Popular Sire Research Articles

Analysis of the level of inbreeding and relatedness of Bull Terrier dogs – the popular stud dog effect

The aim of the study was to analyze the level of homozygosity of a bull terrier dog population due to its small size, forcing mating in kinship and, possibly, overuse of popular stud dogs. The pedigrees of 107 bull terrier dogs (35 males and 72 females), born in 2008-2016 were used to obtain the inbreeding coefficients for all animals and relatedness coefficients between dogs, between bitches and between bitches and dogs. Pedigrees of bull terriers were also analyzed for occurrence the most common stud dogs. The frequency of occurrence of a popular sire was found according to its position in the pedigree. For the most common stud dog, a list of his sons and their progeny was created. In total about 75% of individuals from the studied population were inbred and their average inbreeding was over 0.04. Almost 95% of bull terriers were related with the average relatedness amounting to over 0.07. The highest value of an individual's inbreeding was almost 0.18, and the highest relationship coefficient was between bitches (over 0.61). There was a popular stud dog in the analyzed population that appeared 113 times in the pedigrees of 107 tested animals and his genes were passed on by his 10 sons as well. It should be noticed that the studied population requires constant monitoring of genetic variability and limiting the overuse of popular stud dogs, which should lead to maintain the variability.

The Weight of Genetic Drift: A Pedigree-Based Evaluation of the Breton Horse Population in Brazil.

The genetic diversity of Breton horses in Brazil is a critical concern, mainly due to the small population size and low number of births per year. Given that the inbreeding was overlooked by breeders for multiple generations, we estimated the genetic diversity of this population utilizing pedigree-based measures of population diversity. A total of 1394 six-generation pedigrees representing the full population of registered Breton horses in Brazil defined a total population (TP, N = 2679), with horses born between 2000 and 2022, reproductively active and alive, as reported by the breed association, representing the reference population (RP, N = 731). Using the R package PurgeR, we estimated inbreeding coefficient (F ped ), maternal inbreeding coefficient (F da m ), paternal inbreeding coefficient (F sire ), individual reproductive values, number of equivalents to complete generations (t), and unbiased ancestral inbreeding coefficient (Fa). We established the equivalent complete generations (ECG), effective population size (Ne), total number of founders (Nf), effective number of founders (Nfe), total number of ancestors (Na), effective number of ancestors (Nae), founder genomes (Ng), and the inbreeding coefficient estimated with effective population size (Ne) and generation numbers (t) (F Ne:t ), as well as Nfe/Nae and Nfe/Ng ratios for the RP. The RP inbreeding levels have stabilized, although they are still significantly rising by generation (t), and the Nfe/Ng ratio strongly suggests genetic drift. Pedigree-based analysis demonstrates that only five stallions have sired 52.83% of the RP individuals, which along with the Nae value of 36.73 implies that the observed inbreeding can be arising from patrilines. Our results suggest that observed inbreeding is due to Popular Sire Effect, highlighting the importance of monitoring breeding schemes and genetic diversity to maintain health.

Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach

BackgroundThe Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds.ResultsThe k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne).ConclusionsDistinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.

The importance of historically popular sires on the accuracy of genomic predictions of young animals in the US Holstein population

