Reciprocal Chromosome Translocations in the Domestic Pig, the Prevalence, Genetic and Genomic Factors Associated with Breakpoint Formation

Abstract

Chromosome rearrangements such as reciprocal translocations are prevalent in the domestic pig, estimated to occur in 1/200 live births, and are suspected to be the reason behind 50% of cases of hypoprolificacy. Despite there being over 200 chromosome rearrangements found in the pig, little is known about why rearrangements form in the pig genome. In order to better understand chromosome rearrangements, their breakpoints, and factors influencing their formation a routine cytogenetic screening program was created to identify carriers in Canadian swine herds. Using data from this project and others a comprehensive analysis of rearrangement breakpoints was conducted, and a GWAS and CNV analysis was performed using DNA samples from identified carrier boars. Routine cytogenetic screening of 6491 boars revealed 101 carriers of chromosome rearrangements, with a prevalence of 1.56%. Comprehensive analysis of rearrangement breakpoints in pigs revealed a non-random distribution with hotspots for rearrangement sharing a set of architectural features including a euchromatic composition, as well as higher densities of genes, simple repeats, and tRNA. A GWAS and CNV analysis of carrier boars and their parents revealed five SNP associations, four CNVR and eleven nearby genes each of which played roles in genomic stability or DNA repair. The results of this study show the high prevalence of rearrangements in pigs, as well as the effectiveness of screening efforts. In addition, genomic architectural features along with genetic and genomic variants in the pig genome may be proposed to influence chromosome breakage and promote rearrangement.