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Population Genomic Structure and Genome-Wide Linkage Disequilibrium in Farmed Atlantic Salmon (Salmo salar L.) Using Dense SNP Genotypes

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      Abstract

      Chilean Farmed Atlantic salmon ( Salmo salar) populations were established with individuals of both European and North American origins. These populations are expected to be highly genetically differentiated due to evolutionary history and poor gene flow between ancestral populations from different continents. The extent and decay of linkage disequilibrium (LD) among single nucleotide polymorphism (SNP) impacts the implementation of genome-wide association studies and genomic selection and provides relevant information about demographic processes of fish populations. We assessed the population structure and characterized the extent and decay of LD in three Chilean commercial populations of Atlantic salmon with North American (NAM), Scottish (SCO), and Norwegian (NOR) origin. A total of 123 animals were genotyped using a 159 K SNP Axiom ® myDesign TM Genotyping Array. A total of 32 K SNP markers, representing the common SNPs along the three populations after quality control were used. The principal component analysis explained 78.9% of the genetic diversity between populations, clearly discriminating between populations of North American and European origin, and also between European populations. NAM had the lowest effective population size, followed by SCO and NOR. Large differences in the LD decay were observed between populations of North American and European origin. An r 2 threshold of 0.2 was estimated for marker pairs separated by 7,800, 64, and 50 kb in the NAM, SCO, and NOR populations, respectively. In this study we show that this SNP panel can be used to detect association between markers and traits of interests and also to capture high-resolution information for genome-enabled predictions. Also, we suggest the feasibility to achieve similar prediction accuracies using a smaller SNP data set for the NAM population, compared with samples with European origin which would need a higher density SNP array.

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      Most cited references 62

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      PLINK: a tool set for whole-genome association and population-based linkage analyses.

      Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.
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        Inference of population structure using multilocus genotype data.

        We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
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          Prediction of total genetic value using genome-wide dense marker maps.

          Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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            Author and article information

            Affiliations
            1Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile , La Pintana, Chile
            2Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho , Jaboticabal, Brazil
            3Benchmark Genetic S.A. , Puerto Montt, Chile
            4Nucleo Milenio INVASAL , Concepción, Chile
            Author notes

            Edited by: Paulino Martínez, University of Santiago de Compostela, Spain

            Reviewed by: Silvia Teresa Rodriguez Ramilo, Institut National de la Recherche Agronomique (INRA), France; Roger Luis Vallejo, United States Department of Agriculture, United States

            *Correspondence: José M. Yáñez, jmayanez@ 123456uchile.cl

            These authors have contributed equally to this work

            This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics

            Contributors
            Journal
            Front Genet
            Front Genet
            Front. Genet.
            Frontiers in Genetics
            Frontiers Media S.A.
            1664-8021
            14 December 2018
            2018
            : 9
            6302115 10.3389/fgene.2018.00649
            Copyright © 2018 Barria, López, Yoshida, Carvalheiro, Lhorente and Yáñez.

            This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

            Counts
            Figures: 5, Tables: 3, Equations: 1, References: 66, Pages: 11, Words: 0
            Categories
            Genetics
            Original Research

            Genetics

            population structure, linkage disequilibrium, gwas, selective breeding, salmo salar

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