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Genetics, Selection, Evolution: GSE

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https://www.readbyqxmd.com/read/30314431/genomic-prediction-for-numerically-small-breeds-using-models-with-pre-selected-and-differentially-weighted-markers
#1
Biaty Raymond, Aniek C Bouwman, Yvonne C J Wientjes, Chris Schrooten, Jeanine Houwing-Duistermaat, Roel F Veerkamp
BACKGROUND: Genomic prediction (GP) accuracy in numerically small breeds is limited by the small size of the reference population. Our objective was to test a multi-breed multiple genomic relationship matrices (GRM) GP model (MBMG) that weighs pre-selected markers separately, uses the remaining markers to explain the remaining genetic variance that can be explained by markers, and weighs information of breeds in the reference population by their genetic correlation with the validation breed...
October 10, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30290764/genome-wide-association-scan-for-heterotic-quantitative-trait-loci-in-multi-breed-and-crossbred-beef-cattle
#2
Everestus C Akanno, Liuhong Chen, Mohammed K Abo-Ismail, John J Crowley, Zhiquan Wang, Changxi Li, John A Basarab, Michael D MacNeil, Graham S Plastow
BACKGROUND: Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations. METHODS: Illumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle...
October 5, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30285629/derivation-of-the-economic-value-of-r-0-for-macroparasitic-diseases-and-application-to-sea-lice-in-salmon
#3
Kasper Janssen, Hans Komen, Helmut W Saatkamp, Mart C M de Jong, Piter Bijma
BACKGROUND: Macroparasites, such as ticks, lice, and helminths, are a concern in livestock and aquaculture production, and can be controlled by genetic improvement of the host population. Genetic improvement should aim at reducing the rate at which parasites spread across the farmed population. This rate is determined by the basic reproduction ratio, i.e. [Formula: see text], which is the appropriate breeding goal trait. This study aims at providing a method to derive the economic value of [Formula: see text]...
October 3, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30227828/genetic-selection-against-intrauterine-growth-retardation-in-piglets-a-problem-at-the-piglet-level-with-a-solution-at-the-sow-level
#4
Stephanie M Matheson, Grant A Walling, Sandra A Edwards
BACKGROUND: In polytocous livestock species, litter size and offspring weight act antagonistically; in modern pig breeds, selection for increased litter size has resulted in lower mean birth weights, an increased number of small piglets and an increased number of those affected by varying degrees of intrauterine growth retardation (IUGR). IUGR poses life-long challenges, both mental, with morphological brain changes and altered cognition, and physical, such as immaturity of organs, reduced colostrum intake and weight gain...
September 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30223768/assessment-of-the-performance-of-hidden-markov-models-for-imputation-in-animal-breeding
#5
Andrew Whalen, Gregor Gorjanc, Roger Ros-Freixedes, John M Hickey
BACKGROUND: In this paper, we review the performance of various hidden Markov model-based imputation methods in animal breeding populations. Traditionally, pedigree and heuristic-based imputation methods have been used for imputation in large animal populations due to their computational efficiency, scalability, and accuracy. Recent advances in the area of human genetics have increased the ability of probabilistic hidden Markov model methods to perform accurate phasing and imputation in large populations...
September 17, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30223766/quantifying-genomic-connectedness-and-prediction-accuracy-from-additive-and-non-additive-gene-actions
#6
Mehdi Momen, Gota Morota
BACKGROUND: Genetic connectedness is classically used as an indication of the risk associated with breeding value comparisons across management units because genetic evaluations based on best linear unbiased prediction rely for their success on sufficient linkage among different units. In the whole-genome prediction era, the concept of genetic connectedness can be extended to measure a connectedness level between reference and validation sets. However, little is known regarding (1) the impact of non-additive gene action on genomic connectedness measures and (2) the relationship between the estimated level of connectedness and prediction accuracy in the presence of non-additive genetic variation...
September 17, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30134820/misidentification-of-runs-of-homozygosity-islands-in-cattle-caused-by-interference-with-copy-number-variation-or-large-intermarker-distances
#7
Wilson Nandolo, Yuri T Utsunomiya, Gábor Mészáros, Maria Wurzinger, Negar Khayadzadeh, Rafaela B P Torrecilha, Henry A Mulindwa, Timothy N Gondwe, Patrik Waldmann, Maja Ferenčaković, José F Garcia, Benjamin D Rosen, Derek Bickhart, Curt P van Tassell, Ino Curik, Johann Sölkner
BACKGROUND: Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone...
