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.
Highlights
Transmission ratio distortion (TRD) occurs when two alleles at a heterozygous locus are not transmitted to the offspring, disrupting Mendelian segregation (0.5 probabilities of transmission; [1,2,3])
These missing genotypes in the parental generation can become a major problem using previous methods that need known expected frequencies in the last generation or offspring genotypes anticipated by the experimental cross itself [24,25]
There are more negative TRD values, meaning there is an increase in the transmission of the minor allele
Summary
Transmission ratio distortion (TRD) occurs when two alleles at a heterozygous locus are not transmitted to the offspring, disrupting Mendelian segregation (0.5 probabilities of transmission; [1,2,3]). Different biological mechanisms can cause TRD before or after fertilization [12,13,14,15,16]. There are different mechanisms in sires and dams prior to fertilization. The meiotic drive is restricted to female gametes (asymmetry meiosis), whereas male gametes (symmetric meiosis) have gamete competition [13,17]. In this way, some causes of TRD could not be studied depending on the parents’ data available
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