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Genetics, Selection, Evolution: GSE

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28125975/embryonic-environment-and-transgenerational-effects-in-quail
#10
Sophie Leroux, David Gourichon, Christine Leterrier, Yann Labrune, Vincent Coustham, Sandrine Rivière, Tatiana Zerjal, Jean-Luc Coville, Mireille Morisson, Francis Minvielle, Frédérique Pitel
BACKGROUND: Environmental exposures, for instance to chemicals, are known to impact plant and animal phenotypes on the long term, sometimes across several generations. Such transgenerational phenotypes were shown to be promoted by epigenetic alterations such as DNA methylation, an epigenetic mark involved in the regulation of gene expression. However, it is yet unknown whether transgenerational epigenetic inheritance of altered phenotypes exists in birds. The purpose of this study was to develop an avian model to investigate whether changes to the embryonic environment had a transgenerational effect that could alter the phenotypes of third-generation offspring...
January 26, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28122487/detection-and-validation-of-structural-variations-in-bovine-whole-genome-sequence-data
#11
Long Chen, Amanda J Chamberlain, Coralie M Reich, Hans D Daetwyler, Ben J Hayes
BACKGROUND: Several examples of structural variation (SV) affecting phenotypic traits have been reported in cattle. Currently the identification of SV from whole-genome sequence data (WGS) suffers from a high false positive rate. Our aim was to construct a high quality set of SV calls in cattle using WGS data. First, we tested two SV detection programs, Breakdancer and Pindel, and the overlap of these methods, on simulated sequence data to determine their precision and sensitivity. We then identified population SV from WGS of 252 Holstein and 64 Jersey bulls based on the overlapping calls from the two programs...
January 25, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28118822/genome-wide-association-study-for-conformation-traits-in-three-danish-pig-breeds
#12
Thu H Le, Ole F Christensen, Bjarne Nielsen, Goutam Sahana
BACKGROUND: Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses. METHODS: Data on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses...
January 24, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28107818/multiple-trait-structured-antedependence-model-to-study-the-relationship-between-litter-size-and-birth-weight-in-pigs-and-rabbits
#13
Ingrid David, Hervé Garreau, Elodie Balmisse, Yvon Billon, Laurianne Canario
BACKGROUND: Some genetic studies need to take into account correlations between traits that are repeatedly measured over time. Multiple-trait random regression models are commonly used to analyze repeated traits but suffer from several major drawbacks. In the present study, we developed a multiple-trait extension of the structured antedependence model (SAD) to overcome this issue and validated its usefulness by modeling the association between litter size (LS) and average birth weight (ABW) over parities in pigs and rabbits...
January 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28095776/genetic-and-economic-benefits-of-selection-based-on-performance-recording-and-genotyping-in-lower-tiers-of-multi-tiered-sheep-breeding-schemes
#14
Bruno F S Santos, Julius H J van der Werf, John P Gibson, Timothy J Byrne, Peter R Amer
BACKGROUND: Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, and create additional economic benefits for the breeding structure. METHODS: The genetic change in a multiple-trait breeding objective was predicted for various selection strategies that included performance recording, parentage testing and genomic selection...
January 17, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#15
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093063/whole-genome-sequence-based-genomic-prediction-in-laying-chickens-with-different-genomic-relationship-matrices-to-account-for-genetic-architecture
#16
Guiyan Ni, David Cavero, Anna Fangmann, Malena Erbe, Henner Simianer
BACKGROUND: With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher predictive ability, since such data may contain all genomic variants including causal mutations. Our objective was to compare prediction ability with high-density (HD) array data and WGS data in a commercial brown layer line with genomic best linear unbiased prediction (GBLUP) models using various approaches to weight single nucleotide polymorphisms (SNPs)...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#17
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28073357/long-noncoding-rna-repertoire-in-chicken-liver-and-adipose-tissue
#18
Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf, Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Sandrine Lagarrigue
BACKGROUND: Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity...
January 10, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093062/derivation-of-economic-values-for-production-traits-in-aquaculture-species
#19
Kasper Janssen, Paul Berentsen, Mathieu Besson, Hans Komen
BACKGROUND: In breeding programs for aquaculture species, breeding goal traits are often weighted based on the desired gains but economic gain would be higher if economic values were used instead. The objectives of this study were: (1) to develop a bio-economic model to derive economic values for aquaculture species, (2) to apply the model to determine the economic importance and economic values of traits in a case-study on gilthead seabream, and (3) to validate the model by comparison with a profit equation for a simplified production system...
January 5, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093083/genetic-analysis-of-teat-number-in-pigs-reveals-some-developmental-pathways-independent-of-vertebra-number-and-several-loci-which-only-affect-a-specific-side
#20
Gary A Rohrer, Dan J Nonneman
BACKGROUND: Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n = 1828) had number of teats on each side recorded...
January 4, 2017: Genetics, Selection, Evolution: GSE
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