Abstract
The Manila clam Ruditapes philippinarum, a major cultured shellfish species, is threatened by infection with the microparasite Perkinsus olseni, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against P. olseni, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR. A mixed-family cohort of potentially 1,479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of P. olseni had previously been reported. Growth and parasite load were monitored every month and, after 1 year, more than 1,000 individuals were collected for DNA samples and phenotype recording. A pooled sequencing approach was carried out using DNA samples from the hatchery broodstock and from a Venice lagoon clam population, providing candidate markers used to develop a 245-SNP panel. Parentage assignment for 246 F1 individuals showed sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.23 ± 0.11–0.35 ± 0.13) was estimated for growth traits (shell length, shell weight, total weight), while parasite load showed high heritability, estimated at 0.51 ± 0.20. No significant genetic correlations were found between growth-associated traits and parasite load. Overall, the preliminary results provided by this study show high potential for selecting clams resistant to parasite load. Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.
Highlights
Infectious diseases continue to be a major limit in fish and shellfish aquaculture, with production losses estimated to cost over 6 billion USD per annum, and far more in treatments such as vaccinations, cleaning, and antibiotics [1, 2]
Given the inherent difficulties in eliminating pathogens in the open-water environments most often used in aquaculture, genetic selection provides a feasible and sustainable solution to mitigating the impact of infectious diseases by identifying genetic factors associated with traits of interest such as disease resistance and growth
Most of the studies carried out so far seeking to evaluate the potential for genetic gain in bivalves have focused on traits such as disease resistance, growth rate, meat yield, and visual aspects such as shape and shell color, and relatively few have tackled the estimation of genetic parameters across all traits simultaneously [30]
Summary
Infectious diseases continue to be a major limit in fish and shellfish aquaculture, with production losses estimated to cost over 6 billion USD per annum, and far more in treatments such as vaccinations, cleaning, and antibiotics [1, 2]. Over the past 20 years, a number of commercial and experimental breeding programs have been introduced for mollusks [9,10,11,12,13,14,15,16,17,18], many of which have obtained high genetic gains due to a combination of high heritability for economically favorable traits, high fecundity allowing for high selection pressure, and relatively short generation intervals (1–4 years for most species) [19,20,21,22]. Despite the difficulties associated with obtaining parentage information for shellfish, several recent studies have successfully applied SNP panels for parentage assignment in order to estimate genetic parameters of traits of commercial interest in mollusks [26,27,28,29]. Balancing genetic gain for disease resistance with genetic gain for production traits is an essential step in designing rational breeding programs in order to evaluate the potential for genetic improvement across traits and, more importantly, to avoid selecting for a trait that may negatively affect other traits of interest
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