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

Abstract

Transmission ratio distortion (TRD) is the departure from the expected Mendelian ratio in offspring, a poorly investigated biological phenomenon in livestock species. Given the current availability of specific parametric methods for the analysis of segregation data, this study focused on the screening of TRD in 602 402 single nucleotide polymorphisms covering all autosomal chromosomes in seven Spanish beef cattle breeds. On average, 0.13% (n = 786) and 0.01% (n = 29) of genetic markers evidenced sire- or dam-specific TRD respectively. There were no single nucleotide polymorphisms accounting for both sire- and dam-specific TRD at the same time, and only one marker (rs43147474) accounted for (sire-specific) TRD in all seven breeds. It must be noted that rs43147474 is located in the fourth intronic region of the GTP-binding protein 10 gene, and this locus has been previously linked to the maintenance of mitochondria and nucleolar architectures. Alternatively, other candidate genes surround this hot-spot for sire-specific TRD in the cattle genome, and they are related to embryonic and postnatal lethality as well as prostate cancer, among others. This research characterized the distribution of TRD in the bovine genome, highlighting heterogeneous results when comparing across breeds.

Implementation of Bayesian methods to identify SNP and haplotype regions with transmission ratio distortion across the whole genome: TRDscan v.1.0

“…It is important to note that some biological mechanisms causing TRD can be limited to one of the parental sexes. Sex-dependent TRD has been previously reported in other studies (e.g., Alcaide et al, 2012;Liu et al, 2013;Didion et al, 2015;Casellas et al, 2017). In addition, 4 SNP were detected with sire-and dam-TRD in the opposite direction of preference of transmission.…”

Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach

“…Following Casellas et al (2014Casellas et al ( , 2017, the probability of allele transmission (p) from heterozygous parents to offspring can be parameterized, including TRD effects on allelic basis, as:…”

Discriminating between allele‐ and genotype‐specific transmission ratio distortion

“…Nevertheless, these approaches mask the genetic mechanism involved in TRD departure; they merge additive and dominant genetic effects without discriminating between the sources of genetic variation. The TRD-specific analytical approach developed by Casellas et al (2012) provided a new approach to elucidate the genetic mechanisms underlying distortion (Casellas et al 2014(Casellas et al , 2017. These parametrizations rely on a hierarchical structure that accounts for additive and/or dominance sources of TRD rather than simplifying to overall distortion patterns.…”

“…These parametrizations rely on a hierarchical structure that accounts for additive and/or dominance sources of TRD rather than simplifying to overall distortion patterns. Moreover, the methodologies focus on different genetic points of view, relying on a genotype- (Casellas et al 2012) or a single-allele basis (Casellas et al 2014(Casellas et al , 2017. It is important to note that, unlike standard gene association analyses, genotype-and allele-based parametrizations are not equivalent approaches under TRD analyses and they may provide different results.…”