Review: Assessing available genetic diversity estimates of rare breeds of livestock

The United Kingdom is home to many local and rare livestock breeds. The local breed populations are highly adapted to specific environments in the United Kingdom, and these and other rare breeds provide solutions to niche needs. Rare breeds often contribute more than expected to overall species genetic diversity, which is important because genetic variation is needed for adapting to new challenges. It is therefore very important from both the United Kingdom and global perspectives to maintain genetic diversity of rare livestock breeds in the United Kingdom, and to do this, we need to evaluate the monitoring of genetic diversity to identify gaps in our knowledge and prioritise resources reserved for conservation purposes. The objectives of this study were to survey the literature to: (1) summarise genetic/genomic characterisation (effective population size (N_e) and inbreeding) of domestic populations (livestock and equine) in the United Kingdom and Ireland; (2) compare number of populations on the United Kingdom's Rare Breeds Survival Trust watchlist and the number of United Kingdom and Irish populations in the peer-reviewed literature with inbreeding, genetic diversity and/or N_e estimates; and (3) compare annually reported (census-based) estimates of N_e with (inbreeding- and DNA-based) estimates from peer-reviewed literature. We found a total of 37 publications with N_e or inbreeding estimates for United Kingdom or Ireland livestock populations, published from 1975 to 2024. While many (42%) of the breeds on the Rare Breeds Survival Trust watchlist have been included in publications, there are still many breeds, and a few species (turkey, duck and geese) with no publicly available pedigree- or DNA-based genetic diversity measures. We found census-based N_e estimates were, on average, higher than DNA-based estimates, likely due to violated assumptions when estimating N_e with census-based data because of the way livestock mating systems are designed. Most peer-reviewed papers estimated genetic diversity measures using pedigree, microsatellite markers, or single-nucleotide polymorphism (SNP) markers. To identify breed-unique variants responsible for adaptive traits in rare breeds, more studies using whole-genome sequencing will be needed. Altogether, we have summarised genetic diversity estimates of United Kingdom livestock populations, identifying gaps in knowledge.