title: Linkage group correction using epistatic distorted markers in F2 and backcross populations.
abstract: Epistasis has been frequently observed in all types of mapping populations. However, relatively little is known about the effect of epistatic distorted markers on linkage group construction. In this study, a new approach was proposed to correct the recombination fraction between epistatic distorted markers in backcross and F2 populations under the framework of fitness and liability models. The information for three or four markers flanking with an epistatic segregation distortion locus was used to estimate the recombination fraction by the maximum likelihood method, implemented via an expectation-maximisation algorithm. A set of Monte Carlo simulation experiments along with a real data analysis in rice was performed to validate the new method. The results showed that the estimates from the new method are unbiased. In addition, five statistical properties for the new method in a backcross were summarised and confirmed by theoretical, simulated and real data analyses.
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/Collaborative Innovation Center for Modern Crop Production, Department of Crop Genetics and Breeding, College of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: S-Q
authors.initials: SQ
authors.lastname: Xie
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/Collaborative Innovation Center for Modern Crop Production, Department of Crop Genetics and Breeding, College of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: J-Y
authors.initials: JY
authors.lastname: Feng
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/Collaborative Innovation Center for Modern Crop Production, Department of Crop Genetics and Breeding, College of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Y-M
authors.identifier: 0000000323172190
authors.initials: YM
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D003198:Computer Simulation; D003433:Crosses, Genetic; D004843:Epistasis, Genetic; D005787:Gene Frequency; D056084:Genetic Fitness; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D008957:Models, Genetic; D009010:Monte Carlo Method; D012275:Oryza / Q000235:genetics*; D015203:Reproducibility of Results; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers