Simultaneous estimation of genetic linkage and preferential pairing factor for a triploid population with unphased markers  

作　　者：WANG JianXin DONG XiaoLi PANG XiaoMing LV YaFei YI HuaLin YANG XiaoXia WANG Zhong WU Song WU RongLing 

机构地区：[1]School of Information, Beijing Forestry University, Beijing 100083, China [2]Center for Computational Biology, Beijing Forestry University, Beijing 100083, China [3]National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China [4]Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China [5]The National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China [6]Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA [7]Department of Applied Mathematics ＆ Statistics, State University of New York, Stony Brook, NY 11794, USA

出　　处：《Chinese Science Bulletin》2012年第21期2711-2720,共10页

基　　金：supported by Fundamental Research Funds for the Central Universities(YX2011-30,YX2010-30,BLYX200924and JD2010-5);Special Fund for Forestry-Scientific Research in the Public Interest(201004017);National Natural Science Foundation of China(61170268);China Agricultural Research System-CARS;NSF/IOS-0923975;Changjiang Scholars Award;"Thousand-person Plan"Award

摘　　要：Triploids,recognized to occur more frequently in natural and experimental populations of many species than previously appreciated,display important economic and biological values.Despite this,however,linkage analysis for triploids has not been well explored.We develop a statistical model for estimating and testing the linkage between molecular markers in a triploid population derived from a tetraploid and diploid parent.The model incorporates one important meiotic feature of tetraploids by which more homologous chromosomes pair with a greater likelihood than less homologous chromosomes.By implementing the EM algorithm within the maximum likelihood framework,the model provides a procedure for simultaneous estimation of the linkage and preferential pairing factor.The model accommodates the segregating patterns of pseudotest markers and intercross markers with different amounts of informativeness.The utility of the model was validated through a real data analysis and simulation studies.The model provides a statistical tool for linkage analysis in a triploid population by taking into account meiotic behavior of tetraploids.Results from the model will help to shed light on the genetic diversity and origin of a polyploid population.Triploids,recognized to occur more frequently in natural and experimental populations of many species than previously appreciated,display important economic and biological values.Despite this,however,linkage analysis for triploids has not been well explored.We develop a statistical model for estimating and testing the linkage between molecular markers in a triploid population derived from a tetraploid and diploid parent.The model incorporates one important meiotic feature of tetraploids by which more homologous chromosomes pair with a greater likelihood than less homologous chromosomes.By implementing the EM algorithm within the maximum likelihood framework,the model provides a procedure for simultaneous estimation of the linkage and preferential pairing factor.The model accommodates the segregating patterns of pseudotest markers and intercross markers with different amounts of informativeness.The utility of the model was validated through a real data analysis and simulation studies.The model provides a statistical tool for linkage analysis in a triploid population by taking into account meiotic behavior of tetraploids.Results from the model will help to shed light on the genetic diversity and origin of a polyploid population.

关 键 词：分子标记 同时估计 三倍体 人口 遗传连锁 配对 减数分裂行为 模型估算 

分 类 号：Q343[生物学—遗传学]