Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties

Abstract

Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (n = 129) and Retinto (n = 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (q < 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.

Impact of SNP calling quality on the detection of transmission ratio distortion in goats

“…In strong contrast, allele frequencies of mothers and offspring were highly correlated in the Group 2 of SNPs (r = 0.8656, P -value = 0.0005). This result implies that the method implemented by Casellas et al (2014) and subsequently modified by Vázquez-Gómez et al (2020) works very well in reconstructing allele frequencies in parental individuals without genotypes when SNPs have high GenTrain scores (> 0.80 in our study), which are the vast majority (Fig. 1c).…”

“…In contrast, eleven SNPs have GenTrain scores above such threshold, with an average value of 0.87 ± 0.04 ( Group 2 ). For each of these two groups of SNPs, we have calculated the correlation between allele frequencies of the SNP in the offspring vs allele frequencies inferred for the ungenotyped dams with the methods reported by Vázquez-Gómez et al (2020). In principle, allele frequencies of parents and their offspring should be significantly and positively correlated.…”

“…To estimate TRD, we used a frequentist modification (Vázquez-Gómez et al, 2020) of the Bayesian method implemented by Casellas et al (2014). Assuming two alleles (A1 and A2) and the existence of genotyped heterozygous sires and of ungenotyped dams, this method allows to compute for every marker an α-value which ranges between −0.5 (the A1 allele is not transmitted) and 0.5 (the A2 allele is not transmitted) thus providing an estimate of the magnitude of TRD.…”

“…A few years ago, Casellas et al (2014) implemented a new Bayesian methodology to scan TRD for biallelic markers in diploid organisms. This method was later refined by Vázquez-Gómez et al (2020) to detect TRD even in pedigrees with incomplete trios. This can be achieved by inferring the probability that specific alleles are present in the parent with a missing genotype based on the allele frequencies of the SNP in the overall population.…”

“…The accuracy of such inference might be substantially affected by the quality of SNP genotypes. In previous studies (Abdalla et al, 2020; Casellas et al, 2017, 2020 Gòdia et al, 2020; Lahoucine et al, 2020; Vázquez-Gómez et al, 2020), the filtering of SNPs used in TRD scans relied fundamentally on two parameters (genotype call rate and minimum allele frequency or MAF). Deviation from HWE has never been used for this purpose because SNPs showing TRD are expected to display significant departures from HWE.…”