August 22, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30107792/estimation-of-variance-components-and-prediction-of-breeding-values-based-on-group-records-from-varying-group-sizes
#8
Guosheng Su, Per Madsen, Bjarne Nielsen, Tage Ostersen, Mahmoud Shirali, Just Jensen, Ole F Christensen
BACKGROUND: Records on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake in pigs or beef cattle. Here, we present a model, which handles group records from varying group sizes and involves multiple fixed and random effects, for estimating variance components and predicting BV. Moreover, using simulation, we investigated the efficiency of group records for predicting BV in situations with various group sizes and structures, and factors that affect the trait...
August 14, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30081822/weighted-single-step-gwas-and-gene-network-analysis-reveal-new-candidate-genes-for-semen-traits-in-pigs
#9
Daniele B D Marques, John W M Bastiaansen, Marleen L W J Broekhuijse, Marcos S Lopes, Egbert F Knol, Barbara Harlizius, Simone E F Guimarães, Fabyano F Silva, Paulo S Lopes
BACKGROUND: In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms...
August 6, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30081816/understanding-the-potential-bias-of-variance-components-estimators-when-using-genomic-models
#10
Beatriz C D Cuyabano, A Christian Sørensen, Peter Sørensen
BACKGROUND: Genomic models that link phenotypes to dense genotype information are increasingly being used for infering variance parameters in genetics studies. The variance parameters of these models can be inferred using restricted maximum likelihood, which produces consistent, asymptotically normal estimates of variance components under the true model. These properties are not guaranteed to hold when the covariance structure of the data specified by the genomic model differs substantially from the covariance structure specified by the true model, and in this case, the likelihood of the model is said to be misspecified...
August 6, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30075705/estimates-of-genetic-trend-for-single-step-genomic-evaluations
#11
Karin Meyer, Bruce Tier, Andrew Swan
BACKGROUND: A common measure employed to evaluate the efficacy of livestock improvement schemes is the genetic trend, which is calculated as the means of predicted breeding values for animals born in successive time periods. This implies that different cohorts refer to the same base population. For genetic evaluation schemes integrating genomic information with records for all animals, genotyped or not, this is often not the case: expected means for pedigree founders are zero whereas values for genotyped animals are expected to sum to zero at the (mean) time corresponding to the frequencies that are used to center marker allele counts when calculating genomic relationships...
August 3, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/30037326/the-genetic-architecture-of-socially-affected-traits-a-gwas-for-direct-and-indirect-genetic-effects-on-survival-time-in-laying-hens-showing-cannibalism
#12
Tessa Brinker, Piter Bijma, Addie Vereijken, Esther D Ellen
BACKGROUND: Cannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Previous studies analysed repeated binomial survival, instead of survival time, which improved accuracies of breeding value predictions. Our study aimed at identifying SNPs associated with DGE and IGE for survival time, and comparing results from models that analyse survival time and repeated binomial survival...
July 23, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29996786/whole-genome-snp-analysis-elucidates-the-genetic-structure-of-russian-cattle-and-its-relationship-with-eurasian-taurine-breeds
#13
Alexander A Sermyagin, Arsen V Dotsev, Elena A Gladyr, Alexey A Traspov, Tatiana E Deniskova, Olga V Kostyunina, Henry Reyer, Klaus Wimmers, Mario Barbato, Ivan A Paronyan, Kirill V Plemyashov, Johann Sölkner, Ruslan G Popov, Gottfried Brem, Natalia A Zinovieva
BACKGROUND: The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip...
July 11, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29980171/remapping-of-the-belted-phenotype-in-cattle-on-bta3-identifies-a-multiplication-event-as-the-candidate-causal-mutation
#14
Sophie Rothammer, Elisabeth Kunz, Stefan Krebs, Fanny Bitzer, Andreas Hauser, Natalia Zinovieva, Nikolai Klymiuk, Ivica Medugorac
BACKGROUND: It has been known for almost a century that the belted phenotype in cattle follows a pattern of dominant inheritance. In 2009, the approximate position of the belt locus in Brown Swiss cattle was mapped to a 922-kb interval on bovine chromosome 3 and, subsequently, assigned to a 336-kb haplotype block based on an animal set that included, Brown Swiss, Dutch Belted (Lakenvelder) and Belted Galloway individuals. A possible candidate gene in this region i.e. HES6 was investigated but the causal mutation remains unknown...
