journal
MENU ▼
Read by QxMD icon Read
search

Genetics, Selection, Evolution: GSE

journal
https://www.readbyqxmd.com/read/28427324/genomic-prediction-from-observed-and-imputed-high-density-ovine-genotypes
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
journal
journal
30870
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"