= Expected average number of meioses separating two individuals
calculate r e = min(0.5, power(r,1/M f ))
construct correlation matrix, M , with element
M (k,k) = 1.0
M (k,l) = (1.0 - 2*r e )
unlinked markers: matix M is diagonal
calculate w = ( 1 T M -1 ),
effective number of loci = sum( w )
unlinked markers: vector w is unity => sum( w ) = N loci
10.
WP-C II Account for genetic linkage maps Unlinked markers Loosely linked markers closely linked markers W = 1.0 W = 1.0 W = 0.5 W = 0.7 W = 0.2 W = 0.3 M eff = 5.0 M eff = 2.9 M eff = 1.2 Example!
This leads to the detection of a small region containing the disease gene.
Key-paper: Meuwissen & Goddard (2000) Genetics 155 :421-430 Linkage disequilibrium mapping successful in mapping genetic disorders: = Identify a chromosomal region that is identical by descent ( IBD ) among diseased individuals ( region may contain disease gene ) The IBD region is detected by closely linked marker loci that carry identical alleles at this region in the diseased individuals. Size of IBD region decreases with the number of meioses since the disease mutation occurred and may be small.
effective population size for many discrete generations
phenotypes available for last generation of individuals
Fully inbred individuals (selfed by single seed descent)
(1) Expected correlation matrix among marker haplotypes
Whether two marker haplotypes have identical alleles in a region depends on the position of the QTL . Hence, the covariance between haplotype effects depends on the position of the QTL .
Objective was to find important patterns within the germplasm data set, which are not apparent from visual analysis and to compare and contrast these patterns with those found from the classical statistical analyses
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