By Martijn Derks
Within pig genetics and genome research, we usually rely on a reference genome which we compare to the variations within our breeding lines. However, using a single reference genome has its limitations. Unique genetic variations that are specific to our breeding lines but absent in the reference genome may go unnoticed. The development of line-specific reference genomes addresses this issue, enabling a precise mapping of sequences that are absent in the original reference genome. At Topigs Norsvin, we have produced line-specific reference genomes for our main breeding lines. Additionally, these technologies make it easier to detect a different type of structural variation which would be challenging using conventional methods.
A notable example of the significance of line-specific reference genomes involves the identification of two deletions associated with lower fertility. With this newfound knowledge, we can now eliminate this variant from our breed, enhancing the overall reproductive success.
The use of these new reference genomes enables the identification of novel regions in the DNA that are unique to our breeding lines. This discovery has provided us with a wealth of previously unseen genetic variations, allowing for potential selection and further refinement within our breeding programs. The collection of all these Topigs Norsvin reference genomes will result in the creation of a Topigs Norsvin pan-genome. This pan-genome encompasses all the genetic variations within our main breeding lines.
Using novel sequencing techniques, we can open up the complete genome of our breeding lines and specifically assess structural differences between and within our breeding lines. Future research includes the identification of new variations with important traits and, subsequently, these variations will be included in the selection chip to allow for a fast implementation of the results.
