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

Abstract

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 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 (Ne) and inbreeding) of domestic populations (livestock and equine) in the United Kingdom and Ireland; (2) compare number of populations on the United Kingdoms Rare Breeds Survival Trust watch list and the number of United Kingdom and Irish populations in the peer-reviewed literature with inbreeding, genetic diversity and/or Ne estimates; and (3) compare annually reported (census-based) estimates of Ne with (inbreeding- and DNA-based) estimates from peer-reviewed literature. We found a total of 37 publications with Ne 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 Ne estimates were, on average, higher than DNA-based estimates, likely due to violated assumptions when estimating Ne 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 polymorphisms (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. ImplicationsMaintaining genetic diversity in livestock helps safeguard against future challenges to our food production systems. We surveyed publicly available measures of genetic diversity for farm animal populations in the United Kingdom (including government, Rare Breeds Survival Trust, and peer-reviewed scientific publications) to identify any gaps. We found census-based estimates of genetic diversity, which are used to inform and prioritise resources for conservation efforts, on average, are likely overestimating available genetic diversity. Additionally, most farm animal breeds had only these census-based estimates. Genetic diversity estimates could be improved using pedigree or DNA information, more accurately identifying endangered breeds.