DOI: 10.5061/dryad.rr4xgxd6d
title: SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum

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.
description: 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 &gt;0.3;
 Coverage 25x-100x; Stable flanking region &gt;100 bp, Presence in both
 populations; Biallelic; Max 1 SNP/contig.