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Genetics, Selection, Evolution: GSE

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https://www.readbyqxmd.com/read/29041917/locally-epistatic-models-for-genome-wide-prediction-and-association-by-importance-sampling
#1
Deniz Akdemir, Jean-Luc Jannink, Julio Isidro-Sánchez
BACKGROUND: In statistical genetics, an important task involves building predictive models of the genotype-phenotype relationship to attribute a proportion of the total phenotypic variance to the variation in genotypes. Many models have been proposed to incorporate additive genetic effects into prediction or association models. Currently, there is a scarcity of models that can adequately account for gene by gene or other forms of genetic interactions, and there is an increased interest in using marker annotations in genome-wide prediction and association analyses...
October 17, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28982372/detection-of-two-non-synonymous-snps-in-slc45a2-on-bta20-as-candidate-causal-mutations-for-oculocutaneous-albinism-in-braunvieh-cattle
#2
Sophie Rothammer, Elisabeth Kunz, Doris Seichter, Stefan Krebs, Martina Wassertheurer, Ruedi Fries, Gottfried Brem, Ivica Medugorac
BACKGROUND: Cases of albinism have been reported in several species including cattle. So far, research has identified many genes that are involved in this eye-catching phenotype. Thus, when two paternal Braunvieh half-sibs with oculocutaneous albinism were detected on a private farm, we were interested in knowing whether their phenotype was caused by an already known gene/mutation. RESULTS: Analysis of genotyping data (50K) of the two albino individuals, their mothers and five other relatives identified a 47...
October 5, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28962553/the-genetic-basis-of-novel-water-utilisation-and-drinking-behaviour-traits-and-their-relationship-with-biological-performance-in-turkeys
#3
Julija Rusakovica, Valentin D Kremer, Thomas Plötz, Paige Rohlf, Ilias Kyriazakis
BACKGROUND: There is increasing interest in the definition, measurement and use of traits associated with water use and drinking behaviour, mainly because water is a finite resource and its intake is an important part of animal health and well-being. Analysis of such traits has received little attention, due in part to the lack of appropriate technology to measure drinking behaviour. We exploited novel equipment to collect water intake data in two lines of turkey (A: 27,415 and B: 12,956 birds)...
September 29, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28934948/multi-breed-genomic-prediction-using-bayes-r-with-sequence-data-and-dropping-variants-with-a-small-effect
#4
Irene van den Berg, Phil J Bowman, Iona M MacLeod, Ben J Hayes, Tingting Wang, Sunduimijid Bolormaa, Mike E Goddard
BACKGROUND: The increasing availability of whole-genome sequence data is expected to increase the accuracy of genomic prediction. However, results from simulation studies and analysis of real data do not always show an increase in accuracy from sequence data compared to high-density (HD) single nucleotide polymorphism (SNP) chip genotypes. In addition, the sheer number of variants makes analysis of all variants and accurate estimation of all effects computationally challenging. Our objective was to find a strategy to approximate the analysis of whole-sequence data with a Bayesian variable selection model...
September 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28934946/genome-wide-snp-data-unveils-the-globalization-of-domesticated-pigs
#5
Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P M A Crooijmans, Natalia Zinovieva, Lawrence B Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A M Groenen, Lusheng Huang, Hendrik-Jan Megens
BACKGROUND: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection...
September 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28931372/transcriptional-profile-of-breast-muscle-in-heat-stressed-layers-is-similar-to-that-of-broiler-chickens-at-control-temperature
#6
Imran Zahoor, Dirk-Jan de Koning, Paul M Hocking
BACKGROUND: In recent years, the commercial importance of changes in muscle function of broiler chickens and of the corresponding effects on meat quality has increased. Furthermore, broilers are more sensitive to heat stress during transport and at high ambient temperatures than smaller egg-laying chickens. We hypothesised that heat stress would amplify muscle damage and expression of genes that are involved in such changes and, thus, lead to the identification of pathways and networks associated with broiler muscle and meat quality traits...
