INTER-INDIVIDUAL VARIATION OF DE NOVO ERV TRANSPOSITION RATE IN THE CATTLE GERMLINE

By studying a lethal recessive disease (cholesterol deficiency in Holstein-Friesian cattle breed), we recently discovered a family of endogenous retroviruses (ERV) still active in present-day cattle populations. To study the inter-individual variation of ERV de novo transposition rate (dnTR), we first used a pedigree-based method. As part of a larger project aimed at studying germline de novo mutation rate (Damona project), we generated a dataset of whole-genome sequences for 131 extended trios ((grand-) parents, proband and at least 5 grand-offspring). Here we mined them specifically for germline de novo ERV insertions - defined as insertions (i) detected in the proband, (ii) absent from its parents and (iii) transmitted to the next generation. Five de novo insertions were identified: 1 of maternal origin, 4 paternal, including 3 from the same sire and 2 within the same sperm cell. Thus, the ERV dnTR can be roughly estimated at 1 new insertion every ~50 gametes, yet with major differences between individuals (as 3 from the 5 detected events occurred in the same animal).
To allow us to increase the number of studied gametes, we modified a method (Pooled CRISPR Inverse PCR sequencing: PCIP-seq) initially developed to detect somatic retroviral insertions (Artesi et al, 2020). We optimized it to directly locate and quantify de novo ERV insertional events in the male germline (sperm DNA). We are currently applying it to a large cohort of sires (n > 200). The resulting normalized sire-specific dnTR will be treated as a quantitative molecular phenotype to perform a genome-wide association study in order to pinpoint genomic loci influencing ERV dnTR in the cattle germline. This new quantitative method can easily be adapted to other families of active transposable elements in livestock.