Estimating genetic diversity across the neutral genome with the use of dense marker maps

Autor: Piter Bijma, Jack J. Windig, Mario P. L. Calus, K.A. Engelsma
Rok vydání: 2009
Předmět:
haplotypes
Linkage disequilibrium
Population genetics
Genome
genetische diversiteit
Loss of heterozygosity
computersimulatie
Gene Frequency
Genetics(clinical)
lcsh:SF1-1100
conservation
genetic diversity
General Medicine
respiratory system
populatiegenetica
Wageningen Livestock Research
Heterozygote
lcsh:QH426-470
selection
Animal Breeding and Genomics
Biology
Polymorphism
Single Nucleotide
Genetic variation
computer simulation
Genetics
Animals
Fokkerij en Genomica
Genetic variability
marker genes
Ecology
Evolution
Behavior and Systematics
Probability
Genetic diversity
Research
population genetics
Genetic Variation
prediction
populations
lcsh:Genetics
merkergenen
Genetic marker
Evolutionary biology
WIAS
Animal Science and Zoology
Cattle
lcsh:Animal culture
human activities
linkage disequilibrium
Biomarkers
Onderzoek
Zdroj: Genetics, Selection, Evolution : GSE
Genetics, Selection, Evolution, 42
Genetics, Selection, Evolution 42 (2010)
Genetics Selection Evolution, Vol 42, Iss 1, p 12 (2010)
ISSN: 1297-9686
0999-193X
Popis: Background With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity. Results The simulated population had an average minor allele frequency of 0.28 and an LD (r2) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity. Conclusions Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.
Databáze: OpenAIRE
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