September 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28923017/within-breed-and-multi-breed-gwas-on-imputed-whole-genome-sequence-variants-reveal-candidate-mutations-affecting-milk-protein-composition-in-dairy-cattle
#7
Marie-Pierre Sanchez, Armelle Govignon-Gion, Pascal Croiseau, Sébastien Fritz, Chris Hozé, Guy Miranda, Patrice Martin, Anne Barbat-Leterrier, Rabia Letaïef, Dominique Rocha, Mickaël Brochard, Mekki Boussaha, Didier Boichard
BACKGROUND: Genome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) dairy cattle. Whey protein (α-lactalbumin and β-lactoglobulin) and casein (αs1, αs2, β, and κ) contents were estimated by mid-infrared (MIR) spectrometry, with medium to high accuracy (0.59 ≤ R(2) ≤ 0.92), for 848,068 test-day milk samples from 156,660 cows in the first three lactations...
September 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28899355/genetic-tests-for-estimating-dairy-breed-proportion-and-parentage-assignment-in-east-african-crossbred-cattle
#8
Eva M Strucken, Hawlader A Al-Mamun, Cecilia Esquivelzeta-Rabell, Cedric Gondro, Okeyo A Mwai, John P Gibson
BACKGROUND: Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application...
September 12, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28841821/influence-of-epistasis-on-response-to-genomic-selection-using-complete-sequence-data
#9
Natalia S Forneris, Zulma G Vitezica, Andres Legarra, Miguel Pérez-Enciso
BACKGROUND: The effect of epistasis on response to selection is a highly debated topic. Here, we investigated the impact of epistasis on response to sequence-based selection via genomic best linear prediction (GBLUP) in a regime of strong non-symmetrical epistasis under divergent selection, using real Drosophila sequence data. We also explored the possible advantage of including epistasis in the evaluation model and/or of knowing the causal mutations. RESULTS: Response to selection was almost exclusively due to changes in allele frequency at a few loci with a large effect...
August 25, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28838315/erratum-to-incorporation-of-causative-quantitative-trait-nucleotides-in-single-step-gblup
#10
Breno O Fragomeni, Daniela A L Lourenco, Yutaka Masuda, Andres Legarra, Ignacy Misztal
No abstract text is available yet for this article.
August 24, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28836944/simultaneous-fitting-of-genomic-blup-and-bayes-c-components-in-a-genomic-prediction-model
#11
Oscar O M Iheshiulor, John A Woolliams, Morten Svendsen, Trygve Solberg, Theo H E Meuwissen
BACKGROUND: The rapid adoption of genomic selection is due to two key factors: availability of both high-throughput dense genotyping and statistical methods to estimate and predict breeding values. The development of such methods is still ongoing and, so far, there is no consensus on the best approach. Currently, the linear and non-linear methods for genomic prediction (GP) are treated as distinct approaches. The aim of this study was to evaluate the implementation of an iterative method (called GBC) that incorporates aspects of both linear [genomic-best linear unbiased prediction (G-BLUP)] and non-linear (Bayes-C) methods for GP...
August 24, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28836943/an-efficient-unified-model-for-genome-wide-association-studies-and-genomic-selection
#12
Hengde Li, Guosheng Su, Li Jiang, Zhenmin Bao
BACKGROUND: A quantitative trait is controlled both by major variants with large genetic effects and by minor variants with small effects. Genome-wide association studies (GWAS) are an efficient approach to identify quantitative trait loci (QTL), and genomic selection (GS) with high-density single nucleotide polymorphisms (SNPs) can achieve higher accuracy of estimated breeding values than conventional best linear unbiased prediction (BLUP). GWAS and GS address different aspects of quantitative traits, but, as statistical models, they are quite similar in their description of the genetic mechanisms that underlie quantitative traits...
August 24, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28810834/multiple-trait-qtl-mapping-and-genomic-prediction-for-wool-traits-in-sheep
#13
Sunduimijid Bolormaa, Andrew A Swan, Daniel J Brown, Sue Hatcher, Nasir Moghaddar, Julius H van der Werf, Michael E Goddard, Hans D Daetwyler
BACKGROUND: The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymorphism (SNP) data. Several key traits determine the value of wool and influence a sheep's susceptibility to fleece rot and fly strike. Our aim was to predict genomic estimated breeding values (GEBV) and to compare three methods of combining information across traits to map polymorphisms that affect these traits...
