How will CWD Resistance Breeding impact genetic variation in semi-domesticated reindeer herds?

The first European case of Chronic wasting disease (CWD) was confirmed in a wild reindeer (Rangifer tarandus tarandus) in Norway in 2016. Since then, 20 more cases have been reported in wild reindeer. The potential expansion of CWD in wild reindeer populations and transmission into semi-domesticated reindeer herds is a major concern.

Specific genetic variants in the prion protein gene (PRNP) reduce an individual’s CWD susceptibility and selectively breeding for resistance may enhance herd resilience. This study aims to investigate the potential of breeding for CWD resistance in semi-domesticated reindeer herds.

Since selection for resistance may reduce overall genetic variation, a critical first step is to evaluate the existing genetic diversity within and across herds. To address this, a high-quality reference genome for reindeer was assembled using whole-genome sequencing data generated with Oxford Nanopore technology. To explore population-level variation, 177 semi-domesticated reindeer representing five different herds were whole-genome sequenced using Illumina short-read technology. These sequences were aligned to a novel reindeer genome and compared to identify small genetic variants.

Our analysis identified approximately 16 million short variants (SNPs and indels). A multidimensional scaling plot revealed clear population structure, with all five reindeer herds showing significant clustering. However, fixation index analysis showed low genetic differentiation (<1%), indicating underlying high genetic similarity.

This study represents a significant first step in mapping genetic variation and evaluating how selective breeding for CWD resistance might impact genetic diversity and other traits in Norwegian semi-domesticated reindeer.