By Kelvin Kelles
Inbreeding, defined as mating between closely related animals, can accelerate genetic progress but also poses significant risks, such as the reduction of genetic diversity. One way to better manage inbreeding in pig breeding programs is to analyze the level of runs of homozygosity (ROH). ROH are continuous stretches of DNA where genetic markers are identical on both chromosomes, indicating inherited segments from common ancestors.
However, the parameters used to identify and calculate ROH are not yet standardized. We studied over 600,000 pigs from seven lines, using two types of genetic panels: one with 50k markers and another with 660k. We tested different settings to see how they affect the reliability of ROH detection.
Allowing for heterozygous genetic markers within the ROH DNA stretches is quite common, but we found that excluding heterozygous markers completely improved the accuracy of the results. In general, using more consecutive markers to define a ROH increased reliability but reduced the total number of runs found. In the 50k panel, the best results were observed with 30 to 60 consecutive markers, while in the 660k panel, similar settings performed well, with slight improvements when allowing up to 100 markers. In this study, we found that the high-density SNP panels proved important for more accurate monitoring of inbreeding. The method worked consistently across all pig lines.
This study emphasizes the need to tailor ROH detection parameters based on the data type to improve reliability. The approach developed here establishes optimal standards for identifying ROH, enabling breeding programs to accurately track inbreeding and prevent the loss of genetic diversity, as well as problems like inbreeding depression.