The dairy industry is known for its extensive use of artificial insemination, which has resulted in a population where most animals can be traced back to only a few sires. Due to their relatedness to the population, old influential sires could still contribute to the accuracy of genomic predictions. The objective of the study was to identify the impact of historically influential sires on the recent population. This was tested by constructing a genomic relationship matrix using recursion with different sets of sires. Differences in prediction accuracies with different sets are indicative of how important each set is. Recursion coefficients linking young animals to those sets reveal the relative importance of specific sires to the prediction accuracy of recent animals. The data included ∼10 million scores for stature and fore udder attachment (FUA) measured from 1983. Genotypes of 569,404 animals were available. Sire sets included the 100 most popular sires born within different time periods. Computations were with single-step genomic BLUP. In general, the younger sires had higher prediction accuracies than the oldest sires, even though they generally have fewer progeny. The accuracy of evaluation for stature was increased from 0.54 with the most popular sires born before 1981 to 0.69 with sires born from 2001 to 2010, while the accuracy for FUA increased from 0.47 to 0.61. The accuracy achieved using the overall 100 most used sires was 0.66 for stature and 0.58 for FUA. All 100 sires from each period were combined in a subset to determine the importance of each sire relative to all 400 animals in the combined subset. The highest relative impact of a sire that was born within the different time sets was 1.97 for Valiant (before 1981), 1.94 for Blackstar (1981 to 1990), 4.38 for Shottle (1991 to 2000), and 3.09 for Planet (2001 to 2010). The 3 sires among the 400 with the greatest impact were Shottle, Goldwyn (3.73), and Planet. The relative impact of a sire was not strongly related to the number of progeny. For instance, the relative impact of Durham with 34K progeny was 2.29, whereas the impact of O Man with 15K progeny was 3.13. The impact of a sire is also influenced by whether it was used as a sire of sires. Results show that younger sires are more relevant to the accuracy of breeding value prediction in the recent population.

Inbreeding levels in an open-registry pedigreed dog breed: The Australian working kelpie

The depletion in genetic diversity of closed-pedigree dog breeds can be a contentious topic and can lead to calls for open-registry. However, strong evidence in support of proposed open-registry solutions is lacking, with the reproductive isolation of these breeds unlikely to be the sole cause of elevated inbreeding levels. Human-induced limitations, such as popular sire effects, are unlikely to be confined to closed-registry breeds and conceivably play an important role in maintaining genetic diversity within all breeds. Consequently, the aim of the current study was to explore inbreeding levels in an open-registry breed and determine the impact open-registry has on genetic diversity. Complete pedigree records on all Australian working kelpies (AWKs) were provided by the Working Kelpie Council with the cleaned pedigree consisting of 86,671 individuals with a median pedigree depth of 6.6 generations. The average inbreeding coefficient in the AWK population was 0.049 with an increase in inbreeding coefficient of 0.0016/year. This demonstrates that opening a breed registry can have a beneficial impact on the level of inbreeding within a population over the longer-term. However, allowing for a generation length of 5.1 years yielded an effective population size of 61 for AWKs and demonstrated a pattern consistent with closed-registry dog populations of comparable size.

The use of inbreeding when breeding dogs of Giant schnauzer breed

Inbreeding is a breeding method that is widely used in dog breeding. However, excessive thoughtless use of this method can have a detrimental effect on the health and reproduction of dogs, which under modern environments can occur due to a lack of professional knowledge among people engaged in breeding, lack of publicly available information about the health of sires and their off spring, and widespread breeding use of popular sires. The purpose of the research was to analyze the use of inbreeding in the breeding of dogs of Giant schnauzer breed of exhibition and working directions and its influence on the multiple pregnancy of dogs. The paper analyzes the use of inbreeding in Giant schnauzer breed in two populations that do not intersect due to the direction of use. There was a significant difference between the average indicators of the inbreeding coefficient in the studied groups; in the exhibition direction close inbreeding and incest are more often used during breeding, while in the working direction moderate inbreeding is mainly used, and incest is not used at all. The male dogs and female dogs in the group of the exhibition direction also have a higher indicator of the inbreeding coefficient. Outbred sires in both groups, in group exhibition such companies, outbreeding is less common than in the group working direction. There was no signifi cant difference between the indicators of multiple pregnancy in the groups. On average, female dogs in the working direction group are used more often than female dogs in the exhibition direction group. The frequency of use of male dogs does not differ significantly.

