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Microsatellite data for Atlantic Mackerel

Supplemental Material for Left Ventricular Venting During Extracorporeal Membrane Oxygenation; the Effects on Cardiac Performance in a Porcine Model of Critical Post-cardiotomy Failure by Atle Solholm, Pirjo-Riitta Salminen, Lodve Stangeland, Geir Olav Dahle, Arve Mongstad, Bård Svenheim, Liqun Zhang, Rune Haaverstad and Ketil Grong in Perfusion

Additional file 1. Supplementary material on microsatellite loci used (Appendix 1), PCR conditions (Appendix 2), overview of anadromous trout returning to Guddal River several times during the study period (Appendix 3), and proportion of anadromous trout ascending the river in different weeks in specific years (Appendix 4).

Additional file 6 : Figure S1. α-plot for the determination of optimal number of principal components retained in DAPC with 33 k data. Figure S2. Distribution of observed heterozygosity for the used 33,235 SNP loci over all loci in all populations (main figure). Locus-wise distribution per population is shown in the upper right corner (small figure). Figure S3 a) and b). Assignment plot (a) and compo plot (b) of 60 goldsinny wrasses based on 33 k SNPs. All individuals have very high probability to belong to the same population from where they were sampled. Figure S4 a) and b). Selection test result from the BayeScan analysis shown as figure for a) the whole dataset, and b) for the Scandinavian populations only. Loci on the right side of the vertical line are observed outliers, and thus suggested being under selection. Figure S5 a.-d). Figures related to selection test for the whole genomic dataset (all four populations) with PCadapt a) Scree plot to determine number of Ks. Because the curve plateaus after K = 4, that was the selected number of clusters. b) Histogram of p-values. The excess of small p-values indicates presence of outliers. c) Manhattan plot displays -log10 of the p-values. d) Q-Q plot show that many p-values do not follow expected uniform distribution confirming outliers. Figure S6 a.-d). Figures related to selection test for the Scandinavian genomic dataset (two populations) with PCadapt. Figure S7. Heatmap of linkage between the used 173 SNP loci. Figure S8a-e. Expected vs observed FST between Scandinavian goldsinny wrasse populations. Figure S9. Loading plot showing individual locus contribution of the genetic divergence between the Scandinavian goldsinny wrasse populations. Figure S10. Assignment accuracy divided by populations with different proportions of the 173 SNP loci based on Monte Carlo resampling procedure.

Supplemental material, Supplementary_File_NEW_12.04.18 for Left ventricular dysfunction after two hours of polarizing or depolarizing cardioplegic arrest in a porcine model by Terje Aass, Lodve Stangeland, Christian Arvei Moen, Atle Solholm, Geir Olav Dahle, David J. Chambers, Malte Urban, Knut Nesheim, Rune Haaverstad, Knut Matre and Ketil Grong in Perfusion

Probabilities for heterozygote genetic markers in hybrids . (PDF 29 kb)

Additional file 3: Table S2. Pairwise genetic differentiation (F ST) among adult and juvenile cod samples.

Additional file 2: Figure S1. Comparison of population differentiation (F ST) and heterozygosity (H E) among 15 samples of cod in eight microsatellite loci to identify outliers and potential candidates for selection using LOSITAN. All loci are candidates to be selectively neutral.

Additional file 4: Table S3. Pair-wise genetic differentiation between cod reference samples.

Additional file 1: Table S1. Overall genetic differentiation (F ST) among cod samples for eight microsatellite loci.

Additional file 5: Table S4. Assessment of sample size in reference samples for genetic assignment of migratory fish.

Supplemental Materials. (DOC 2321 kb)

Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1–5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a genome wide association study (GWAS) using a pool sequencing approach (20 individuals per river and phenotype) of male salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNPs in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33–36% phenotypic variation. A single locus was found to have a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in humans (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates., Author Summary For most species the factors that contribute to the genetic predisposition for age at maturity are currently unknown. In salmon aquaculture early maturation is negative for the growth, disease resistance and flesh quality. In addition, using populations of salmon selected to mature late may limit the genetic impact of aquaculture escapees, as these late maturing fish are more likely to die before they reach maturity. The aim of this study was to elucidate the genetic predisposition for salmon maturation. We determined the sequences of genomes from Atlantic salmon maturing early and late in six Norwegian rivers. This methodology enabled us to identify a short genomic region involved in determining the age at maturity in male Atlantic salmon. This region has also previously been linked to time of puberty in humans–supporting a general mechanism behind age at maturity in vertebrates. The results of this study may be used to breed salmon that are genetically predisposed to mature late which will improve welfare and production in aquaculture industry and aid in the management of escaped farmed salmon.

Havforskningsinstituttet fikk høsten 2010 i oppdrag fra Fiskeridirektoratet å gjennomføre en omfattende utredning av oppdrettet torsk sin innflytelse på vill torsk for å vurdere mulige effektindikatorer i forbindelse med rømming fra oppdrettsanlegg. Dette gjaldt både påvirkning fra gyting i merd og effekter av konkrete rømminger. I denne forbindelse ble Havforsk-ningsinstituttet bedt om å gjennomføre en vitenskapelig undersøkelse, med spesielt fokus på Skjerstadfjorden i Nordland. Denne rapporten presenterer det arbeidet som ble gjennomført i Skjerstadfjorden høsten 2010 og våren 2011. For å få et helhetlig bilde av situasjonen i fjordsystemet, ble prøver tatt på gytefelt i Skjerstadfjorden i 2004 og 2005, i tillegg til en prøve samlet inn av Fiskeri-direktoratet i 2009 fra et oppdrettsanlegg i fjorden, inkludert i analysene. De første oppdrettskonsesjonene ble gitt i 2007, og man kan derfor anta at det ikke har vært satt ut oppdrettsfisk i merd av betydning i fjorden før 2008. Den siste oppdrettsfisken ble slaktet ut desember 2010. Det ble funnet signifikant forskjell mellom oppdrettsfisken og villfisken i området, mens prøver tatt av gytefisk i 2011 ikke er forskjellig fra gytefisk fanget inn før oppdrett ble etablert i fjorden (2004 og 2005). Det er heller ikke mulig å påvise tilstedeværelse av oppdrettstorsk i fjorden utenom gytesesongen med genetiske metoder, og analysene viser ingen tegn til innblanding av oppdrettsfisk i yngelen produsert på gytefeltet i 2011