title: Reconstruction of Genome Ancestry Blocks in Multiparental Populations.
abstract: We present a general hidden Markov model framework called R: econstructing A: ncestry B: locks BIT: by bit (RABBIT) for reconstructing genome ancestry blocks from single-nucleotide polymorphism (SNP) array data, a required step for quantitative trait locus (QTL) mapping. The framework can be applied to a wide range of mapping populations such as the Arabidopsis multiparent advanced generation intercross (MAGIC), the mouse Collaborative Cross (CC), and the diversity outcross (DO) for both autosomes and X chromosomes if they exist. The model underlying RABBIT accounts for the joint pattern of recombination breakpoints between two homologous chromosomes and missing data and allelic typing errors in the genotype data of both sampled individuals and founders. Studies on simulated data of the MAGIC and the CC and real data of the MAGIC, the DO, and the CC demonstrate that RABBIT is more robust and accurate in reconstructing recombination bin maps than some commonly used methods.
authors.affiliation: Biometris, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands chaozhi.zheng@wur.nl.
authors.forename: Chaozhi
authors.initials: C
authors.lastname: Zheng
authors.affiliation: Biometris, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands.
authors.forename: Martin P
authors.initials: MP
authors.lastname: Boer
authors.affiliation: Biometris, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands.
authors.forename: Fred A
authors.initials: FA
authors.lastname: van Eeuwijk
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping; D023281:Genomics / Q000379:methods*; D008390:Markov Chains; D051379:Mice; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D012984:Software
keywords: Collaborative Cross (CC); Multiparent Advanced Generation Inter-Cross (MAGIC); diversity outcross (DO); haplotype reconstruction; hidden Markov model; multiparental populations; MPP