Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data

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.

16 Years of breed management brings substantial improvement in population genetics of the endangered Cleveland Bay Horse

“…Genetic and demographic analyses reported in previous studies (Dell et al, 2020b;Walling, 1994) suggest that even at the time of formation of the Society in 1884, the genetic resources within the breed were secure. Many founder animals were no longer represented in the then living population, and other lines were lost soon afterward.…”

“…Although the need for management to prevent the continued loss of diversity was highlighted, what was not clear was the manner in which this would deliver a real-world impact to support the genetic resources within the breed. The difficulties being experienced by the Cleveland Bay population as an endangered breed had more in common with those experienced in the field of wildlife and captive animal conservation than livestock breeding because of the limited number of animals of breeding age, the limited number of founders, and the loss of founder representation (Dell et al, 2020b). However, computer systems being used by zoological parks had not proven suitable in the management of equine breeds (Hall, 2004).…”

“…management programs to control the rate of increase in inbreeding (Dell et al, 2020b), maximize effective population size (N e ), and limit the expression of deleterious alleles (Dell et al, 2020a(Dell et al, , 2020b.…”

“…Previously reported evaluation of the studbook (Dell et al, 2020b) has shown that the Cleveland Bay horse has a very deep and robust studbook extending back over 36 generations.…”

Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse

“…The average level of inbreeding for the Cleveland Bay is estimated as 22.5%, substantially higher than for the majority of domestic horse breeds (6.55–12.55%) and the current effective population size is calculated at 32; substantially lower than the United Nations FAO critical threshold of 50. Indeed, we have recently outlined a comparative analysis of the population employing both pedigree evaluation and molecular methods, whilst formulating a pedagogically-based strategy for conservation assessments of such breeds going forward and allowing for our framework to be employed for the conservation of endangered breeds going forward [ 4 ]. Furthermore, this work develops on our previous assessment of pedigree records and indicates that the small size of the population and high levels of inbreeding constitute a powerful argument for establishing a robust understanding of the genetic diversity of the breed in order to secure its survival.…”