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Genetics, Selection, Evolution: GSE

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https://www.readbyqxmd.com/read/28532460/selection-for-environmental-variance-of-litter-size-in-rabbits
#1
Agustín Blasco, Marina Martínez-Álvaro, Maria-Luz García, Noelia Ibáñez-Escriche, María-José Argente
BACKGROUND: In recent years, there has been an increasing interest in the genetic determination of environmental variance. In the case of litter size, environmental variance can be related to the capacity of animals to adapt to new environmental conditions, which can improve animal welfare. RESULTS: We developed a ten-generation divergent selection experiment on environmental variance. We selected one line of rabbits for litter size homogeneity and one line for litter size heterogeneity by measuring intra-doe phenotypic variance...
May 22, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28521728/a-method-for-the-allocation-of-sequencing-resources-in-genotyped-livestock-populations
#2
Serap Gonen, Roger Ros-Freixedes, Mara Battagin, Gregor Gorjanc, John M Hickey
BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level...
May 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28511677/a-strategy-to-improve-phasing-of-whole-genome-sequenced-individuals-through-integration-of-familial-information-from-dense-genotype-panels
#3
Pierre Faux, Tom Druet
BACKGROUND: Haplotype reconstruction (phasing) is an essential step in many applications, including imputation and genomic selection. The best phasing methods rely on both familial and linkage disequilibrium (LD) information. With whole-genome sequence (WGS) data, relatively small samples of reference individuals are generally sequenced due to prohibitive sequencing costs, thus only a limited amount of familial information is available. However, reference individuals have many relatives that have been genotyped (at lower density)...
May 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28499352/novel-optimum-contribution-selection-methods-accounting-for-conflicting-objectives-in-breeding-programs-for-livestock-breeds-with-historical-migration
#4
Yu Wang, Jörn Bennewitz, Robin Wellmann
BACKGROUND: Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles...
May 12, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28499351/prediction-of-the-reliability-of-genomic-breeding-values-for-crossbred-performance
#5
Jérémie Vandenplas, Jack J Windig, Mario P L Calus
BACKGROUND: In crossbreeding programs, various genomic prediction models have been proposed for using phenotypic records of crossbred animals to increase the selection response for crossbred performance in purebred animals. A possible model is a model that assumes identical single nucleotide polymorphism (SNP) effects for the crossbred performance trait across breeds (ASGM). Another model is a genomic model that assumes breed-specific effects of SNP alleles (BSAM) for crossbred performance...
May 12, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28499345/exploring-the-genetic-architecture-and-improving-genomic-prediction-accuracy-for-mastitis-and-milk-production-traits-in-dairy-cattle-by-mapping-variants-to-hepatic-transcriptomic-regions-responsive-to-intra-mammary-infection
#6
Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
BACKGROUND: A better understanding of the genetic architecture of complex traits can contribute to improve genomic prediction. We hypothesized that genomic variants associated with mastitis and milk production traits in dairy cattle are enriched in hepatic transcriptomic regions that are responsive to intra-mammary infection (IMI). Genomic markers [e.g. single nucleotide polymorphisms (SNPs)] from those regions, if included, may improve the predictive ability of a genomic model. RESULTS: We applied a genomic feature best linear unbiased prediction model (GFBLUP) to implement the above strategy by considering the hepatic transcriptomic regions responsive to IMI as genomic features...
May 12, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28464791/higher-heritabilities-for-gait-components-than-for-overall-gait-scores-may-improve-mobility-in-ducks
#7
Brendan M Duggan, Anne M Rae, Dylan N Clements, Paul M Hocking
BACKGROUND: Genetic progress in selection for greater body mass and meat yield in poultry has been associated with an increase in gait problems which are detrimental to productivity and welfare. The incidence of suboptimal gait in breeding flocks is controlled through the use of a visual gait score, which is a subjective assessment of walking ability of each bird. The subjective nature of the visual gait score has led to concerns over its effectiveness in reducing the incidence of suboptimal gait in poultry through breeding...
