Reconstruction of genome ancestry blocks in multiparental populations

Chaozhi Zheng*, M.P. Boer, F.A. van Eeuwijk

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

Abstract

We present a general hidden Markov model framework called reconstructing ancestry blocks 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.

Original languageEnglish
Pages (from-to)1073-1087
JournalGenetics
Volume200
Issue number4
DOIs
Publication statusPublished - 2015

Keywords

  • Collaborative cross (CC)
  • Diversity outcross (DO)
  • Haplotype reconstruction
  • Hidden Markov model
  • MPP
  • Multiparent advanced generation inter-cross (MAGIC)
  • Multiparental populations

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