Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids

Chaozhi Zheng, R.E. Voorrips, J. Jansen, C.A. Hackett, J. Ho, M.C.A.M. Bink

Research output: Contribution to journalArticleAcademicpeer-review

25 Citations (Scopus)

Abstract

For both plant (e.g., potato) and animal (e.g., salmon) species, unveiling the genetic architecture of complex traits is key to
the genetic improvement of polyploids in agriculture. F1 progenies of a biparental cross are often used for quantitative trait loci (QTL)
mapping in outcrossing polyploids, where haplotype reconstruction by identifying the parental origins of marker alleles is necessary. In
this paper, we build a novel and integrated statistical framework for multilocus haplotype reconstruction in a full-sib tetraploid family
from biallelic marker dosage data collected from single-nucleotide polymorphism (SNP) arrays or next-generation sequencing technology
given a genetic linkage map. Compared to diploids, in tetraploids, additional complexity needs to be addressed, including double
reduction and possible preferential pairing of chromosomes. We divide haplotype reconstruction into two stages: parental linkage phasing for reconstructing the most probable parental haplotypes and ancestral inference for probabilistically reconstructing the offspring haplotypes conditional on the reconstructed parental haplotypes. The simulation studies and the application to real data from potato show that the parental linkage phasing is robust to, and that the subsequent ancestral inference is accurate for, complex chromosome pairing behaviors during meiosis, various marker segregation types, erroneous genetic maps except for long-range disturbances of marker ordering, various amounts of offspring dosage errors (up to 20%), and various fractions of missing data in parents and offspring dosages
Original languageEnglish
Pages (from-to)119-131
JournalGenetics
Volume203
Issue number1
DOIs
Publication statusPublished - 2016

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