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Genetics, Selection, Evolution: GSE

Mahmoud Shirali, Patrick Francis Varley, Just Jensen
BACKGROUND: This study aimed at (1) deriving Bayesian methods to predict breeding values for ratio (i.e. feed conversion ratio; FCR) or linear (i.e. residual feed intake; RFI) traits; (2) estimating genetic parameters for average daily feed consumption (ADFI), average daily weight gain (ADG), lean meat percentage (LMP) along with the derived traits of RFI and FCR; and (3) deriving Bayesian estimates of direct and correlated responses to selection on RFI, FCR, ADG, ADFI, and LMP. Response to selection was defined as the difference in additive genetic mean of the selected top individuals, expected to be parents of the next generation, and the total population after integrating genetic trends out of the posterior distribution of selection responses...
June 20, 2018: Genetics, Selection, Evolution: GSE
Ali Toosi, Rohan L Fernando, Jack C M Dekkers
BACKGROUND: Population stratification and cryptic relationships have been the main sources of excessive false-positives and false-negatives in population-based association studies. Many methods have been developed to model these confounding factors and minimize their impact on the results of genome-wide association studies. In most of these methods, a two-stage approach is applied where: (1) methods are used to determine if there is a population structure in the sample dataset and (2) the effects of population structure are corrected either by modeling it or by running a separate analysis within each sub-population...
June 19, 2018: Genetics, Selection, Evolution: GSE
Marc Teissier, Hélène Larroque, Christèle Robert-Granié
BACKGROUND: In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain the same fraction of genetic variance. However, ssGBLUP is not suitable for protein content, which is controlled by a major gene, i.e. α s 1 casein. This gene explains about 40% of the genetic variation in protein content. In this study, we evaluated the accuracy of genomic prediction using different genomic methods to include the effect of the α s 1 casein gene...
June 15, 2018: Genetics, Selection, Evolution: GSE
Christos Palaiokostas, Sophie Cariou, Anastasia Bestin, Jean-Sebastien Bruant, Pierrick Haffray, Thierry Morin, Joëlle Cabon, François Allal, Marc Vandeputte, Ross D Houston
BACKGROUND: European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding...
June 8, 2018: Genetics, Selection, Evolution: GSE
Tatiana E Deniskova, Arsen V Dotsev, Marina I Selionova, Elisabeth Kunz, Ivica Medugorac, Henry Reyer, Klaus Wimmers, Mario Barbato, Alexei A Traspov, Gottfried Brem, Natalia A Zinovieva
BACKGROUND: Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip...
May 24, 2018: Genetics, Selection, Evolution: GSE
Naomi Duijvesteijn, Sunduimijid Bolormaa, Hans D Daetwyler, Julius H J van der Werf
BACKGROUND: In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene...
May 22, 2018: Genetics, Selection, Evolution: GSE
Kim E Grashei, Jørgen Ødegård, Theo H E Meuwissen
BACKGROUND: Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage assignment are exclusion-based (i.e. based on loci that violate Mendelian inheritance) or likelihood-based, assuming independent inheritance of loci. For true parent-offspring relations, genotyping errors cause apparent violations of Mendelian inheritance. Thus, the maximum proportion of such violations must be determined, which is complicated by variable call- and genotype error rates among loci and individuals...
May 18, 2018: Genetics, Selection, Evolution: GSE
Biaty Raymond, Aniek C Bouwman, Chris Schrooten, Jeanine Houwing-Duistermaat, Roel F Veerkamp
BACKGROUND: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. METHODS: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands...
May 18, 2018: Genetics, Selection, Evolution: GSE
David M Howard, Ricardo Pong-Wong, Pieter W Knap, Valentin D Kremer, John A Woolliams
BACKGROUND: Optimal contributions selection (OCS) provides animal breeders with a framework for maximising genetic gain for a predefined rate of inbreeding. Simulation studies have indicated that the source of the selective advantage of OCS is derived from breeding decisions being more closely aligned with estimates of Mendelian sampling terms ([Formula: see text]) of selection candidates, rather than estimated breeding values (EBV). This study represents the first attempt to assess the source of the selective advantage provided by OCS using a commercial pig population and by testing three hypotheses: (1) OCS places more emphasis on [Formula: see text] compared to EBV for determining which animals were selected as parents, (2) OCS places more emphasis on [Formula: see text] compared to EBV for determining which of those parents were selected to make a long-term genetic contribution (r), and (3) OCS places more emphasis on [Formula: see text] compared to EBV for determining the magnitude of r...
May 10, 2018: Genetics, Selection, Evolution: GSE
Ingrid David, Juan-Pablo Sánchez, Miriam Piles
BACKGROUND: Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have investigated how IGE vary over time for traits under selection in livestock species. To overcome this issue, our aim was: (1) to analyze longitudinal records of average daily gain (ADG) in rabbits subjected to a 5-week period of feed restriction using a structured antedependence (SAD) model that includes IGE and (2) to evaluate, by simulation, the response to selection when IGE are present and genetic evaluation is based on a SAD model that includes IGE or not...
