title: A flexible bayesian model for testing for transmission ratio distortion.
abstract: Current statistical approaches to investigate the nature and magnitude of transmission ratio distortion (TRD) are scarce and restricted to the most common experimental designs such as F2 populations and backcrosses. In this article, we describe a new Bayesian approach to check TRD within a given biallelic genetic marker in a diploid species, providing a highly flexible framework that can accommodate any kind of population structure. This model relies on the genotype of each offspring and thus integrates all available information from either the parents' genotypes or population-specific allele frequencies and yields TRD estimates that can be corroborated by the calculation of a Bayes factor (BF). This approach has been evaluated on simulated data sets with appealing statistical performance. As a proof of concept, we have also tested TRD in a porcine population with five half-sib families and 352 offspring. All boars and piglets were genotyped with the Porcine SNP60 BeadChip, whereas genotypes from the sows were not available. The SNP-by-SNP screening of the pig genome revealed 84 SNPs with decisive evidences of TRD (BF > 100) after accounting for multiple testing. Many of these regions contained genes related to biological processes (e.g., nucleosome assembly and co-organization, DNA conformation and packaging, and DNA complex assembly) that are critically associated with embryonic viability. The implementation of this method, which overcomes many of the limitations of previous approaches, should contribute to fostering research on TRD in both model and nonmodel organisms.
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain joaquim.casellas@uab.cat.
authors.forename: Joaquim
authors.initials: J
authors.lastname: Casellas
authors.affiliation: Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
authors.forename: Arianna
authors.initials: A
authors.lastname: Manunza
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Mercader
authors.affiliation: IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Quintanilla
authors.affiliation: Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
authors.forename: Marcel
authors.initials: M
authors.lastname: Amills
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D001499:Bayes Theorem; D033481:Chromosomes, Mammalian; D066264:Datasets as Topic; D005787:Gene Frequency; D005819:Genetic Markers; D016678:Genome; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D040582:Inheritance Patterns; D008957:Models, Genetic; D009010:Monte Carlo Method; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D013552:Swine
chemical_list: D005819:Genetic Markers
keywords: Bayes factor; Duroc; genome scan; multinomial distribution; transmission ratio distortion