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      Genome-Wide Association Study and Cost-Efficient Genomic Predictions for Growth and Fillet Yield in Nile Tilapia ( Oreochromis niloticus)

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          Abstract

          Fillet yield (FY) and harvest weight (HW) are economically important traits in Nile tilapia production. Genetic improvement of these traits, especially for FY, are lacking, due to the absence of efficient methods to measure the traits without sacrificing fish and the use of information from relatives to selection. However, genomic information could be used by genomic selection to improve traits that are difficult to measure directly in selection candidates, as in the case of FY. The objectives of this study were: (i) to perform genome-wide association studies (GWAS) to dissect the genetic architecture of FY and HW, (ii) to evaluate the accuracy of genotype imputation and (iii) to assess the accuracy of genomic selection using true and imputed low-density (LD) single nucleotide polymorphism (SNP) panels to determine a cost-effective strategy for practical implementation of genomic information in tilapia breeding programs. The data set consisted of 5,866 phenotyped animals and 1,238 genotyped animals (108 parents and 1,130 offspring) using a 50K SNP panel. The GWAS were performed using all genotyped and phenotyped animals. The genotyped imputation was performed from LD panels (LD0.5K, LD1K and LD3K) to high-density panel (HD), using information from parents and 20% of offspring in the reference set and the remaining 80% in the validation set. In addition, we tested the accuracy of genomic selection using true and imputed genotypes comparing the accuracy obtained from pedigree-based best linear unbiased prediction (PBLUP) and genomic predictions. The results from GWAS supports evidence of the polygenic nature of FY and HW. The accuracy of imputation ranged from 0.90 to 0.98 for LD0.5K and LD3K, respectively. The accuracy of genomic prediction outperformed the estimated breeding value from PBLUP. The use of imputation for genomic selection resulted in an increased relative accuracy independent of the trait and LD panel analyzed. The present results suggest that genotype imputation could be a cost-effective strategy for genomic selection in Nile tilapia breeding programs.

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          Most cited references 77

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          Hot topic: a unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score.

          The first national single-step, full-information (phenotype, pedigree, and marker genotype) genetic evaluation was developed for final score of US Holsteins. Data included final scores recorded from 1955 to 2009 for 6,232,548 Holsteins cows. BovineSNP50 (Illumina, San Diego, CA) genotypes from the Cooperative Dairy DNA Repository (Beltsville, MD) were available for 6,508 bulls. Three analyses used a repeatability animal model as currently used for the national US evaluation. The first 2 analyses used final scores recorded up to 2004. The first analysis used only a pedigree-based relationship matrix. The second analysis used a relationship matrix based on both pedigree and genomic information (single-step approach). The third analysis used the complete data set and only the pedigree-based relationship matrix. The fourth analysis used predictions from the first analysis (final scores up to 2004 and only a pedigree-based relationship matrix) and prediction using a genomic based matrix to obtain genetic evaluation (multiple-step approach). Different allele frequencies were tested in construction of the genomic relationship matrix. Coefficients of determination between predictions of young bulls from parent average, single-step, and multiple-step approaches and their 2009 daughter deviations were 0.24, 0.37 to 0.41, and 0.40, respectively. The highest coefficient of determination for a single-step approach was observed when using a genomic relationship matrix with assumed allele frequencies of 0.5. Coefficients for regression of 2009 daughter deviations on parent-average, single-step, and multiple-step predictions were 0.76, 0.68 to 0.79, and 0.86, respectively, which indicated some inflation of predictions. The single-step regression coefficient could be increased up to 0.92 by scaling differences between the genomic and pedigree-based relationship matrices with little loss in accuracy of prediction. One complete evaluation took about 2h of computing time and 2.7 gigabytes of memory. Computing times for single-step analyses were slightly longer (2%) than for pedigree-based analysis. A national single-step genetic evaluation with the pedigree relationship matrix augmented with genomic information provided genomic predictions with accuracy and bias comparable to multiple-step procedures and could account for any population or data structure. Advantages of single-step evaluations should increase in the future when animals are pre-selected on genotypes. Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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            Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach

            Background The prediction of the genetic disease risk of an individual is a powerful public health tool. While predicting risk has been successful in diseases which follow simple Mendelian inheritance, it has proven challenging in complex diseases for which a large number of loci contribute to the genetic variance. The large numbers of single nucleotide polymorphisms now available provide new opportunities for predicting genetic risk of complex diseases with high accuracy. Methodology/Principal Findings We have derived simple deterministic formulae to predict the accuracy of predicted genetic risk from population or case control studies using a genome-wide approach and assuming a dichotomous disease phenotype with an underlying continuous liability. We show that the prediction equations are special cases of the more general problem of predicting the accuracy of estimates of genetic values of a continuous phenotype. Our predictive equations are responsive to all parameters that affect accuracy and they are independent of allele frequency and effect distributions. Deterministic prediction errors when tested by simulation were generally small. The common link among the expressions for accuracy is that they are best summarized as the product of the ratio of number of phenotypic records per number of risk loci and the observed heritability. Conclusions/Significance This study advances the understanding of the relative power of case control and population studies of disease. The predictions represent an upper bound of accuracy which may be achievable with improved effect estimation methods. The formulae derived will help researchers determine an appropriate sample size to attain a certain accuracy when predicting genetic risk.
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              A new approach for efficient genotype imputation using information from relatives

              Background Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally challenging. Popular imputation methods are based upon the Hidden Markov model and have computational constraints due to an intensive sampling process. A fast, deterministic approach, which makes use of both family and population information, is presented here. All individuals are related and, therefore, share haplotypes which may differ in length and frequency based on their relationships. The method starts with family imputation if pedigree information is available, and then exploits close relationships by searching for long haplotype matches in the reference group using overlapping sliding windows. The search continues as the window size is shrunk in each chromosome sweep in order to capture more distant relationships. Results The proposed method gave higher or similar imputation accuracy than Beagle and Impute2 in cattle data sets when all available information was used. When close relatives of target individuals were present in the reference group, the method resulted in higher accuracy compared to the other two methods even when the pedigree was not used. Rare variants were also imputed with higher accuracy. Finally, computing requirements were considerably lower than those of Beagle and Impute2. The presented method took 28 minutes to impute from 6 k to 50 k genotypes for 2,000 individuals with a reference size of 64,429 individuals. Conclusions The proposed method efficiently makes use of information from close and distant relatives for accurate genotype imputation. In addition to its high imputation accuracy, the method is fast, owing to its deterministic nature and, therefore, it can easily be used in large data sets where the use of other methods is impractical.
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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
                6 June 2019
                August 2019
                : 9
                : 8
                : 2597-2607
                Affiliations
                [* ]Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820808 Chile,
                []Benchmark Genetics Chile, Puerto Montt, Chile, and
                []Grupo Acuacorporacion Internacional (GACI), Cañas, Costa Rica
                Author notes
                [1 ]Corresponding author: Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, Santiago, Chile. E-mail: jmayanez@ 123456uchile.cl
                Article
                GGG_400116
                10.1534/g3.119.400116
                6686944
                31171566
                Copyright © 2019 Yoshida 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.

                Page count
                Figures: 4, Tables: 4, Equations: 4, References: 88, Pages: 11
                Product
                Categories
                Genomic Prediction

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