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      Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout

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          Abstract

          A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

            More than a thousand disease susceptibility loci have been identified via genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings generally remain to be defined. We utilize pooled next-generation sequencing to study 56 genes in regions associated to Crohn’s Disease in 350 cases and 350 controls. Follow up genotyping of 70 rare and low-frequency protein-altering variants (MAF ~ .001-.05) in nine independent case-control series (16054 CD patients, 12153 UC patients, 17575 healthy controls) identifies four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association to a novel, protective splice variant in CARD9 (p < 1e-16, OR ~ 0.29), as well as additional associations to coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by providing novel, rare, and likely functional variants that will empower functional experiments and predictive models.
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              Guidelines for estimating repeatability

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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                09 July 2019
                September 2019
                : 9
                : 9
                : 2887-2896
                Affiliations
                [* ]Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
                []Department of Biology, University of Turku, FI- 20014, Turku, Finland
                []Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
                [§ ]Natural Resources Institute Finland, Manamansalontie 90, FI-88300, Paltamo, Finland
                [** ]Institute of Integrative Biology, University of Liverpool, Bioscience building, Crown street, L69 7BZ Liverpool, UK
                [†† ]Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia, and
                [‡‡ ]Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, 17893 Drottningholm, Sweden
                Author notes
                [1 ]Corresponding author: E-mail: lemopoulos.alexandre@ 123456gmail.com
                [2]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-7997-5526
                http://orcid.org/0000-0003-2723-1012
                http://orcid.org/0000-0001-9001-581X
                Article
                GGG_400369
                10.1534/g3.119.400369
                6723140
                31289024
                de51fe99-a1bd-4c33-aa93-641023b06db0
                Copyright © 2019 Lemopoulos et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 20 May 2019
                : 02 July 2019
                Page count
                Figures: 3, Tables: 1, Equations: 0, References: 100, Pages: 10
                Categories
                Investigations

                Genetics
                life-history strategies,radseq,gwas,salmonids
                Genetics
                life-history strategies, radseq, gwas, salmonids

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