Background
Bivalve molluscs aquaculture has steadily increased over the past decades as a source of healthy food rich in omega-3 and omega-6 fatty acids, with a relatively low carbon footprint. However, like other sessile species, molluscs cannot escape unfavourable environmental conditions and are therefore particularly vulnerable to climate change (CC)-induced stressors such as marine heatwaves (MHWs) and pathogen outbreaks. These events can cause massive mortality, as observed during the 2003 MHW and 2024 (summer period), which led to widespread losses of benthic invertebrates across the Northwestern Mediterranean.
Within this context, selective breeding represents a promising strategy to produce mollusc seed with enhanced tolerance to CC-related stressors. This potential is largely driven by the high within-species genetic diversity of molluscs, which remains only partially exploited.
Methods
To test this potential, within the EU-funded project ShellFishBoost, we experimentally assessed tolerance to key CC-related stressors in the Manila clam, Ruditapes philippinarum. We produced an F1 population from controlled crosses involving 20 dams and 20 sires, and exposed juveniles to: i) a simulated MHW in the laboratory lasting 21 days, with temperatures oscillating between 31 and 35 °C to mimic natural daily cycles; and ii) a natural infection challenge by seeding individuals in the Venice lagoon and monitoring infection by the endemic protozoan parasite Perkinsus olsenii.
For the MHW experiment, approximately 1,000 individuals were randomly distributed across 10 aquaria. Tissue samples were collected twice daily from dead or moribund (i.e. susceptible) individuals. After 21 days, water temperature was reduced to 25 °C and mortality was monitored for an additional 8 days. Surviving individuals were classified as resistant and sampled accordingly. Overall mortality reached 55% by the end of the experiment.
For the infection experiment, approximately 10,000 individuals were deployed in the Venice lagoon and P. olsenii prevalence was monitored monthly. When prevalence reached ~50%, 1,000 individuals were randomly sampled and preserved in ethanol. Gill tissue was used to quantify infection intensity.
Results
Samples from both experiments were genotyped using a newly developed multi-species Axiom SNP array (~49K SNPs for Manila clam). Of the 1,920 genotyped individuals, 1,905 (>99%) passed dish quality control and call rate thresholds, with an average call rate of 98.5%. A total of 35,284 SNPs (71.4%) were classified as poly-high-resolution and used to reconstruct pedigree and family structure. Combined pedigree and phenotypic data (i.e. MHW survival as a binary trait; Perkinsus load as a continuous trait) were used to estimate heritability of "MHW tolerance" and "Perkinsus resistance." Analyses are ongoing, with to goal to assess the feasibility of selective breeding programs to enhance resilience to these stressors in Manila clams.