May 10, 2018: Genetics, Selection, Evolution: GSE
Anna Wolc, Wioleta Drobik-Czwarno, Janet E Fulton, Jesus Arango, Tomasz Jankowski, Jack C M Dekkers
Avian influenza (AI) is a devastating poultry disease that currently can be controlled only by liquidation of affected flocks. In spite of typically very high mortality rates, a group of survivors was identified and genotyped on a 600K single nucleotide polymorphism (SNP) chip to identify genetic differences between survivors, and age- and genetics-matched controls from unaffected flocks. In a previous analysis of this dataset, a heritable component was identified and several regions that are associated with outcome of the infection were localized but none with a large effect...
May 2, 2018: Genetics, Selection, Evolution: GSE
Diercles F Cardoso, Lucia Galvão de Albuquerque, Christian Reimer, Saber Qanbari, Malena Erbe, André V do Nascimento, Guilherme C Venturini, Daiane C Becker Scalez, Fernando Baldi, Gregório M Ferreira de Camargo, Maria E Zerlotti Mercadante, Joslaine N do Santos Gonçalves Cyrillo, Henner Simianer, Humberto Tonhati
BACKGROUND: This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection...
May 2, 2018: Genetics, Selection, Evolution: GSE
Siri S Horn, Bente Ruyter, Theo H E Meuwissen, Borghild Hillestad, Anna K Sonesson
BACKGROUND: The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids (n-3 LC-PUFA) eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) in their filets. Previous studies showed the potential of selective breeding to increase n-3 LC-PUFA levels in salmon tissues, but knowledge on the genetic parameters for individual muscle fatty acids (FA) and their relationships with other traits is still lacking...
May 2, 2018: Genetics, Selection, Evolution: GSE
Stephen J Bush, Charity Muriuki, Mary E B McCulloch, Iseabail L Farquhar, Emily L Clark, David A Hume
BACKGROUND: mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human...
April 24, 2018: Genetics, Selection, Evolution: GSE
Gabriela Padilla-Jacobo, Horacio Cano-Camacho, Rigoberto López-Zavala, María E Cornejo-Pérez, María G Zavala-Páramo
BACKGROUND: The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M...
April 17, 2018: Genetics, Selection, Evolution: GSE
John W M Bastiaansen, Henk Bovenhuis, Martien A M Groenen, Hendrik-Jan Megens, Han A Mulder
BACKGROUND: Genome editing technologies provide new tools for genetic improvement and have the potential to become the next game changer in animal and plant breeding. The aim of this study was to investigate how genome editing in combination with genomic selection can accelerate the introduction of a monogenic trait in a livestock population as compared to genomic selection alone. METHODS: A breeding population was simulated under genomic selection for a polygenic trait...
April 16, 2018: Genetics, Selection, Evolution: GSE
Martijn F L Derks, Hendrik-Jan Megens, Mirte Bosse, Jeroen Visscher, Katrijn Peeters, Marco C A M Bink, Addie Vereijken, Christian Gross, Dick de Ridder, Marcel J T Reinders, Martien A M Groenen
BACKGROUND: Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken lines for deleterious and functional variations, combining genotype and whole-genome sequence data. RESULTS: We analysed over 22,000 animals that were genotyped on a 60 K SNP chip from four purebred lines (two white egg and two brown egg layer lines) and two crossbred lines...
April 16, 2018: Genetics, Selection, Evolution: GSE
Johannes W R Martini, Matias F Schrauf, Carolina A Garcia-Baccino, Eduardo C G Pimentel, Sebastian Munilla, Andres Rogberg-Muñoz, Rodolfo J C Cantet, Christian Reimer, Ning Gao, Valentin Wimmer, Henner Simianer
BACKGROUND: The single-step covariance matrix H combines the pedigree-based relationship matrix [Formula: see text] with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix [Formula: see text]. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights [Formula: see text] and [Formula: see text] have been introduced in the definition of [Formula: see text], which blend the inverse of a part of [Formula: see text] with the inverse of [Formula: see text]...
April 13, 2018: Genetics, Selection, Evolution: GSE
Harmen P Doekes, Roel F Veerkamp, Piter Bijma, Sipke J Hiemstra, Jack J Windig
BACKGROUND: In recent decades, Holstein-Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015...
April 11, 2018: Genetics, Selection, Evolution: GSE
Chunyan Zhang, Robert Alan Kemp, Paul Stothard, Zhiquan Wang, Nicholas Boddicker, Kirill Krivushin, Jack Dekkers, Graham Plastow
BACKGROUND: Increasing marker density was proposed to have potential to improve the accuracy of genomic prediction for quantitative traits; whole-sequence data is expected to give the best accuracy of prediction, since all causal mutations that underlie a trait are expected to be included. However, in cattle and chicken, this assumption is not supported by empirical studies. Our objective was to compare the accuracy of genomic prediction of feed efficiency component traits in Duroc pigs using single nucleotide polymorphism (SNP) panels of 80K, imputed 650K, and whole-genome sequence variants using GBLUP, BayesB and BayesRC methods, with the ultimate purpose to determine the optimal method to increase genetic gain for feed efficiency in pigs...
April 6, 2018: Genetics, Selection, Evolution: GSE
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