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Genetics, Selection, Evolution: GSE

Hanne Gro Olsen, Tim Martin Knutsen, Anna M Lewandowska-Sabat, Harald Grove, Torfinn Nome, Morten Svendsen, Mariann Arnyasi, Marte Sodeland, Kristil K Sundsaasen, Sandra Rinne Dahl, Bjørg Heringstad, Hanne H Hansen, Ingrid Olsaker, Matthew Peter Kent, Sigbjørn Lien
BACKGROUND: Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms that underlie these traits would be valuable to improve both of them simultaneously through breeding. A quantitative trait locus (QTL) that affects both clinical mastitis and milk production has recently been fine-mapped to around 89 Mb on bovine chromosome 6 (BTA6), but identification of the gene that underlies this QTL was not possible due to the strong linkage disequilibrium between single nucleotide polymorphisms (SNPs) within this region...
October 19, 2016: Genetics, Selection, Evolution: GSE
Gesine Lühken, Stefan Krebs, Sophie Rothammer, Julia Küpper, Boro Mioč, Ingolf Russ, Ivica Medugorac
BACKGROUND: The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3'-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2)...
October 19, 2016: Genetics, Selection, Evolution: GSE
Xiaochen Sun, Rohan Fernando, Jack Dekkers
BACKGROUND: Traditional genomic prediction models using multiple regression on single nucleotide polymorphisms (SNPs) genotypes exploit associations between genotypes of quantitative trait loci (QTL) and SNPs, which can be created by historical linkage disequilibrium (LD), recent co-segregation (CS) and pedigree relationships. Results from field data analyses show that prediction accuracy is usually much higher for individuals that are close relatives of the training population than for distantly related individuals...
October 11, 2016: Genetics, Selection, Evolution: GSE
Minhui Chen, Dunfei Pan, Hongyan Ren, Jinluan Fu, Junya Li, Guosheng Su, Aiguo Wang, Li Jiang, Qin Zhang, Jian-Feng Liu
BACKGROUND: The identification of signals left by recent positive selection provides a feasible approach for targeting genomic variants that underlie complex traits and fitness. A better understanding of the selection mechanisms that occurred during the evolution of species can also be gained. In this study, we simultaneously detected the genome-wide footprints of recent positive selection that occurred within and between Chinese Holstein and Simmental populations, which have been subjected to artificial selection for distinct purposes...
October 6, 2016: Genetics, Selection, Evolution: GSE
Mohammad H Ferdosi, John Henshall, Bruce Tier
BACKGROUND: As genomic data becomes more abundant, genomic prediction is more routinely used to estimate breeding values. In genomic prediction, the relationship matrix ([Formula: see text]), which is traditionally used in genetic evaluations is replaced by the genomic relationship matrix ([Formula: see text]). This paper considers alternative ways of building relationship matrices either using single markers or haplotypes of different lengths. We compared the prediction accuracies and log-likelihoods when using these alternative relationship matrices and the traditional [Formula: see text] matrix, for real and simulated data...
September 29, 2016: Genetics, Selection, Evolution: GSE
Androniki Psifidi, Georgios Banos, Oswald Matika, Takele T Desta, Judy Bettridge, David A Hume, Tadelle Dessie, Rob Christley, Paul Wigley, Olivier Hanotte, Pete Kaiser
BACKGROUND: The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are hampered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability...
September 29, 2016: Genetics, Selection, Evolution: GSE
Laura Plieschke, Christian Edel, Eduardo C G Pimentel, Reiner Emmerling, Jörn Bennewitz, Kay-Uwe Götz
BACKGROUND: Extending the reference set for genomic predictions in dairy cattle by adding large numbers of cows with genotypes and phenotypes has been proposed as a means to increase reliability of selection decisions for candidates. METHODS: In this study, we explored the potential of increasing the reliability of breeding values of young selection candidates by genotyping a fixed number of first-crop daughters of each sire from one or two generations in a balanced and regular system of genotyping...
September 28, 2016: Genetics, Selection, Evolution: GSE
Laurence Puillet, Denis Réale, Nicolas C Friggens
BACKGROUND: Feed efficiency of farm animals has greatly improved through genetic selection for production. Today, we are faced with the limits of our ability to predict the effect of selection on feed efficiency, partly because the relative importance of the components of this complex phenotype changes across environments. Thus, we developed a dairy cow model that incorporates the dynamic interplay between life functions and evaluated its behaviour with a global sensitivity analysis on two definitions of feed efficiency...
September 26, 2016: Genetics, Selection, Evolution: GSE
Ricardo V Ventura, Stephen P Miller, Ken G Dodds, Benoit Auvray, Michael Lee, Matthew Bixley, Shannon M Clarke, John C McEwan
BACKGROUND: Genotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical directions on the implementation of imputation strategies in a multi-breed sheep population genotyped with three single nucleotide polymorphism (SNP) panels: 5K, 50K and HD (600K SNPs). RESULTS: Imputation from 5K to HD was slightly better (0.6 %) than imputation from 5K to 50K...
2016: Genetics, Selection, Evolution: GSE
Binyam S Dagnachew, Theo H E Meuwissen
BACKGROUND: The management of genetic variation in a breeding scheme relies very much on the control of the average relationship between selected parents. Optimum contribution selection is a method that seeks the optimum way to select for genetic improvement while controlling the rate of inbreeding. METHODS: A novel iterative algorithm, Gencont2, for calculating optimum genetic contributions was developed. It was validated by comparing it with a previous program, Gencont, on three datasets that were obtained from practical breeding programs in three species (cattle, pig and sheep)...
