title: Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing.
abstract: Gilthead sea bream (Sparus aurata) is a species of paramount importance to the Mediterranean aquaculture industry, with an annual production exceeding 140,000 metric tons. Pasteurellosis due to the Gram-negative bacteriumPhotobacterium damselaesubsp.piscicida(Phdp) causes significant mortality, especially during larval and juvenile stages, and poses a serious threat to bream production. Selective breeding for improved resistance to pasteurellosis is a promising avenue for disease control, and the use of genetic markers to predict breeding values can improve the accuracy of selection, and allow accurate calculation of estimated breeding values of nonchallenged animals. In the current study, a population of 825 sea bream juveniles, originating from a factorial cross between 67 broodfish (32 sires, 35 dams), were challenged by 30 min immersion with 1 × 105CFU virulent Phdp. Mortalities and survivors were recorded and sampled for genotyping by sequencing. The restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. A high-density linkage map containing 12,085 SNPs grouped into 24 linkage groups (consistent with the karyotype) was constructed. The heritability of surviving days (censored data) was 0.22 (95% highest density interval: 0.11-0.36) and 0.28 (95% highest density interval: 0.17-0.4) using the pedigree and the genomic relationship matrix respectively. A genome-wide association study did not reveal individual SNPs significantly associated with resistance at a genome-wide significance level. Genomic prediction approaches were tested to investigate the potential of the SNPs obtained by 2b-RAD for estimating breeding values for resistance. The accuracy of the genomic prediction models (r= 0.38-0.46) outperformed the traditional BLUP approach based on pedigree records (r= 0.30). Overall results suggest that major quantitative trait loci affecting resistance to pasteurellosis were not present in this population, but highlight the effectiveness of 2b-RAD genotyping by sequencing for genomic selection in a mass spawning fish species.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG Scotland, United Kingdom christos.palaiokostas@roslin.ed.ac.uk luca.bargelloni@unipd.it.
authors.forename: Christos
authors.identifier: http://orcid.org/0000-0002-4480-4612
authors.initials: C
authors.lastname: Palaiokostas
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy.
authors.forename: Serena
authors.identifier: http://orcid.org/0000-0001-5928-9361
authors.initials: S
authors.lastname: Ferraresso
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy.
authors.forename: Rafaella
authors.identifier: http://orcid.org/0000-0002-1333-0733
authors.initials: R
authors.lastname: Franch
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG Scotland, United Kingdom.
authors.forename: Ross D
authors.identifier: http://orcid.org/0000-0003-1805-0762
authors.initials: RD
authors.lastname: Houston
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy christos.palaiokostas@roslin.ed.ac.uk luca.bargelloni@unipd.it.
authors.forename: Luca
authors.identifier: http://orcid.org/0000-0003-4351-2826
authors.initials: L
authors.lastname: Bargelloni
keywords: 2b-RAD; Aquaculture; Breeding; GenPred; Genomic Selection; High-Throughput sequencing; Shared Data Resources