earliest life stage for which oysters are able to develop disease resistance. Wild stocks and selected families were tested using experimental infections by both pathogens at the larval, spat and juvenile stages.Oyster families could be evaluated for OsHV-1 as soon as the larval stage by a bath method, but this only highlighted the most resistant families; those that showed the highest resistance to V. aestuarianus could be determined using the cohabitation method at the juvenile stage.The second objective of this study was to determine if selection to increase/decrease the resistance to OsHV-1 and V. aestuarianus could have an impact on other major pathogens currently detected in hatchery at the larval stage, and in nursery and field at the spat/juveniles stages (V. coralliilyticus, V. crassostreae, V. tasmaniensis, V.neptunius, V. europaeus, V. harveyi, V. chagasi). No relationship was found between mortality caused by V. aestuarianus/OsHV-1 and the mortality caused by the other virulent bacterial strains tested regardless the stages, except between OsHV-1 and V. tasmaniensis at the juvenile stage.Finally, miscellaneous findings were evidenced such as (1) bath for bacterial challenges was not adapted for spat, (2) the main pathogens at the larval stage were OsHV-1 and V. coralliilyticus using bath, while it was V. coralliilyticus, V. europaeus, and V. neptunius at the juvenile stage by injection, and (4) variation in mortality was observed among families/wild controls for all pathogens at larval and juvenile stages, except for V. harveyi for larvae.

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A genome-wide association study for host resistance to Ostreid Herpesvirus in Pacific oysters (Crassostrea gigas)

Cited by 18 publications

References 41 publications

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

Genomic selection in salmonids: new discoveries and future perspectives

Susceptibility variation to the main pathogens of Crassostrea gigas at the larval, spat and juvenile stages using unselected and selected oysters to OsHV-1 and/or V. aestuarianus

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