Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
Reads0
Chats0
TLDR
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.read more
Citations
More filters
Journal ArticleDOI
The pattern of linkage disequilibrium in German Holstein cattle.
Saber Qanbari,E. C. G. Pimentel,Jens Tetens,Georg Thaller,P. Lichtner,Ahmad Reza Sharifi,Henner Simianer +6 more
TL;DR: It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r(2) estimates, and a lower level of LD for SNP pairs at the distance < or =100 kb than previously thought.
Journal ArticleDOI
Toward a Theory of Marker-Assisted Gene Pyramiding
TL;DR: An algorithm is provided that generates and compares pedigrees on the basis of the population sizes they require and on their total duration and finds the best gene-pyramiding scheme.
Genomic prediction in maize breeding populations with genotyping-by-
Vanessa S. Windhausen,Edward S. Buckler,M. A. Lopez Cruz,Raman Babu,José Crossa,Yoseph Beyene,Semagn Kassa,Charles Chen,Juan Burgueño,Lopez Cruz,Paulino Pérez,John M. Hickey +11 more
TL;DR: Crossa et al. as discussed by the authors used genotyping-by-1 sequencing to predict maize breeding populations with genotype-by1 sequencing, and showed that the predicted maize genomes are similar to those of maize kernels.
Journal ArticleDOI
Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.
TL;DR: It was found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates.
Journal ArticleDOI
Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy
Gabriele Marras,Gabriele Marras,Giustino Gaspa,Silvia Sorbolini,Corrado Dimauro,Paolo Ajmone-Marsan,Alessio Valentini,John L. Williams,Nicolò Pietro Paolo Macciotta +8 more
TL;DR: ROH are a direct measure of autozygosity at the DNA level and can overcome approximations and errors resulting from incomplete pedigree data, and in populations with low LD and ancient inbreeding, marker density would have to be increased to identify short ROH that are identical by descent more precisely.
References
More filters
Book
Introduction to quantitative genetics
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.
BookDOI
Markov Chain Monte Carlo in Practice
TL;DR: The Markov Chain Monte Carlo Implementation Results Summary and Discussion MEDICAL MONITORING Introduction Modelling Medical Monitoring Computing Posterior Distributions Forecasting Model Criticism Illustrative Application Discussion MCMC for NONLINEAR HIERARCHICAL MODELS.
Book
Genetics and Analysis of Quantitative Traits
Michael Lynch,Bruce Walsh +1 more
TL;DR: This book discusses the genetic Basis of Quantitative Variation, Properties of Distributions, Covariance, Regression, and Correlation, and Properties of Single Loci, and Sources of Genetic Variation for Multilocus Traits.
Journal ArticleDOI
An Introduction to Population Genetics Theory
James F. Crow,Motoo Kimura +1 more
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics Theory, Population Genetics theory, Population genetics theory as discussed by the authors, Population genetics, population genetics, and population genetics theories, Population Genetic Theory
Book
An introduction to population genetics theory
James F. Crow,Motoo Kimura +1 more
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics theory, and more.