An investigation into the critically endangered Cleveland Bay horse reveals a worrying loss of diversity and high levels of relatedness and inbreeding in the surviving stock.
The Cleveland Bay horse is one of the oldest equines in Britain, with pedigree data going back almost 300 years.
It is a heritage British breed which has its origins in the Cleveland Hills of northern England.
Over the years the breed has been used extensively as both a workhorse and a riding horse, and has been crossed with other breeds to produce carriage horses.
The first studbook was published in 1885, containing retrospective pedigrees of animals dating back to 1732, providing a closed non-Thoroughbred studbook covering more than 38 generations.
The studbook is essentially closed.
It one of five horse breeds listed as critical by the UK Rare Breeds Survival Trust in its annual watchlist, meaning there are fewer than 300 registered adult breeding females.
Researchers Andrew Dell, Mark Curry, Kelly Yarnell, Gareth Starbuck and Philippe Wilson worked with both genealogical and molecular data in their study to assess founder representation, lineage, and genetic diversity.
The Cleveland Bay Horse Society provided the study team with access to 535 microsatellite parentage testing reports. Using the studbook data, census records and the genetic information within the microsatellite parentage testing reports, they identified a reference population of 402 Cleveland Bay horses.
Their work on the available data for the reference population determined that 91% of the stallion lines and 48% of the dam lines had been lost within the breed.
Just three ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from three founder females. All paternal lineages trace back to a single founder stallion.
The findings reveal a substantial loss of genetic diversity and high levels of relatedness and inbreeding, mostly in the last century, they said.
“The results of this study highlight the importance of the Cleveland Bay Horse community implementing an effective and sustainable breed management plan,” they said.
Average inbreeding for the Cleveland Bay Horse within the reference population was calculated at 20.64%, which is substantially higher than most of the values reported in the literature for other breeds, which typically range from 6.5% to 12.5%.
However, most of these inbreeding values have been computed in breeds with deep pedigrees such as Andalusian, Lipizzana or Thoroughbred horses.
“There are significant differences in population sizes, and the accumulation of inbreeding in populations of restricted size will occur at a greater rate,” they said.
Discussing their findings, the researchers said there has been considerable debate about the most effective methods of conserving and managing endangered populations.
Before the era of DNA analysis, the accepted strategy involved minimizing inbreeding, whilst managing mean kinship and average relatedness.
The use of molecular methods has been proposed. However, where pedigree data is robust and complete over a significant number of generations, it appears that genealogical data remains the preferred method by which to manage founder contributions, inbreeding and relatedness.
Members of the study team are variously affiliated with Lincoln University, Nottingham Trent University and the Rare Breeds Survival Trust.
Dell A, Curry M, Yarnell K, Starbuck G, Wilson PB (2020) Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data. PLoS ONE 15(10): e0240410. https://doi.org/10.1371/journal.pone.0240410