Modeling segregation distortion for viability selection I. Reconstruction of linkage maps with distorted markers |
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Authors: | Chengsong Zhu Chunming Wang Yuan-Ming Zhang |
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Institution: | (1) Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People’s Republic of China;(2) Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore |
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Abstract: | Molecular markers have been widely used to map quantitative trait loci (QTL). The QTL mapping partly relies on accurate linkage
maps. The non-Mendelian segregation of markers, which affects not only the estimation of genetic distance between two markers
but also the order of markers on a same linkage group, is usually observed in QTL analysis. However, these distorted markers
are often ignored in the real data analysis of QTL mapping so that some important information may be lost. In this paper,
we developed a multipoint approach via Hidden Markov chain model to reconstruct the linkage maps given a specified gene order
while simultaneously making use of distorted, dominant and missing markers in an F2 population. The new method was compared with the methods in the MapManager and Mapmaker programs, respectively, and verified
by a series of Monte Carlo simulation experiments along with a working example. Results showed that the adjusted linkage maps
can be used for further QTL or segregation distortion locus (SDL) analysis unless there are strong evidences to prove that
all markers show normal Mendelian segregation. |
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Keywords: | EM algorithm Genetic linkage map Hidden Markov chain Segregation distortion Viability selection |
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