GENETIC ANALYSIS AND BREED MANAGEMENT
OF THE
ENDANGERED CLEVELAND BAY HORSE

A thesis submitted in partial fulfilment of the requirements of the University of Lincoln for the degree of Doctor of Philosophy

Andrew C. Dell

December 2010

ABSTRACT

The Cleveland Bay Horse is one of the oldest breeds of horse in the United Kingdom, with pedigree data going back almost 300 years. The breed is one of three equines listed as “Critical” by the UK Rare Breeds Survival Trust. The studbook is essentially closed and because of this there are concerns about loss of genetic variation. The reported analysis assesses the genetic diversity in the Cleveland Bay Horse population using both genealogical and molecular methods.
Pedigree analysis shows high levels of inbreeding, which reach 25% when corrected for pedigree completeness. Founder analysis shows 182 founders contributed to the breed, but the number of ancestors explaining 50% of the genome of the living population was 3. Three founder females make up 70% of maternal lineages in the living population whilst all paternal lineages can be traced back to one founder stallion. Effective Population Size (Ne) was at approximately 20 from 1910 to 1960. A 6 year breed management programme to control the rate of accumulation of inbreeding through minimising coancestry and mean kinship has demonstrated some success at increasing effective population size above FAO minimum recommendations.
Data from 16 microsatellite loci from a reference population of 402 horses was assessed for allelic diversity showing mean number of alleles (MNA) = 5.625. Bottleneck analysis suggests that the breed experienced a genetic bottleneck between 75 and 1000 years bp., and that the reduction in population size in the late 1950s was a demographic and not a genetic bottleneck as had previously been believed.
Mitochondrial d-loop sequencing shows limited matrilineal diversity, with only 4 haplotypes being found in the pure-bred population. Haplotype sharing with other breeds suggests that not all Cleveland Bay horses are descended from the now extinct Chapman horse, as was the previous understanding.
This study reveals that high levels of inbreeding, limited effective population size and genetic bottlenecking were already compromising the population at the time of formation of the Cleveland Bay Horse Society in 1884 and continue to be issues that affect and endanger the breed today.