SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum

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 1479 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 one year, more than 1000 individuals were
collected and DNA and phenotype records. A 245-SNP panel was developed
using candidate markers obtained from a pooled sequencing approach on two
DNA samples from all the potential parents and from a Venice lagoon clam
population. For 246 individuals of the mixed-family F1, sire and dam
representation were high (75 and 85%, respectively), indicating a very
limited risk of inbreeding. Moderate heritability (0.20 – 0.30) was
estimated for growth traits, while parasite load showed high heritability,
estimated at 0.52. No significant genetic correlations were found between
growth-associated traits and parasite load. Overall, the study shows 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.