August 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28764638/contribution-of-rare-and-low-frequency-whole-genome-sequence-variants-to-complex-traits-variation-in-dairy-cattle
#14
Qianqian Zhang, Mario P L Calus, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
BACKGROUND: Whole-genome sequencing and imputation methodologies have enabled the study of the effects of genomic variants with low to very low minor allele frequency (MAF) on variation in complex traits. Our objective was to estimate the proportion of variance explained by imputed sequence variants classified according to their MAF compared with the variance explained by the pedigree-based additive genetic relationship matrix for 17 traits in Nordic Holstein dairy cattle. RESULTS: Imputed sequence variants were grouped into seven classes according to their MAF (0...
August 1, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28747171/incorporation-of-causative-quantitative-trait-nucleotides-in-single-step-gblup
#15
Breno O Fragomeni, Daniela A L Lourenco, Yutaka Masuda, Andres Legarra, Ignacy Misztal
BACKGROUND: Much effort is put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, empowered by the availability of dense single nucleotide polymorphism (SNP) information. Genomic selection using traditional SNP information is easily implemented for any number of genotyped individuals using single-step genomic best linear unbiased predictor (ssGBLUP) with the algorithm for proven and young (APY). Our aim was to investigate whether ssGBLUP is useful for genomic prediction when some or all QTN are known...
July 26, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28728597/interaction-of-direct-and-social-genetic-effects-with-feeding-regime-in-growing-rabbits
#16
Miriam Piles, Ingrid David, Josep Ramon, Laurianne Canario, Oriol Rafel, Mariam Pascual, Mohamed Ragab, Juan P Sánchez
BACKGROUND: Most rabbit production farms apply feed restriction at fattening because of its protective effect against digestive diseases that affect growing rabbits. However, it leads to competitive behaviour between cage mates, which is not observed when animals are fed ad libitum. Our aim was to estimate the contribution of direct ([Formula: see text]) and social ([Formula: see text]) genetic effects (also known as indirect genetic effects) to total heritable variance of average daily gain ([Formula: see text]) in rabbits on different feeding regimens (FR), and the magnitude of the interaction between genotype and FR (G × FR)...
July 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28709397/use-of-haplotypes-to-identify-regions-harbouring-lethal-recessive-variants-in-pigs
#17
David M Howard, Ricardo Pong-Wong, Pieter W Knap, John A Woolliams
BACKGROUND: Lethal recessive genetic variants are maintained at relatively low frequencies in a population in the heterozygous state, but by definition are fatal and therefore unobserved in the homozygous state. Since haplotypes allow the tagging of rare and untyped genetic variants, they have potential for studying lethal recessive variants. In this study, we used a large commercial population to identify putative lethal recessive haplotypes that impact either the total number born (TNB) or the number born alive (NBA) as a proportion of the total number born (NBA/TNB)...
July 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28683716/putative-enhancer-sites-in-the-bovine-genome-are-enriched-with-variants-affecting-complex-traits
#18
Min Wang, Timothy P Hancock, Iona M MacLeod, Jennie E Pryce, Benjamin G Cocks, Benjamin J Hayes
BACKGROUND: Enhancers are non-coding DNA sequences, which when they are bound by specific proteins increase the level of gene transcription. Enhancers activate unique gene expression patterns within cells of different types or under different conditions. Enhancers are key contributors to gene regulation, and causative variants that affect quantitative traits in humans and mice have been located in enhancer regions. However, in the bovine genome, enhancers as well as other regulatory elements are not yet well defined...
July 6, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28676070/the-potential-of-shifting-recombination-hotspots-to-increase-genetic-gain-in-livestock-breeding
#19
Serap Gonen, Mara Battagin, Susan E Johnston, Gregor Gorjanc, John M Hickey
BACKGROUND: This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs. METHODS: We simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots)...
July 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28673233/fixed-length-haplotypes-can-improve-genomic-prediction-accuracy-in-an-admixed-dairy-cattle-population
#20
Melanie Hess, Tom Druet, Andrew Hess, Dorian Garrick
BACKGROUND: Fitting covariates representing the number of haplotype alleles rather than single nucleotide polymorphism (SNP) alleles may increase genomic prediction accuracy if linkage disequilibrium between quantitative trait loci and SNPs is inadequate. The objectives of this study were to evaluate the accuracy, bias and computation time of Bayesian genomic prediction methods that fit fixed-length haplotypes or SNPs. Genotypes at 37,740 SNPs that were common to Illumina BovineSNP50 and high-density panels were phased for ~58,000 New Zealand dairy cattle...
July 3, 2017: Genetics, Selection, Evolution: GSE
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