2016: Genetics, Selection, Evolution: GSE
Isabel Cervantes, Juan Pablo Gutiérrez, Theo H E Meuwissen
BACKGROUND: Rare breeds represent a valuable resource for future market demands. These populations are usually well-adapted, but their low census compromises the genetic diversity and future of these breeds. Since improvement of a breed for commercial traits may also confer higher probabilities of survival for the breed, it is important to achieve good responses to artificial selection. Therefore, efficient genetic management of these populations is essential to ensure that they respond adequately to genetic selection in possible future artificial selection scenarios...
2016: Genetics, Selection, Evolution: GSE
Setegn W Alemu, Mario P L Calus, William M Muir, Katrijn Peeters, Addie Vereijken, Piter Bijma
BACKGROUND: Mortality due to cannibalism causes both economic and welfare problems in laying hens. To limit mortality due to cannibalism, laying hens are often beak-trimmed, which is undesirable for animal welfare reasons. Genetic selection is an alternative strategy to increase survival and is more efficient by taking heritable variation that originates from social interactions into account, which are modelled as the so-called indirect genetic effects (IGE). Despite the considerable heritable variation in survival time due to IGE, genetic improvement of survival time in laying hens is still challenging because the detected heritable variation of the trait with IGE is still limited, ranging from 0...
2016: Genetics, Selection, Evolution: GSE
Xiangyu Guo, Ole Fredslund Christensen, Tage Ostersen, Yachun Wang, Mogens Sandø Lund, Guosheng Su
BACKGROUND: Dominance and imprinting genetic effects have been shown to contribute to genetic variance for certain traits but are usually ignored in genomic prediction of complex traits in livestock. The objectives of this study were to estimate variances of additive, dominance and imprinting genetic effects and to evaluate predictions of genetic merit based on genomic data for average daily gain (DG) and backfat thickness (BF) in Danish Duroc pigs. METHODS: Corrected phenotypes of 8113 genotyped pigs from breeding and multiplier herds were used...
2016: Genetics, Selection, Evolution: GSE
Anh T Quach, Tamas Revay, Daniel A F Villagomez, Mariana P Macedo, Alison Sullivan, Laurence Maignel, Stefanie Wyss, Brian Sullivan, W Allan King
BACKGROUND: Structural chromosome abnormalities are well known as factors that reduce fertility rate in domestic pigs. According to large-scale national cytogenetic screening programs that are implemented in France, it is estimated that new chromosome abnormalities occur at a rate of 0.5 % in fertility-unproven boars. RESULTS: This work aimed at estimating the prevalence and consequences of chromosome abnormalities in commercial swine operations in Canada. We found pig carriers at a frequency of 1...
2016: Genetics, Selection, Evolution: GSE
Strahil Ristov, Vladimir Brajkovic, Vlatka Cubric-Curik, Ivan Michieli, Ino Curik
BACKGROUND: Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis...
2016: Genetics, Selection, Evolution: GSE
Chontida Phuthaworn, Nguyen Hong Nguyen, Jane Quinn, Wayne Knibb
BACKGROUND: In shrimp farming, major production losses are caused by viruses. Hepatopancreatic parvovirus (HPV) is one of the viral pathogens that infect banana shrimp (Fenneropenaeus merguiensis). HPV is thought to slow down growth and cause mortality in the juvenile stages of banana shrimp. Genetic improvement through selection of shrimp resistant to viral diseases is one approach to address this issue. This is the first detailed report on an aquaculture species that investigates whether viral titre varies among families and is heritable, and thus whether viral titre per se is a possible candidate trait for selection to produce resistant stock...
2016: Genetics, Selection, Evolution: GSE
Vinzent Boerner, Bruce Tier
BACKGROUND: The advent of genomic marker data has triggered the development of various Bayesian algorithms for estimation of marker effects, but software packages implementing these algorithms are not readily available, or are limited to a single algorithm, uni-variate analysis or a limited number of factors. Moreover, script based environments like R may not be able to handle large-scale genomic data or exploit model properties which save computing time or memory (RAM). RESULTS: BESSiE is a software designed for best linear unbiased prediction (BLUP) and Bayesian Markov chain Monte Carlo analysis of linear mixed models allowing for continuous and/or categorical multivariate, repeated and missing observations, various random and fixed factors and large-scale genomic marker data...
2016: Genetics, Selection, Evolution: GSE
Xing Guo, Qi Fang, Chendong Ma, Bangyuan Zhou, Yi Wan, Runshen Jiang
BACKGROUND: Selective breeding for genetic improvement is expected to leave distinctive selection signatures within genomes. The identification of selection signatures can help to elucidate the mechanisms of selection and accelerate genetic improvement. Fighting chickens have undergone extensive artificial selection, resulting in modifications to their morphology, physiology and behavior compared to wild species. Comparing the genomes of fighting chickens and wild species offers a unique opportunity for identifying signatures of artificial selection...
2016: Genetics, Selection, Evolution: GSE
Jérémie Vandenplas, Mario P L Calus, Claudia A Sevillano, Jack J Windig, John W M Bastiaansen
BACKGROUND: For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions...
2016: Genetics, Selection, Evolution: GSE
Qianqian Zhang, Bernt Guldbrandtsen, Mario P L Calus, Mogens Sandø Lund, Goutam Sahana
BACKGROUND: There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map rare variants. Besides, livestock populations have large half-sib families and the occurrence of rare variants may be confounded with family structure, which makes it difficult to disentangle their effects from family mean effects...
2016: Genetics, Selection, Evolution: GSE
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