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Genetics, Selection, Evolution: GSE

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https://www.readbyqxmd.com/read/30107792/estimation-of-variance-components-and-prediction-of-breeding-values-based-on-group-records-from-varying-group-sizes
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/29793424/population-structure-and-genetic-diversity-of-25-russian-sheep-breeds-based-on-whole-genome-genotyping
#14
Tatiana E Deniskova, Arsen V Dotsev, Marina I Selionova, Elisabeth Kunz, Ivica Medugorac, Henry Reyer, Klaus Wimmers, Mario Barbato, Alexei A Traspov, Gottfried Brem, Natalia A Zinovieva
BACKGROUND: Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip...
May 24, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29788905/genomic-prediction-of-the-polled-and-horned-phenotypes-in-merino-sheep
#15
Naomi Duijvesteijn, Sunduimijid Bolormaa, Hans D Daetwyler, Julius H J van der Werf
BACKGROUND: In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene...
May 22, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29776335/using-genomic-relationship-likelihood-for-parentage-assignment
#16
Kim E Grashei, Jørgen Ødegård, Theo H E Meuwissen
BACKGROUND: Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage assignment are exclusion-based (i.e. based on loci that violate Mendelian inheritance) or likelihood-based, assuming independent inheritance of loci. For true parent-offspring relations, genotyping errors cause apparent violations of Mendelian inheritance. Thus, the maximum proportion of such violations must be determined, which is complicated by variable call- and genotype error rates among loci and individuals...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29776327/utility-of-whole-genome-sequence-data-for-across-breed-genomic-prediction
#17
Biaty Raymond, Aniek C Bouwman, Chris Schrooten, Jeanine Houwing-Duistermaat, Roel F Veerkamp
BACKGROUND: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. METHODS: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29747576/selective-advantage-of-implementing-optimal-contributions-selection-and-timescales-for-the-convergence-of-long-term-genetic-contributions
#18
David M Howard, Ricardo Pong-Wong, Pieter W Knap, Valentin D Kremer, John A Woolliams
BACKGROUND: Optimal contributions selection (OCS) provides animal breeders with a framework for maximising genetic gain for a predefined rate of inbreeding. Simulation studies have indicated that the source of the selective advantage of OCS is derived from breeding decisions being more closely aligned with estimates of Mendelian sampling terms ([Formula: see text]) of selection candidates, rather than estimated breeding values (EBV). This study represents the first attempt to assess the source of the selective advantage provided by OCS using a commercial pig population and by testing three hypotheses: (1) OCS places more emphasis on [Formula: see text] compared to EBV for determining which animals were selected as parents, (2) OCS places more emphasis on [Formula: see text] compared to EBV for determining which of those parents were selected to make a long-term genetic contribution (r), and (3) OCS places more emphasis on [Formula: see text] compared to EBV for determining the magnitude of r...
May 10, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29747574/longitudinal-analysis-of-direct-and-indirect-effects-on-average-daily-gain-in-rabbits-using-a-structured-antedependence-model
#19
Ingrid David, Juan-Pablo Sánchez, Miriam Piles
BACKGROUND: Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have investigated how IGE vary over time for traits under selection in livestock species. To overcome this issue, our aim was: (1) to analyze longitudinal records of average daily gain (ADG) in rabbits subjected to a 5-week period of feed restriction using a structured antedependence (SAD) model that includes IGE and (2) to evaluate, by simulation, the response to selection when IGE are present and genetic evaluation is based on a SAD model that includes IGE or not...
May 10, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29720082/genomic-prediction-of-avian-influenza-infection-outcome-in-layer-chickens
#20
Anna Wolc, Wioleta Drobik-Czwarno, Janet E Fulton, Jesus Arango, Tomasz Jankowski, Jack C M Dekkers
Avian influenza (AI) is a devastating poultry disease that currently can be controlled only by liquidation of affected flocks. In spite of typically very high mortality rates, a group of survivors was identified and genotyped on a 600K single nucleotide polymorphism (SNP) chip to identify genetic differences between survivors, and age- and genetics-matched controls from unaffected flocks. In a previous analysis of this dataset, a heritable component was identified and several regions that are associated with outcome of the infection were localized but none with a large effect...
May 2, 2018: Genetics, Selection, Evolution: GSE
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