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

Dell, Andrew; Curry, Mark; Hunter, Elena; Dalton, Ruth; Yarnell, Kelly; Starbuck, Gareth; Wilson, Philippe B.

doi:10.1002/ece3.8118

Cited by 7 publications

(6 citation statements)

References 71 publications

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“…The pedigrees of Arabian Horses, English Thoroughbreds and some European breeds [ 61 , 70 , 75 , 77 , 84 , 111 , 122 ] have been deeply described in the dedicated studbooks, showing a notable influence of Arabian, Spanish and Thoroughbred stallions. However, the information included in studbooks is not always error free, and genetic analyses are essential for an accurate characterization of patrilines in a breed [ 77 ].…”

Section: The Debate About Stallion Pedigreesmentioning

confidence: 99%

“…Recently, many studies have been focused on the loss of biodiversity [ 23 , 24 , 25 ] or the increase in deleterious genotypes [ 26 ] caused by such inbreeding (as reviewed in [ 7 ]). In the last 200 years, the inbreeding practice led to the phenotypical expression at homozygous sites of deleterious variants [ 27 ], as highlighted when the coefficients are calculated in order to evaluate the genetic diversity among different horse breeds [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ,…”

Section: Introductionmentioning

confidence: 99%

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Unlocking Horse Y Chromosome Diversity

Cardinali

Giontella

Tommasi

et al. 2022

Genes

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The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.

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Section: The Debate About Stallion Pedigreesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Unlocking Horse Y Chromosome Diversity

Cardinali

Giontella

Tommasi

et al. 2022

Genes

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“…In the United States, there were less than 200 registered Cleveland Bay horses in 2009, resulting in the breed being listed as critically endangered by the Livestock Conservancy (Khanshour et al., 2019 ). Thus, there is a loss of genetic diversity due to the decreasing number of breeding stock horses and resultant increased levels of inbreeding (Dell et al., 2020 ; Dell et al., 2021 ). A recent genetic study on Cleveland Bay horses found that 70% of the living maternal lineage is derived from three founding mares, and all living paternal lineages can be traced back to a single founder stud (Dell et al., 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Bilateral patellar aplasia in a foal

Ludwig

Hallowell

Womble

et al. 2023

Veterinary Medicine & Sci

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A 2-day-old Cleveland Bay colt was referred to the Equine Emergency Service of the Farm Animal and Equine Veterinary Medical Center at North Carolina State University's College of Veterinary Medicine for evaluation of decreased nursing behaviour and right hindlimb lameness of 2 days' duration. When assisted to stand, the foal was unable to extend either hindlimb or bear weight on the hindlimbs, the right patella was luxated laterally and unable to be reduced, and the foal assumed a crouched position.Stifle radiographs revealed minimal, heterogeneous, ill-defined ossification of both patellae. Due to the severity of the musculoskeletal defects, humane euthanasia was elected. Post-mortem examination identified a congenital malformation of both patella bones with failure of ossification and cardiac changes suggestive of right atrioventricular valve dysplasia. Histology of the patellae showed no evidence of osteoid deposition or ossification. To our knowledge, bilateral congenital patellar aplasia has not been previously described in foals.

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“…The current recommendation of the United Nations Farm Animal Organization (FAO) is to maintain breeds with a maximum rate of accumulation of 1% inbreeding per generation. In order to achieve this, it is necessary to maintain a minimum Ne of 50 animals (the rate of inbreeding ∆F = 1/2Ne) [28]. In 2021, the highest effective population size (Ne (based on the number of parents) was determined in LBWP (4449) and LRWP (3855) and the lowest in LR_pure (42).…”

Section: Discussionmentioning

confidence: 99%

“…This study presents four methods for estimating the effective population size (Ne). For details, see Groeneveld et al [24,28] and Gutiérrez et al [29]. Based on the rates computed, the Ne is estimated as Ne = 1/2 × ∆F* for the pedigree-based methods (Table 1):…”

mentioning

confidence: 99%

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations

Marašinskienė,

Šveistienė,

Razmaitė

et al. 2023

Animals

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The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR’s ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

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

Cited by 7 publications

References 71 publications

Unlocking Horse Y Chromosome Diversity

Unlocking Horse Y Chromosome Diversity

Bilateral patellar aplasia in a foal

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations

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