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Genetics, Selection, Evolution: GSE

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https://www.readbyqxmd.com/read/28283016/metafounders-are-related-to-f-st-fixation-indices-and-reduce-bias-in-single-step-genomic-evaluations
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/28245808/erratum-to-commentary-on-the-6th-international-symposium-of-animal-functional-genomics
#7
Paolo Ajmone-Marsan, Alessandra Stella
No abstract text is available yet for this article.
February 28, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28245807/erratum-to-application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#8
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
No abstract text is available yet for this article.
February 28, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28245804/estimating-the-genetic-merit-of-sires-by-using-pooled-dna-from-progeny-of-undetermined-pedigree
#9
Amy M Bell, John M Henshall, Laercio R Porto-Neto, Sonja Dominik, Russell McCulloch, James Kijas, Sigrid A Lehnert
BACKGROUND: DNA-based predictions for hard-to-measure production traits hold great promise for selective breeding programs. DNA pooling might provide a cheap genomic approach to use phenotype data from commercial flocks which are commonly group-mated with parentage unknown. This study on sheep explores if genomic breeding values for stud sires can be estimated from genomic relationships that were obtained from pooled DNA in combination with phenotypes from commercial progeny. METHODS: Phenotypes used in this study were categorical data...
February 28, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28235410/tcf21-is-related-to-testis-growth-and-development-in-broiler-chickens
#10
Hui Zhang, Wei Na, Hong-Li Zhang, Ning Wang, Zhi-Qiang Du, Shou-Zhi Wang, Zhi-Peng Wang, Zhiwu Zhang, Hui Li
BACKGROUND: Large amounts of fat deposition often lead to loss of reproductive efficiency in humans and animals. We used broiler chickens as a model species to conduct a two-directional selection for and against abdominal fat over 19 generations, which resulted in a lean and a fat line. Direct selection for abdominal fat content also indirectly resulted in significant differences (P < 0.05) in testis weight (TeW) and in TeW as a percentage of total body weight (TeP) between the lean and fat lines...
February 24, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28222685/evaluation-of-the-accuracy-of-imputed-sequence-variant-genotypes-and-their-utility-for-causal-variant-detection-in-cattle
#11
Hubert Pausch, Iona M MacLeod, Ruedi Fries, Reiner Emmerling, Phil J Bowman, Hans D Daetwyler, Michael E Goddard
BACKGROUND: The availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large datasets consisting of tens of thousands of individuals with genotypes at millions of polymorphic sites that may enhance the power of genomic analyses. The imputation of missing genotypes ensures that all individuals have genotypes for a shared set of variants. RESULTS: We evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 249 Fleckvieh and 450 Holstein cattle using Minimac and FImpute...
February 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28201985/genetic-parameters-of-resistance-to-vibrio-aestuarianus-and-oshv-1-infections-in-the-pacific-oyster-crassostrea-gigas-at-three-different-life-stages
#12
Patrick Azéma, Jean-Baptiste Lamy, Pierre Boudry, Tristan Renault, Marie-Agnès Travers, Lionel Dégremont
BACKGROUND: In France, two main diseases threaten Pacific oyster production. Since 2008, Crassostrea gigas spat have suffered massive losses due to the ostreid herpesvirus OsHV-1, and since 2012, significant mortalities in commercial-size adults have been related to infection by the bacterium Vibrio aestuarianus. The genetic basis for resistance to V. aestuarianus and OsHV-1 and the nature of the genetic correlation between these two traits were investigated by using 20 half-sib sire families, each containing two full-sib families...
February 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28196485/rapid-evolution-of-genetic-and-phenotypic-divergence-in-atlantic-salmon-following-the-colonisation-of-two-new-branches-of-a-watercourse
#13
Arne Johan Jensen, Lars Petter Hansen, Bjørn Ove Johnsen, Sten Karlsson
BACKGROUND: Selection acts strongly on individuals that colonise a habitat and have phenotypic traits that deviate from the local optima. Our objective was to investigate the evolutionary rates in Atlantic salmon (Salmo salar) in a river system (the Vefsna watershed in Norway), fewer than 15 generations after colonisation of two new branches of the watercourse for spawning, which were made available by construction of fish ladders in 1889. METHODS: Differences in age and size were analysed using scale samples collected by anglers...
