Gene retrocopies are commonly found in mammalian genomes where they are typically presumed to be nonfunctional pseudogenes. However, active LINE-1 is capable of inserting new gene retrocopies, which can be functional via direct expression or through altering the expression patterns of nearby genes at the insertion site. Challenging their designation as pseudogenes, recent studies have implicated retrocopies in cancer and other disorders. Presented here is an in investigation into the recent, polymorphic retrocopies in canids. First, the effects of two canine FGF4 retrocopies were investigated. While two separate FGF4 retrocopies are both associated with two distinct forms of disproportionate dwarfism, the FGF4 retrocopy on CFA12 alone was shown to be associated with calcification of the intervertebral disc and increased susceptibility to intervertebral disc disease, a phenotype known as chondrodystrophy. While multiple additional FGF4 retrocopy insertions located elsewhere in the genome have been discovered in canids with unknown phenotypic associations, the complete landscape of retrocopies in the species was unclear. Thus, a method for the identification of recent, polymorphic retrocopies from whole genome sequencing data was developed and applied to canids. A large number of gene retrocopies insertions were identified, showing that gene retrotransposition events are a common occurrence in the canid genome and not unique to the FGF4 gene. Target-site duplications, which are a characteristic of LINE-1 mediated retrotransposition, were identified at the insertion sites of the retrocopies, conforming they were a consequence of LINE-1 activity. In addition to the expressed and functional FGF4 retrocopies, many other canine retrocopies were also shown to be expressed and under selection, alluding towards possible functions. A polymorphic SNN retrocopy associated with red coat color in Poodles was identified and characterized, where it was shown to alter the expression pattern of a nearby gene, GPR22. Lastly, after the identification of numerous polymorphic canine retrocopies, a similar analysis using the same methodology was performed in equine genomes for comparison. Equids have fewer gene retrocopy insertions on average then canids, indicating that LINE-1 is more active within canids. These findings highlight the contribution of LINE-1 mediated retrotransposition events to the genomic and phenotypic diversity of dogs.
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