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

Citation

Smits, Morgan (2020), SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum, Dryad, Dataset, https://doi.org/10.5061/dryad.rr4xgxd6d

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 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.

Methods

Samples from the Venice lagoon (50 individuals) and from a French hatchery (109 individuals) were sequenced as two pools using Illumina HiSeq 4000. 150 PE reads were aligned to the draft genome of the Manila clam provided by collaborators from the University of Bologna (Ghiselli et al., 2017; doi:10.7287/peerj.preprints.3096) using CLC Genomics Workbench, and SNP identification carried out using PoPoolation2 pipeline. Candidate SNPs were selected according to the following criteria: MAF >0.3; Coverage 25x-100x; Stable flanking region >100 bp, Presence in both populations; Biallelic; Max 1 SNP/contig.

Funding

Horizon 2020 Framework Programme, Award: VIVALDI 678589

Regione del Veneto, Award: POR-FESR 10062983

Agence Nationale de la Recherche, Award: ANR-10-LABX-19

Agence Nationale de la Recherche, Award: ANR-17-EURE-0015

Fondazione Cassa di Risparmio di Padova e Rovigo, Award: Borsa Dottorato di Ricerca 32° Ciclo UNIPD