February 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28196480/genome-wide-detection-of-genetic-markers-associated-with-growth-and-fatness-in-four-pig-populations-using-four-approaches
#14
Yuanmei Guo, Yixuan Huang, Lijuan Hou, Junwu Ma, Congying Chen, Huashui Ai, Lusheng Huang, Jun Ren
BACKGROUND: Genome-wide association studies (GWAS) have been extensively used to identify genomic regions associated with a variety of phenotypic traits in pigs. Until now, most GWAS have explored single-trait association models. Here, we conducted both single- and multi-trait GWAS and a meta-analysis for nine fatness and growth traits on 2004 pigs from four diverse populations, including a White Duroc × Erhualian F2 intercross population and Chinese Sutai, Laiwu and Erhualian populations...
February 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28193175/genome-wide-association-mapping-for-milk-fat-composition-and-fine-mapping-of-a-qtl-for-de-novo-synthesis-of-milk-fatty-acids-on-bovine-chromosome-13
#15
Hanne Gro Olsen, Tim Martin Knutsen, Achim Kohler, Morten Svendsen, Lars Gidskehaug, Harald Grove, Torfinn Nome, Marte Sodeland, Kristil Kindem Sundsaasen, Matthew Peter Kent, Harald Martens, Sigbjørn Lien
BACKGROUND: Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle...
February 13, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28187715/unveiling-genomic-regions-that-underlie-differences-between-afec-assaf-sheep-and-its-parental-awassi-breed
#16
Eyal Seroussi, Alexander Rosov, Andrey Shirak, Alon Lam, Elisha Gootwine
BACKGROUND: Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software...
February 10, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28158968/a-genome-wide-association-study-in-a-large-f2-cross-of-laying-hens-reveals-novel-genomic-regions-associated-with-feather-pecking-and-aggressive-pecking-behavior
#17
Vanessa Lutz, Patrick Stratz, Siegfried Preuß, Jens Tetens, Michael A Grashorn, Werner Bessei, Jörn Bennewitz
BACKGROUND: Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines...
February 3, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28148241/a-predictive-assessment-of-genetic-correlations-between-traits-in-chickens-using-markers
#18
Mehdi Momen, Ahmad Ayatollahi Mehrgardi, Ayoub Sheikhy, Ali Esmailizadeh, Masood Asadi Fozi, Andreas Kranis, Bruno D Valente, Guilherme J M Rosa, Daniel Gianola
BACKGROUND: Genomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be used to improve several correlated traits simultaneously via multiple-trait prediction, which exploits correlations between traits. However, few studies have explored multiple-trait genomic selection. Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness...
February 1, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28148220/genomic-selection-models-double-the-accuracy-of-predicted-breeding-values-for-bacterial-cold-water-disease-resistance-compared-to-a-traditional-pedigree-based-model-in-rainbow-trout-aquaculture
#19
Roger L Vallejo, Timothy D Leeds, Guangtu Gao, James E Parsons, Kyle E Martin, Jason P Evenhuis, Breno O Fragomeni, Gregory D Wiens, Yniv Palti
BACKGROUND: Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation. METHODS: We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model...
February 1, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28143593/the-use-of-genomic-information-increases-the-accuracy-of-breeding-value-predictions-for-sea-louse-caligus-rogercresseyi-resistance-in-atlantic-salmon-salmo-salar
#20
Katharina Correa, Rama Bangera, René Figueroa, Jean P Lhorente, José M Yáñez
Sea lice infestations caused by Caligus rogercresseyi are a main concern to the salmon farming industry due to associated economic losses. Resistance to this parasite was shown to have low to moderate genetic variation and its genetic architecture was suggested to be polygenic. The aim of this study was to compare accuracies of breeding value predictions obtained with pedigree-based best linear unbiased prediction (P-BLUP) methodology against different genomic prediction approaches: genomic BLUP (G-BLUP), Bayesian Lasso, and Bayes C...
January 31, 2017: Genetics, Selection, Evolution: GSE
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