Genomic diversity and population structure of the Leonberger dog breed

BackgroundLeonberger is a giant dog breed formed in the 1850s in Germany. Its post-World War II popularity has resulted in a current global population of ~ 30,000 dogs. The breed has predispositions to neurodegenerative disorders and cancer, which is likely due in large part to limited genetic diversity. However, to date there is no scientific literature on the overall demography and genomic architecture of this breed.ResultsWe assessed extensive pedigree records, SNP array genotype data, and whole-genome sequences (WGS) on 142,072, 1203 and 39 Leonberger dogs, respectively. Pedigree analyses identified 22 founder animals and revealed an apparent popular sire effect. The average pedigree-based inbreeding coefficient of 0.29 and average kinship of 0.31 show a dramatic loss of genetic diversity. The observed average life span decreased over time from 9.4 years in 1989 to 7.7 years in 2004. A global health survey confirmed a high prevalence of cancer and neurological disorders. Analysis of SNP-based runs of homozygosity (ROH) identified 125,653 ROH with an average length of 5.88 Mb, and confirmed an average inbreeding coefficient of 0.28. Genome-wide filtering of the WGS data revealed 28 non-protein-changing variants that were present in all Leonberger individuals and a list of 22 potentially pathogenic variants for neurological disorders of which 50% occurred only in Leonbergers and 50% occurred rarely in other breeds. Furthermore, one of the two mtDNA haplogroups detected was present in one dog only.ConclusionsThe increasing size of the Leonberger population has been accompanied by a considerable loss of genetic diversity after the bottleneck that occurred in the 1940s due to the intensive use of popular sires resulting in high levels of inbreeding. This might explain the high prevalence of certain disorders; however, genomic data provide no evidence for fixed coding variants that explain these predispositions. The list of candidate causative variants for polyneuropathy needs to be further evaluated. Preserving the current genetic diversity is possible by increasing the number of individuals for breeding while restricting the number of litters per sire/dam. In addition, outcrossing would help optimize long-term genetic diversity and contribute to the sustainability and health of the population.

The dog 2.0: Lessons learned from the past

In recent years, concerns have been raised on the diversity, health and welfare of our (pedigree) dog population. Somewhat justified, the popular sire effect, population bottlenecks, the founder effect and inbreeding have left their marks on the dog as we know it. In order to improve the health and welfare of the canine population in general, individual breeding programs should adhere to the concept of ethical breeding (i.e. “the use of healthy animals true to their species in behaviour and looks, and when applicable, showing a sustainable performance”) when population-specific breeding goals are defined. Even though every population has its own problems, the approach to get to possible solution(s) is similar. The starting point will always be the identification of which (un)desirable pheno- and genotypes are segregating and what their prevalence is, followed by an evaluation of the genetic diversity. Based on that information and, when applicable, additional criteria like breed standards, breeding goals can be defined. It is of critical importance that these goals are put forward with a long term vision in mind and with consensus from the stakeholders to ensure collaboration. Upon prioritization of the most important goals, when necessary with the help of specifically developed tools, the final step is choosing the most optimal combination of breeding strategies. This paper aims to provide a stepwise approach to identify and tackle population-specific problems encountered in breeding programs.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FISR2 = 0.942, P = 2.19 × 10−13; FROHR2 = 0.88, P = 1.81 × 10−10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

PSIV-19 Live and carcass production traits for progeny of an F1 USDA Prime – yield grade 1 carcass clone sire in comparison with progeny of popular reference sires

Abstract The cloning of beef carcasses that grade USDA Prime – Yield Grade 1 (P1) has produced a sire that ranked well against high performing bulls from multiple breeds. An F1 (P1 x P1) sire would ideally exhibit heterosis and outperform its high performing parents. A terminal sire study was conducted comparing progeny of an F1 (P1 x P1) sire (AxG1) against progeny (heifers and steers) of four high performing sires of varying breeds {P1 (Alpha); Angus; Simmental; Angus x Simmental}. Production traits included morbidity and mortality frequencies, weaning weight, and feedlot arrival weight; carcass traits included edible liver and normal lung frequencies, hot carcass weight, longissimus muscle area, 12th rib fat thickness, and marbling score. A completely randomized experimental design was used; data was analyzed using a mixed model with a fixed effect of sire and random effects of harvest date, sex, and pen. Feedlot arrival weight, frequencies of morbidity and mortality, 12th rib fat thickness, and frequency of grading Certified Angus Beef or USDA Select did not differ (P ≥ 0.16) between sires. Weaning weight and frequency of normal lungs tended (P ≤ 0.08) to differ amongst sires. Differences in hot carcass weight (P &amp;lt; 0.01), longissimus muscle area (P &amp;lt; 0.01), marbling score (P &amp;lt; 0.01), and frequencies of normal lungs (P &amp;lt; 0.01) was detected among sires. Additionally, sire differences in USDA yield grade (P &amp;lt; 0.01), and frequencies of carcasses grading USDA Prime (P &amp;lt; 0.01) and USDA Choice (P &amp;lt; 0.01) were observed. AxG1 progeny exhibited the least 12th rib fat thickness and lowest USDA yield grade in addition to the largest longissimus muscle area, highest marbling score, and greatest frequency of USDA Prime. These data suggest that AxG1 competed extremely well against other high performing industry sires.

