University of Padua

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

Smits, Morgan (2020) SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum. [Data Collection]

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Collection description

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.

DOI: 10.5061/dryad.rr4xgxd6d
Keywords: Ruditapes philippinarum, shellfish specie, microparasite Perkinsus olseni
Subjects: Life Sciences > Ecology, Evolution and Environmental Biology: Population, community and ecosystem ecology, evolutionary biology, behavioural ecology, microbial ecology > Marine biology and ecology
Life Sciences > Applied Life Sciences, Biotechnology and Molecular and Biosystems engineering: Applied plant and animal sciences; forestry; food sciences; applied biotechnology; environmental, and marine biotechnology; applied bioengineering; biomass, biofuels; biohazard > Marine Biotechnology (including marine bioproducts, feed resources, genome mining)
Department: Departments > Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente (DAFNAE)
Depositing User: Research Data Unipd
Date Deposited: 17 Oct 2023 15:29
Last Modified: 17 Oct 2023 15:29
Type of data: Text
Research funder: Horizon 2020 Framework Programme, Regione del Veneto, University of Padua - Phd Fellowship 32° Cycle Phd School, Agence Nationale de la Recherche, Fondazione Cassa di Risparmio di Padova e Rovigo
Collection period:
Resource language: en
Metadata language: en
Publisher: Dryad
Status: Published
Related publications:
Date: 2020
Date type: Publication
Copyright holders: The Authors

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