TY - JOUR
T1 - Trilocus disequilibrium analysis of multiallelic markers in outcrossing populations
AU - Berg, Arthur
AU - He, Qiuling
AU - Shen, Ye
AU - Chen, Ying
AU - Huang, Minren
AU - Wu, Rongling
N1 - Funding Information:
KEYWORDS: EM algorithm, linkage disequilibrium, multiallelic marker, natural population, trigenic disequilibrium Author Notes: The preparation of this manuscript is partially supported by NSF/NIH Mathematical Biology grant (No. 0540745) and the Changjiang Scholars Award at Beijing Forestry University. We also wish give thanks to an anonymous referee who provided several useful suggestions that have considerably improved this manuscript.
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
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U2 - 10.2202/1544-6115.1528
DO - 10.2202/1544-6115.1528
M3 - Article
C2 - 20196751
AN - SCOPUS:77649088986
SN - 1544-6115
VL - 9
JO - Statistical Applications in Genetics and Molecular Biology
JF - Statistical Applications in Genetics and Molecular Biology
IS - 1
M1 - 16
ER -