Distinct linkage disequilibrium (LD) runs of single nucleotide polymorphisms and microsatellite markers; implications for use of mixed marker haplotypes in LD-based mapping.
It has been suggested that the haplotypic relationship between microsatellite markers and single nucleotide polymorphisms (SNPs) is of considerable importance, as microsatellite markers can potentially be incorporated into haplotypes containing SNPs to increase marker density across a region of interest. However, SNPs and microsatellite markers have different mutation rates and durations, and it is conceivable that the linkage disequilibrium (LD) patterns between the genetic markers may considerably differ. We assessed the LD patterns using 1,661 SNPs and 65 microsatellite markers along chromosome 22 and investigated whether common patterns of LD between the two genetic markers are deduced from the results. The results demonstrated that the patterns of LD among microsatellite markers varied considerably and the LD runs of SNPs and microsatellite markers showed distinct patterns. Microsatellite markers have a much higher mutation rate and the evolution of microsatellite markers is a more complex process which has distinct mutation properties from those of SNPs. We consider that these might contribute to the different LD patterns between the two genetic markers. Therefore, it would seem inadvisable to make assumptions about persistence of LD across even a relatively small genetic distance among microsatellite markers and to construct mixed marker haplotypes/LD maps employing microsatellite markers.
Lee
Kyung-A
KA
Department of Laboratory Medicine, College of Medicine, Hallym University, Chunchon, Korea.
Sohn
Kwang-Min
KM
Cho
Seung-Hee
SH
Hwang
Hyokkee
H
Kim
Sun Woo
SW
Won
Hong-Hee
HH
Kim
Hee-Jin
HJ
Kim
Min Ji
MJ
Cho
Sang Sun
SS
Park
Jun Hee
JH
Kim
Jong-Won
JW
D000465:Algorithms; D002874:Chromosome Mapping; D002892:Chromosomes, Human, Pair 22; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D007055:Iceland; D007723:Korea; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats / Q000235:genetics*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D006113:United Kingdom