Oyster Gene Marker for Herpesvirus Resistance Offers No Shield Against Bacterial Pathogen

The Pacific oyster, Crassostrea (Magallana) gigas, dominates global oyster aquaculture, accounting for more than 98 percent of all oyster production worldwide with over five million metric tons produced annually. Its production, however, is threatened by two major pathogens: ostreid herpesvirus 1 (OsHV-1), a virus capable of causing mass mortality events, and the bacterium Vibrio aestuarianus, which has caused recurrent oyster mortalities in Europe since 2001 and is emerging as a serious threat to oyster aquaculture in British Columbia, Canada. A new study published in Aquaculture Science and Management reports that a genetic marker long used to breed OsHV-1-resistant oysters does not influence susceptibility to V. aestuarianus, a finding with direct consequences for selective breeding programs on the west coast of North America.

The marker in question sits on chromosome 8 of the Pacific oyster genome and is associated with an upregulated interferon regulatory factor antiviral gene, irf2, which is thought to increase resistance to OsHV-1 infection. Oysters carrying the alternate allele of this locus may be genetically primed to defend against viral infections. Marker-assisted selective breeding, using a fluorescence-based rhAmp genotyping assay, has already produced oyster families with increased survivorship to OsHV-1 through the Molluscan Broodstock Program (MBP) at Oregon State University. But selective breeding for one trait can carry fitness trade-offs, and a recent study by Lunda and colleagues found that the same Chr8 marker was associated with increased survivorship of heterozygous larvae and spat to a different bacterial pathogen, Vibrio coralliilyticus. That raised an open question: would the marker help, harm, or leave untouched resistance to V. aestuarianus?

To answer it, researchers produced sixteen oyster families with various Chr8 marker genotypes through the MBP in February 2023. Four of these families, designated F114 through F117, had parents that were both heterozygous at the marker, meaning their offspring carried all possible genotypic states: homozygous reference, heterozygous, and homozygous alternate. Six families produced offspring that were all homozygous reference and six were all heterozygous. No families were produced from crosses where both parents were homozygous for the alternate allele. An additional family from the Vancouver Island University oyster breeding program, which has not been selected for OsHV-1 resistance, was included as a comparison. Spat from all families were shipped to Vancouver Island University’s Deep Bay Marine Field Station and Centre for Shellfish Research in British Columbia for the disease challenge.

The challenge itself was designed to mimic realistic conditions. Rather than injecting bacteria directly, which bypasses natural immune barriers, or using co-habitation, which gives unreliable timing and magnitude of mortality, the team used a bath exposure. Forty-eight spat, each five to ten millimeters in shell length, from each family were placed individually into wells of twelve-well plates containing filtered, UV-sterilized seawater. A V. aestuarianus suspension, strain BS032 2018, was added to reach a final concentration of 2.45 × 10⁷ colony-forming units per milliliter, and the temperature was raised from 16 to 23 degrees Celsius for five days to simulate a marine heatwave event before returning to 16 degrees on the sixth day. Algae were added to encourage feeding and bacterial uptake. A non-exposed control group of 48 oysters from multiple families was treated identically except for the bacteria. Morbidity was measured daily for six days, and oysters were considered dead or moribund when their shell valves gaped and failed to close after gentle probing.

The results showed substantial mortality overall. No deaths occurred in the first two days. Among the 516 exposed, selectively bred oysters, 37.8 percent died on day three and 67.2 percent had died by day six, leaving 252 survivors. The unexposed control group exhibited 100 percent survival, indicating the mortality was caused by the bacterium. Family-level variation was striking: cumulative mortality averaged 67.2 plus or minus 9.5 percent, ranging from 47.9 percent in family F116 to 85.4 percent in family F106. Kaplan-Meier survival analysis confirmed that survival distributions differed significantly among families, with F106 oysters dying more rapidly than those in five other families.

Before the challenge even began, the researchers observed something unexpected. In the four families with heterozygous parents, genotype frequencies at the Chr8 marker departed from the expected Mendelian ratio of 1:2:1. Across the four families, heterozygotes were most common at 57 percent, homozygous reference at 25 percent, and homozygous alternate at only 18 percent. Family F115 had significantly more homozygous alternate individuals than expected at 35 percent, while F114 and F117 had significantly fewer, at 11 and 7 percent respectively. Such genotype distortions are well documented in oysters, and although the deficit in two families might suggest the homozygous alternate genotype is less fit, the opposite trend in F115 points to other unknown factors that could matter for future breeding decisions around this marker.

