A simulation study on the accuracy of position and effect estimates of linked QTL and their asymptotic standard deviations using multiple interval mapping in an F2 scheme

Autor: M. Mayer, Gertraude Freyer, Yuefu Liu
Rok vydání: 2004
Předmět:
Genetic Markers
0106 biological sciences
lcsh:QH426-470
Genetic Linkage
QTL
Quantitative Trait Loci
Coverage probability
Asymptotic distribution
Biology
Quantitative trait locus
01 natural sciences
Standard deviation
03 medical and health sciences
Resampling
Statistics
Confidence Intervals
Genetics
Animals
Computer Simulation
Inbreeding
asymptotic standard error
Genetics(clinical)
mapping
Statistical theory
Crosses
Genetic
Ecology
Evolution
Behavior and Systematics
lcsh:SF1-1100
030304 developmental biology
Likelihood Functions
0303 health sciences
Models
Statistical
Models
Genetic
Research
Homozygote
Chromosome Mapping
Epistasis
Genetic
simulation
confidence interval
General Medicine
Confidence interval
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
lcsh:Genetics
Standard error
Animal Science and Zoology
lcsh:Animal culture
Animals
Inbred Strains
010606 plant biology & botany
Zdroj: Genetics Selection Evolution, Vol 36, Iss 4, Pp 455-479 (2004)
Genetics, selection, evolution, 36(4): 455–479
Genetics, Selection, Evolution : GSE
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2004, 36 (4), pp.455-479. ⟨10.1051/gse:2004011⟩
ISSN: 1297-9686
0999-193X
DOI: 10.1186/1297-9686-36-4-455
Popis: International audience; Approaches like multiple interval mapping using a multiple-QTL model for simultaneously mapping QTL can aid the identification of multiple QTL, improve the precision of estimating QTL positions and effects, and are able to identify patterns and individual elements of QTL epistasis. Because of the statistical problems in analytically deriving the standard errors and the distributional form of the estimates and because the use of resampling techniques is not feasible for several linked QTL, there is the need to perform large-scale simulation studies in order to evaluate the accuracy of multiple interval mapping for linked QTL and to assess confidence intervals based on the standard statistical theory. From our simulation study it can be concluded that in comparison with a monogenetic background a reliable and accurate estimation of QTL positions and QTL effects of multiple QTL in a linkage group requires much more information from the data. The reduction of the marker interval size from 10 cM to 5 cM led to a higher power in QTL detection and to a remarkable improvement of the QTL position as well as the QTL effect estimates. This is different from the findings for (single) interval mapping. The empirical standard deviations of the genetic effect estimates were generally large and they were the largest for the epistatic effects. These of the dominance effects were larger than those of the additive effects. The asymptotic standard deviation of the position estimates was not a good criterion for the accuracy of the position estimates and confidence intervals based on the standard statistical theory had a clearly smaller empirical coverage probability as compared to the nominal probability. Furthermore the asymptotic standard deviation of the additive, dominance and epistatic effects did not reflect the empirical standard deviations of the estimates very well, when the relative QTL variance was smaller/equal to 0.5. The implications of the above findings are discussed.
Databáze: OpenAIRE
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