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 F 2 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.

Bayesian analysis of parent-specific transmission ratio distortion in seven Spanish beef cattle breeds

“…germ‐line selection, meiotic drive and gametic competition) or the differential viability of embryos (both before and after implantation), fetuses or even neonates (Casellas et al . ). Within this context, TRD should be considered as a relevant issue with potential outcomes in multiple research fields where its incidence, biological nature and magnitude should be accurately screened across whole genomes.…”

“…; Casellas et al . ). To the best of our knowledge, very little is known about this biological phenomenon in cattle (Murphy et al .…”

“…Sire‐ and dam‐specific TRD phenomena were evaluated across all SNPs by applying the Bayesian approach developed by Casellas et al . (). The parameterization used took advantage of heterozygous parents (i.e.…”

“…; Casellas et al . , ) has opened the gate to new research opportunities for the screening and characterization of TRD across the whole genome of the bovine species. Most of former TRD studies were carried out on standard mating patterns such as backcrosses (Shendure et al .…”

“…Nevertheless, the model developed by Casellas et al . () overcame these limitations and allowed for a more flexible parameterization of TRD by accommodating open pedigrees and all possible genotypes in both parental and offspring generations, without restrictions apart from the mandatory Mendelian inheritance of the alleles. The objective of this research was to screen for TRD across the whole genome of seven Spanish beef cattle breeds, with a special emphasis on the parental origin of TRD.…”