Detection of parental reciprocal translocations via inter-chromosomal linkage disequilibrium in offspring genotype

Reciprocal translocations (RTs) are among the most common structural chromosomal abnormalities observed in both humans and livestock, characterized by the exchange of DNA segments between two non-homologous chromosomes and associated with reduced fertility in carriers. In pigs, this is most commonly observed as a reduction in litter size. 

RTs and other chromosomal abnormalities can be identified by cytogenetic testing – for example through karyotyping and fluorescence in situ hybridization – but these tests are costly and labor-intensive. This motivated the search for alternative, more cost-effective methods, such as the detection of RTs by short-read sequencing. Another recent study successfully detected RTs in cattle using genotype data of offspring to find abnormal linkage disequilibrium (LD) patterns. The researchers from WUR-ABG decided to build on this idea and investigated whether RTs produce similar, significant effects on inter-chromosomal LD patterns in pig populations.

“We performed extensive LD analyses on progeny groups from seven RT-positive boars and compared the results to a reference dataset of 1,000 RT-negative boars,” Anne Boshove, first author of the study, explains. Our findings demonstrate that RTs can be reliably detected when genotype data from at least 30 offspring are available, with a false positive rate of 0.1%.” In addition, fertility analysis revealed that RT-carriers have significantly reduced litter sizes, on average 35% lower than their respective breed averages, emphasizing the relevance of RT identification in breeding programs. 

Overall, the study confirms that LD patterns offer a practical and cost-efficient method for RT-screening in pigs without the use of cytogenetic testing, provided offspring genotype data is available. Anne: “While cytogenetic testing remains the gold standard for RT identification, it is costly. This method provides a practical and cost-effective screening tool that can be applied to large populations using existing genotype data. By preventing the unintentional use of RT carriers, known to have reduced fertility and cause reproductive losses, this approach can help minimize economic losses and improve reproductive efficiency in pig breeding.”

This study was financially supported by the Dutch Ministry of Economic Affairs (TKI Agri & Food project LWV20054) and the Breed4Food partners Cobb Europe, CRV, Hendrix Genetics, and Topigs Norsvin.