July 6, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29940848/conservation-status-and-historical-relatedness-of-italian-cattle-breeds
#15
Salvatore Mastrangelo, Elena Ciani, Paolo Ajmone Marsan, Alessandro Bagnato, Luca Battaglini, Riccardo Bozzi, Antonello Carta, Gennaro Catillo, Martino Cassandro, Sara Casu, Roberta Ciampolini, Paola Crepaldi, Mariasilvia D'Andrea, Rosalia Di Gerlando, Luca Fontanesi, Maria Longeri, Nicolò P Macciotta, Roberto Mantovani, Donata Marletta, Donato Matassino, Marcello Mele, Giulio Pagnacco, Camillo Pieramati, Baldassare Portolano, Francesca M Sarti, Marco Tolone, Fabio Pilla
BACKGROUND: In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array...
June 26, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29940846/snprune-an-efficient-algorithm-to-prune-large-snp-array-and-sequence-datasets-based-on-high-linkage-disequilibrium
#16
Mario P L Calus, Jérémie Vandenplas
BACKGROUND: High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, this warrants pruning of genotyping data for high LD. We developed an algorithm, named SNPrune, which enables the rapid detection of any pair of SNPs in complete or high LD throughout the genome. METHODS: LD, measured as the squared correlation between phased alleles (r2 ), can only reach a value of 1 when both loci have the same count of the minor allele...
June 26, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29925306/bayesian-estimation-of-direct-and-correlated-responses-to-selection-on-linear-or-ratio-expressions-of-feed-efficiency-in-pigs
#17
Mahmoud Shirali, Patrick Francis Varley, Just Jensen
BACKGROUND: This study aimed at (1) deriving Bayesian methods to predict breeding values for ratio (i.e. feed conversion ratio; FCR) or linear (i.e. residual feed intake; RFI) traits; (2) estimating genetic parameters for average daily feed consumption (ADFI), average daily weight gain (ADG), lean meat percentage (LMP) along with the derived traits of RFI and FCR; and (3) deriving Bayesian estimates of direct and correlated responses to selection on RFI, FCR, ADG, ADFI, and LMP. Response to selection was defined as the difference in additive genetic mean of the selected top individuals, expected to be parents of the next generation, and the total population after integrating genetic trends out of the posterior distribution of selection responses...
June 20, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29914353/genome-wide-mapping-of-quantitative-trait-loci-in-admixed-populations-using-mixed-linear-model-and-bayesian-multiple-regression-analysis
#18
Ali Toosi, Rohan L Fernando, Jack C M Dekkers
BACKGROUND: Population stratification and cryptic relationships have been the main sources of excessive false-positives and false-negatives in population-based association studies. Many methods have been developed to model these confounding factors and minimize their impact on the results of genome-wide association studies. In most of these methods, a two-stage approach is applied where: (1) methods are used to determine if there is a population structure in the sample dataset and (2) the effects of population structure are corrected either by modeling it or by running a separate analysis within each sub-population...
June 19, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29907084/weighted-single-step-genomic-blup-improves-accuracy-of-genomic-breeding-values-for-protein-content-in-french-dairy-goats-a-quantitative-trait-influenced-by-a-major-gene
#19
COMPARATIVE STUDY
Marc Teissier, Hélène Larroque, Christèle Robert-Granié
BACKGROUND: In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain the same fraction of genetic variance. However, ssGBLUP is not suitable for protein content, which is controlled by a major gene, i.e. α s 1 casein. This gene explains about 40% of the genetic variation in protein content. In this study, we evaluated the accuracy of genomic prediction using different genomic methods to include the effect of the α s 1 casein gene...
June 15, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29884113/genome-wide-association-and-genomic-prediction-of-resistance-to-viral-nervous-necrosis-in-european-sea-bass-dicentrarchus-labrax-using-rad-sequencing
#20
Christos Palaiokostas, Sophie Cariou, Anastasia Bestin, Jean-Sebastien Bruant, Pierrick Haffray, Thierry Morin, Joëlle Cabon, François Allal, Marc Vandeputte, Ross D Houston
BACKGROUND: European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding...
June 8, 2018: Genetics, Selection, Evolution: GSE
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