May 2, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28454565/combined-gwas-and-guilt-by-association-based-prioritization-analysis-identifies-functional-candidate-genes-for-body-size-in-sheep
#8
Antonios Kominakis, Ariadne L Hager-Theodorides, Evangelos Zoidis, Aggeliki Saridaki, George Antonakos, George Tsiamis
BACKGROUND: Body size in sheep is an important indicator of productivity, growth and health as well as of environmental adaptation. It is a composite quantitative trait that has been studied with high-throughput genomic methods, i.e. genome-wide association studies (GWAS) in various mammalian species. Several genomic markers have been associated with body size traits and genes have been identified as causative candidates in humans, dog and cattle. A limited number of related GWAS have been performed in various sheep breeds and have identified genomic regions and candidate genes that partly account for body size variability...
April 28, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28427324/genomic-prediction-from-observed-and-imputed-high-density-ovine-genotypes
#9
Nasir Moghaddar, Andrew A Swan, Julius H J van der Werf
BACKGROUND: Genomic prediction using high-density (HD) marker genotypes is expected to lead to higher prediction accuracy, particularly for more heterogeneous multi-breed and crossbred populations such as those in sheep and beef cattle, due to providing stronger linkage disequilibrium between single nucleotide polymorphisms and quantitative trait loci controlling a trait. The objective of this study was to evaluate a possible improvement in genomic prediction accuracy of production traits in Australian sheep breeds based on HD genotypes (600k, both observed and imputed) compared to prediction based on 50k marker genotypes...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28427323/detection-of-qtl-for-traits-related-to-adaptation-to-sub-optimal-climatic-conditions-in-chickens
#10
Ching-Yi Lien, Michèle Tixier-Boichard, Shih-Wen Wu, Woei-Fuh Wang, Chen Siang Ng, Chih-Feng Chen
BACKGROUND: Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS: An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption)...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28424056/use-of-multi-trait-and-random-regression-models-to-identify-genetic-variation-in-tolerance-to-porcine-reproductive-and-respiratory-syndrome-virus
#11
Graham Lough, Hamed Rashidi, Ilias Kyriazakis, Jack C M Dekkers, Andrew Hess, Melanie Hess, Nader Deeb, Antti Kause, Joan K Lunney, Raymond R R Rowland, Han A Mulder, Andrea Doeschl-Wilson
BACKGROUND: A host can adopt two response strategies to infection: resistance (reduce pathogen load) and tolerance (minimize impact of infection on performance). Both strategies may be under genetic control and could thus be targeted for genetic improvement. Although there is evidence that supports a genetic basis for resistance to porcine reproductive and respiratory syndrome (PRRS), it is not known whether pigs also differ genetically in tolerance. We determined to what extent pigs that have been shown to vary genetically in resistance to PRRS also exhibit genetic variation in tolerance...
April 19, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28424047/deciphering-mechanisms-underlying-the-genetic-variation-of-general-production-and-liver-quality-traits-in-the-overfed-mule-duck-by-pqtl-analyses
#12
Yoannah François, Alain Vignal, Caroline Molette, Nathalie Marty-Gasset, Stéphane Davail, Laurence Liaubet, Christel Marie-Etancelin
BACKGROUND: The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified...
April 19, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28359261/single-step-snp-blup-with-on-the-fly-imputed-genotypes-and-residual-polygenic-effects
#13
Matti Taskinen, Esa A Mäntysaari, Ismo Strandén
BACKGROUND: Single-step genomic best linear unbiased prediction (BLUP) evaluation combines relationship information from pedigree and genomic marker data. The inclusion of the genomic information into mixed model equations requires the inverse of the combined relationship matrix [Formula: see text], which has a dense matrix block for genotyped animals. METHODS: To avoid inversion of dense matrices, single-step genomic BLUP can be transformed to single-step single nucleotide polymorphism BLUP (SNP-BLUP) which have observed and imputed marker coefficients...
