Detection of Parental Reciprocal Translocations via Inter-Chromosomal Linkage Disequilibrium in Offspring Genotypes

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. Live-born offspring of RT-carriers have an approximately 50% chance of inheriting a balanced translocation, increasing the linkage disequilibrium (LD) between the affected chromosomes. In this study, we explored the potential for detecting RTs in pigs by identifying abnormal LD patterns in offspring populations. We performed extensive LD analyses on progeny groups from seven RT-positive boars and compared the results to a reference dataset comprising 1000 RT-negative boars. Additionally, we evaluated the impact of RTs on fertility using phenotypes from 15 RT-positive boars. 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%. 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, this 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.