The central finding, however, was a null result with practical weight. Challenged oysters from families F114 through F117 were individually genotyped at the Chr8 marker, and mortality was analyzed both as days to death and as a simple dead-or-alive outcome, with each family analyzed separately to avoid confounding interfamily effects. No significant association was found between offspring genotype and mortality in any family. In other words, neither the presence nor the allelic dosage of the OsHV-1 resistance allele affected survival to V. aestuarianus at this life stage. The authors interpret this as an absence of pleiotropy, meaning the marker carries no positive or negative effect on survivorship to this bacterial pathogen, and as evidence of no genetic correlation between OsHV-1 and V. aestuarianus survivorship through the mechanism associated with this marker.

The team went further, using reduced-representation sequencing of the challenged oysters to conduct a genome-wide association study for V. aestuarianus survivorship. Double-digest RAD sequencing produced hundreds of millions of reads aligned to a chromosome-level reference genome, ultimately yielding 8,193 single-nucleotide polymorphisms for analysis of 136 oysters from the four segregating families, 49 survivors and 87 that died. Using both unimputed and mean-imputed genotypes, and testing both the binary survival phenotype and days-to-death, the GWAS identified no loci significantly associated with survivorship at a Bonferroni-corrected threshold. The authors caution that the sample size is too small to detect moderate or low-effect loci, since GWAS typically requires thousands of individuals for such variants, but they note that resistance to Vibrio in marine bivalves has repeatedly shown polygenic architecture, consistent with their results.

The null result aligns with independent lines of evidence. Two French studies found no genetic correlation between resistance to OsHV-1 and V. aestuarianus, and transcriptome work has shown that the immune genes deployed against the virus and the bacterium are distinct. Notably, susceptibility to the two pathogens shifts in opposite directions with age: vulnerability to OsHV-1 decreases as oysters grow, while vulnerability to V. aestuarianus increases. The lack of increased susceptibility here is also notable because constitutive overexpression of antiviral immunity through irf2 might have been expected to impose a cost against bacterial infection, yet no such trade-off appeared. At the same time, the earlier V. coralliilyticus finding shows this is not a universal pattern, and the authors suggest that species-specific immune evasion strategies, or the ability of some intracellular bacteria to trigger interferon-like host responses, may explain why one Vibrio species responds to the marker’s effects and the other does not.

For breeding programs, the message is cautiously reassuring. Combining this study with the V. coralliilyticus results, there appears to be no negative trade-off from using the Chr8 marker in marker-assisted selection with respect to Vibrio resistance. Because the marker is independent of V. aestuarianus resistance, identifying loci for that trait separately could eventually allow selection for resistance to both viral and bacterial threats. The authors suggest, however, that given the likely polygenic basis of Vibrio resistance, genomic selection may ultimately serve better than marker-assisted selection for this trait. They also note unmeasured avenues for future work, including growth rates and other energetic trade-offs, epigenetic factors that a recent GWAS on Pacific oyster mortality syndrome suggested can outweigh genetic ones, and whether V. coralliilyticus triggers an interferon-like response in the oyster. Significant family differences in susceptibility persisted even within MBP families selectively bred for at least six generations, underscoring how much remains to be learned about the genetics of bacterial disease resistance in this globally important species.

Subject of Research: Effect of an OsHV-1 resistance marker on Pacific oyster susceptibility to Vibrio aestuarianus

Article Title: The presence of a marker associated with Pacific oyster resistance to OsHV-1 does not affect susceptibility to Vibrio aestuarianus

Article References: Surry, L. B., Sutherland, B. J. G., Lunda, S. L., Loudon, A. H., Divilov, K., Langdon, C. J., & Green, T. J. (2026). The presence of a marker associated with Pacific oyster resistance to OsHV-1 does not affect susceptibility to Vibrio aestuarianus. Aquaculture Science and Management, 3(1), Article 10. https://doi.org/10.1186/s44365-026-00038-6

Image Credits: AI Generated

DOI: 10.1186/s44365-026-00038-6

Keywords: Pacific oyster, OsHV-1, Vibrio aestuarianus, marker-assisted selection, disease resistance, aquaculture, GWAS, genetics, selective breeding, molluscan broodstock, presence, marker