It is reputed to have evolved in the matriline from the now extinct Chapman horse, which early records show were being bred on the monastic estates of the region well before the dissolution of the monasteries in the mid 16th century. The Cleveland Bay is a warm-blooded equine a product of a cross of hot-blooded Oriental / Barb /Turkish or Mediterranean stock on the cold-blooded Northern European heavy draught horse. Unrestricted access to the microsatellite test data, as well as the stud book records provides a rare opportunity to evaluate both methods of assessing genetic diversity within the breed and, in turn, provides comprehensive guidance to breeders in terms of conservation practice for this endangered breed, whilst providing an important and potentially wide-ranging tool for wider conservation practices both in situ and ex situ in vivo. In addition, the breed Society now has a mandatory policy of microsatellite-based parentage testing at the time of registration. The first studbook was published in 1885, and this contains retrospective pedigrees of animals dating back to 1732 providing a closed non-Thoroughbred studbook dating back almost 300 years and for more than 38 generations. The Cleveland Bay horse is a heritage British breed which has its origins in the Cleveland Hills of Northern England. The effectiveness of the use of both data types in the understanding and management of rare and native equine breeds have been investigated using both theoretical modelling, and studies of closed studbooks. In recent years there has been substantial interest in quantifying the genetic diversity of equine breeds using pedigree, molecular data or a combination of both sources in order to implement effective breed management strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed and offer a perspective on implementing this data in considered breed management strategies. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Data from 15 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. The breed is one of five equine breeds listed as “critical” (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years.
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