March 30, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28356075/genome-wide-association-study-and-accuracy-of-genomic-prediction-for-teat-number-in-duroc-pigs-using-genotyping-by-sequencing
#14
Cheng Tan, Zhenfang Wu, Jiangli Ren, Zhuolin Huang, Dewu Liu, Xiaoyan He, Dzianis Prakapenka, Ran Zhang, Ning Li, Yang Da, Xiaoxiang Hu
BACKGROUND: The number of teats in pigs is related to a sow's ability to rear piglets to weaning age. Several studies have identified genes and genomic regions that affect teat number in swine but few common results were reported. The objective of this study was to identify genetic factors that affect teat number in pigs, evaluate the accuracy of genomic prediction, and evaluate the contribution of significant genes and genomic regions to genomic broad-sense heritability and prediction accuracy using 41,108 autosomal single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing on 2936 Duroc boars...
March 29, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28283016/metafounders-are-related-to-f-st-fixation-indices-and-reduce-bias-in-single-step-genomic-evaluations
#15
Carolina A Garcia-Baccino, Andres Legarra, Ole F Christensen, Ignacy Misztal, Ivan Pocrnic, Zulma G Vitezica, Rodolfo J C Cantet
BACKGROUND: Metafounders are pseudo-individuals that encapsulate genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses the estimation and usefulness of metafounder relationships in single-step genomic best linear unbiased prediction (ssGBLUP). RESULTS: We show that ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, such as [Formula: see text] fixation indexes...
March 10, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28270100/estimation-of-breeding-values-for-uniformity-of-growth-in-atlantic-salmon-salmo-salar-using-pedigree-relationships-or-single-step-genomic-evaluation
#16
Panya Sae-Lim, Antti Kause, Marie Lillehammer, Han A Mulder
BACKGROUND: In farmed Atlantic salmon, heritability for uniformity of body weight is low, indicating that the accuracy of estimated breeding values (EBV) may be low. The use of genomic information could be one way to increase accuracy and, hence, obtain greater response to selection. Genomic information can be merged with pedigree information to construct a combined relationship matrix ([Formula: see text] matrix) for a single-step genomic evaluation (ssGBLUP), allowing realized relationships of the genotyped animals to be exploited, in addition to numerator pedigree relationships ([Formula: see text] matrix)...
March 7, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28270096/selecting-sequence-variants-to-improve-genomic-predictions-for-dairy-cattle
#17
Paul M VanRaden, Melvin E Tooker, Jeffrey R O'Connell, John B Cole, Derek M Bickhart
BACKGROUND: Millions of genetic variants have been identified by population-scale sequencing projects, but subsets of these variants are needed for routine genomic predictions or genotyping arrays. Methods for selecting sequence variants were compared using simulated sequence genotypes and real July 2015 data from the 1000 Bull Genomes Project. METHODS: Candidate sequence variants for 444 Holstein animals were combined with high-density (HD) imputed genotypes for 26,970 progeny-tested Holstein bulls...
March 7, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28257629/erratum-to-detection-and-validation-of-structural-variations-in-bovine-whole-genome-sequence-data
#18
Long Chen, Amanda J Chamberlain, Coralie M Reich, Hans D Daetwyler, Ben J Hayes
No abstract text is available yet for this article.
March 3, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28253858/a-hybrid-method-for-the-imputation-of-genomic-data-in-livestock-populations
#19
Roberto Antolín, Carl Nettelblad, Gregor Gorjanc, Daniel Money, John M Hickey
BACKGROUND: This paper describes a combined heuristic and hidden Markov model (HMM) method to accurately impute missing genotypes in livestock datasets. Genomic selection in breeding programs requires high-density genotyping of many individuals, making algorithms that economically generate this information crucial. There are two common classes of imputation methods, heuristic methods and probabilistic methods, the latter being largely based on hidden Markov models. Heuristic methods are robust, but fail to impute markers in regions where the thresholds of heuristic rules are not met, or the pedigree is inconsistent...
March 3, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28253844/estimation-of-genetic-connectedness-diagnostics-based-on-prediction-errors-without-the-prediction-error-variance-covariance-matrix
#20
John B Holmes, Ken G Dodds, Michael A Lee
BACKGROUND: An important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic connectedness. While various measures of connectedness have been proposed in the literature, there is general agreement that the most appropriate measure is some function of the prediction error variance-covariance matrix. However, obtaining the prediction error variance-covariance matrix is computationally demanding for large-scale genetic evaluations...
March 2, 2017: Genetics, Selection, Evolution: GSE
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