Trilocus disequilibrium analysis of multiallelic markers in outcrossing populations.
Multiallelic markers, such as microsatellites, provide a powerful tool for studying the genetic structure and organization of an outcrossing population. However, statistical methods of analyzing multiallelic markers in current literature are limited in scope due to the complexity of the multiple alleles. We present a closed-form EM algorithm framework to estimate trigenic linkage disequilibria coefficients of three multiallelic markers and present joint and separate statistical hypothesis tests of different linkage disequilibria. Linkage disequilibria analysis with three multiallelic markers is shown to be considerably more powerful than a two marker analysis or a three marker analysis that treats the multiallelic markers as biallelic markers. A three multiallelic marker model was used to analyze marker data from Lycoris longituba, a tulip-like ornamental plant in China, where each marker consisted of two to four distinct alleles. This algorithm will be useful for studying the pattern of genetic variation for outcrossing populations.
Berg
Arthur
A
Pennsylvania State University and Beijing Forestry University. berg@psu.edu
He
Qiuling
Q
Shen
Ye
Y
Chen
Ying
Y
Huang
Minren
M
Wu
Rongling
R
D000465:Algorithms; D000483:Alleles; D056808:Biostatistics; D003198:Computer Simulation; D003433:Crosses, Genetic; D005819:Genetic Markers; D005828:Genetics, Population / Q000706:statistics & numerical data; D015810:Linkage Disequilibrium; D031426:Lycoris / Q000235:genetics; D018895:Microsatellite Repeats; D008957:Models, Genetic; D015233:Models, Statistical
D005819:Genetic Markers