title: Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids.
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.
authors.affiliation: Biometris, Wageningen University and Research Centre, 6708 PB Wageningen, Netherlands chaozhi.zheng@wur.nl.
authors.forename: Chaozhi
authors.initials: C
authors.lastname: Zheng
authors.affiliation: Plant Breeding, Wageningen University and Research Centre, 6708 PB Wageningen, Netherlands.
authors.forename: Roeland E
authors.initials: RE
authors.lastname: Voorrips
authors.affiliation: Biometris, Wageningen University and Research Centre, 6708 PB Wageningen, Netherlands.
authors.forename: Johannes
authors.initials: J
authors.lastname: Jansen
authors.affiliation: Biomathematics and Statistics Scotland, Dundee DD2 5DA, Scotland.
authors.forename: Christine A
authors.initials: CA
authors.lastname: Hackett
authors.affiliation: Forage Genetics International, Inc., Davis, California 95618-0505.
authors.forename: Julie
authors.initials: J
authors.lastname: Ho
authors.affiliation: Biometris, Wageningen University and Research Centre, 6708 PB Wageningen, Netherlands.
authors.forename: Marco C A M
authors.initials: MC
authors.lastname: Bink
mesh_terms: D000465:Algorithms; D023902:Chromosome Pairing; D003198:Computer Simulation; D003433:Crosses, Genetic; D019143:Evolution, Molecular; D018628:Gene Dosage; D008040:Genetic Linkage; D006239:Haplotypes; D008957:Models, Genetic; D011336:Probability; D040641:Quantitative Trait Loci; D011198:Solanum tuberosum / Q000235:genetics; D057891:Tetraploidy; D015053:Zygote
keywords: ancestral inference; double reduction; outbred population; polyploidy; preferential pairing