Distribution and location of genetic effects for dairy traits
TL;DR: A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects as discussed by the authors.
About: This article is published in Journal of Dairy Science.The article was published on 2009-06-01 and is currently open access. It has received 224 citations till now. The article focuses on the topics: Quantitative trait locus & Allele.
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TL;DR: This research presents a new approach to estimate and compare breeding values using the conventional method (BLUP) and genomic breeding values (MEBV and GEBV) estimated through the bioinformatics method (Objetive) and shows good agreement between the methods.
Abstract: Objetive. To estimate and compare breeding values (EBV) using the conventional method (BLUP) and genomic breeding values (MEBV and GEBV) estimated through ba...
6 citations
01 Apr 2019-Cab Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources
TL;DR: This review focuses on the application of genetic engineering and genome engineering tools to livestock population improvement through the management of genetic load and the promotion of desirable alleles in the population associated with both monogenic and polygenic traits.
Abstract: Abstract
Traditional genetic selection programmes based on pedigree and performance information have been used to improve livestock populations for decades. The introduction of high-density single nucleotide polymorphism genotyping about 10 years ago supported increased rates of gain through more accurate prediction of genetic merit earlier in life. Recent continued technological advances enable the routine use of genetic engineering and gene editing tools in livestock research and, increasingly, production systems. Livestock geneticists have responded by proposing new breeding schemes that combine traditional selection methodology with these new tools to substantially increase rates of genetic gain while reducing harmful effects due to decreased heterozygosity. Genetic improvement strategies based on gene drives have the potential further increase rates of gain but pose risks that may not be acceptable to the public. Intense debate about the use of these technologies in the animal food chain is being driven by regulatory agencies and consumer advocates, and it is not clear if genetically modified animals will be acceptable to consumers. This review focuses on the application of genetic engineering and genome engineering tools to livestock population improvement through the management of genetic load and the promotion of desirable alleles in the population associated with both monogenic and polygenic traits. Limitations of the current technology, such as limited knowledge of true causal variants, are discussed, as are regulatory and consumer acceptance issues.
6 citations
01 Jan 2018
TL;DR: This work presents a novel and scalable approach called “Smart Gene Regulation” that allows for real-time assessment of the status of individual cells as well as their status as to whether or not they can be passed on to the immune system.
Abstract: 1 Immunology Unit, University of Veterinary Medicine Hannover, 30173 Hannover, Germany Clinic for Ruminants, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany Leibniz Institute for Farm Animal Biology, Genome Biology, 18196 Dummerstorf, Germany Clinic for Cattle, University of Veterinary Medicine Hannover, 30173 Hannover, Germany 5 Institute for Microbiology, Technical University Braunschweig, 38124 Braunschweig, Germany 6 Microbial Proteomics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany Agricultural and Environmental Faculty, University Rostock, 18059 Rostock, Germany kuehn@fbn-dummerstorf.de (Corresponding Author)
6 citations
TL;DR: An a posteriori granddaughter design was applied to estimate quantitative trait loci genotypes of sires with many sons in the US Holstein population and can be used as a first step to determine the actual polymorphisms responsible for observed quantitative variation in dairy cattle.
Abstract: An a posteriori granddaughter design was applied to estimate quantitative trait loci genotypes of sires with many sons in the US Holstein population. The results of this analysis can be used to determine concordance between specific polymorphisms and segregating quantitative trait loci. Determination of the actual polymorphisms responsible for observed genetic variation should increase the accuracy of genomic evaluations and rates of genetic gain. A total of 52 grandsire families, each with ⩾100 genotyped sons with genetic evaluations based on progeny tests, were analyzed for 33 traits (milk, fat and protein yields; fat and protein percentages; somatic cell score (SCS); productive life; daughter pregnancy rate; heifer and cow conception rates; service-sire and daughter calving ease; service-sire and daughter stillbirth rates; 18 conformation traits; and net merit). Of 617 haplotype segments spanning the entire bovine genome and each including ~5×10 6 bp, 5 cM and 50 genes, 608 autosomal segments were analyzed. A total of 19 335 unique haplotypes were found among the 52 grandsires. There were a total of 133 chromosomal segment-by-trait combinations, for which the nominal probability of significance for the haplotype effect was −8 , which corresponds to genome-wide significance of −4 . The number of chromosomal regions that met this criterion by trait ranged from one for rear legs (rear view) to seven for net merit. For each of the putative quantitative trait loci, at least one grandsire family had a within-family contrast with a t -value of >3. Confidence intervals (CIs) were estimated by the nonparametric bootstrap for the largest effect for each of nine traits. The bootstrap distribution generated by 100 samples was bimodal only for net merit, which had the widest 90% CI (eight haplotype segments). This may be due to the fact that net merit is a composite trait. For all other chromosomes, the CI spanned less than a third of the chromosome. The narrowest CI (a single haplotype segment) was found for SCS. It is likely that analysis by more advanced methods could further reduce CIs at least by half. These results can be used as a first step to determine the actual polymorphisms responsible for observed quantitative variation in dairy cattle.
5 citations
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References
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Book•
01 Jan 1981
TL;DR: The genetic constitution of a population: Hardy-Weinberg equilibrium and changes in gene frequency: migration mutation, changes of variance, and heritability are studied.
Abstract: Part 1 Genetic constitution of a population: Hardy-Weinberg equilibrium. Part 2 Changes in gene frequency: migration mutation. Part 3 Small populations - changes in gene frequency under simplified conditions. Part 4 Small populations - less simplified conditions. Part 5 Small populations - pedigreed populations and close inbreeding. Part 6 Continuous variation. Part 7 Values and means. Part 8 Variance. Part 9 Resemblance between relatives. Part 10 Heritability. Part 11 Selection - the response and its prediction. Part 12 Selection - the results of experiments. Part 13 Selection - information from relatives. Part 14 Inbreeding and crossbreeding - changes of mean value. Part 15 Inbreeding and crossbreeding - changes of variance. Part 16 Inbreeding and crossbreeding - applications. Part 17 Scale. Part 18 Threshold characters. Part 19 Correlated characters. Part 20 Metric characters under natural selection.
20,288 citations
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
Abstract: Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of ∼50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size (Ne = 100), the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
6,036 citations
TL;DR: Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously, and a blend of first- and second-order Jacobi iteration using 2 separate relaxation factors converged well for allele frequencies and effects.
4,196 citations
TL;DR: Genotypes for 38,416 markers and August 2003 genetic evaluations for 3,576 Holstein bulls born before 1999 were used to predict January 2008 daughter deviations and genomic prediction improves reliability by tracing the inheritance of genes even with small effects.
1,166 citations