Modeling segregation distortion for viability selection. I. Reconstruction of linkage maps with distorted markers.
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 F(2) 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.
Zhu
Chengsong
C
Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
Wang
Chunming
C
Zhang
Yuan-Ming
YM
D002874:Chromosome Mapping / Q000379:methods; D020090:Chromosome Segregation / Q000235:genetics*; D008040:Genetic Linkage; D005819:Genetic Markers; D008957:Models, Genetic; D012641:Selection, Genetic
D005819:Genetic Markers