Abstract
The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. 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. 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. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. 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. 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. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation 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.
Highlights
In recent years there has been substantial interest in quantifying the genetic diversity of equine breeds using pedigree [1], molecular data [2] or a combination of both sources [3] in order to implement effective breed management strategies
The aim of this study was to develop a comparative analysis of the genetic diversity in the Cleveland Bay Horse population using both genealogical and molecular methods and provide recommendations in order to support a global breed conservation strategy for the Cleveland Bay Horse, whilst sequentially detailing the theory and practice inherent in our approach leading to its applicability in the conservation of endangered breeds and species in vivo
The reference population of 402 individual animals consisted of 193 male and 209 females for which microsatellite data as well as pedigree data was available
Summary
In recent years there has been substantial interest in quantifying the genetic diversity of equine breeds using pedigree [1], molecular data [2] or a combination of both sources [3] in order to implement effective breed management strategies. 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. Population genetics of the Cleveland Bay Horse 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. 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 [5], whilst providing an important and potentially wideranging tool for wider conservation practices both in situ and ex situ in vivo
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