Study on Hematological and Biochemical Characters of Cloned Duroc Pigs and Their Progeny.

Simple SummaryCloning is the most promising technique for passing the excellent phenotypes of the best individuals in the population. Here we studied the effects of cloning on Duroc pig, which is the most popular sire used in pig production due to its good growth and meat quality. Understanding the changes of cloned Duroc pigs and their progenies is of great importance for animal breeding and public acceptance. The results of this study suggested that there were no difference in blood parameters between the cloned Duroc and the conventionally bred Duroc and their progenies.To increase public understanding in cloned animals produced by somatic cell nuclear transfer technology, our previous study investigated the carcass trait and meat quality of the clones (paper accepted), and this study we further evaluate differences by investigating the blood parameters in cloned pigs and their progeny. We collected blood samples from the clones and conventionally bred non-clones and their progeny, and investigated their hematological and blood biochemical characters. Our results supported the hypothesis that there was no significant difference between clones and non-clones, or their progeny. Taken together, the data demonstrated that the clones or their progeny were similar with their controls in terms of blood parameters, although there were still other kinds of disorders, such as abnormal DNA methylation or histone modifications that needs further investigation. The data in this study agreed that cloning technique could be used to preserve and enlarge the genetics of the superior boars in pig breeding industry, especially in facing of the deadly threat of African Swine fever happened in China.

Complex patterns of sex-biased demography in canines.

The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to have experienced a popular sire effect, where a small number of males father many offspring with a large number of females. Here we use genetic variation data to test how widespread sex-biased mating practices in canines are during different evolutionary time points. Using whole-genome sequence data from 33 dogs and wolves, we show that patterns of diversity on the X chromosome and autosomes are consistent with a higher number of reproducing males than females over ancient evolutionary history in both dogs and wolves, suggesting that mating practices did not change during early dog domestication. By contrast, since breed formation, we found evidence for a larger number of reproducing females than males in breed dogs, consistent with the popular sire effect. Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history. The signatures observed in genetic data are consistent with documented sex-biased mating practices in both the wild and domesticated populations, suggesting that these mating practices are pervasive.

Battle of the Sexes in Best of Breed: Sex Influences Dogs' Success in the Show Ring.

Simple SummaryWhen breeding dogs, the dam and the sire contribute equally to the genetics of each of their puppies, and so each parent should be equally important to show-ring success. The current study collated samples of dog show results to explore relationships between sex and the likelihood of success in the show ring. It focused on toy and giant breeds to explore any differences in equity, if it existed, at either end of the size spectrum. It revealed that the rate at which male and female dogs were exhibited were similar but that male dogs were a significant advantage of winning Best of Breed titles.Much of the research on pedigree dog breeding has been directed towards understanding the implications of reduced genetic diversity and the prevalence of inherited disorders. An example is the potential role of the popular sire effect in perpetuating genetic defects. If male dogs are more likely than bitches to be identified as examples of members of a breed that align with breed standard, they may be selected for breeding earlier. This may contribute to the influence of individual males and contribute to popular sire effect. Conversely, if breed standards are written in a sex-neutral fashion, and if dogs are entered, exhibited, and judged in a sex-neutral fashion, then we would expect the success of female dogs in the show ring to be equal to that of their male counterparts. With a focus on toy and giant breeds, the current pilot study collated samples of dog show results to explore relationships between sex and the likelihood of success in the show ring. It focused on toy and giant breeds to explore any differences in equity, if it existed, at either end of the size and concomitant age-at-maturation spectrum. For the purpose of this study, toy breeds were those that weigh < 10 kg at maturity while giant breed dogs were those that exceed 45 kg. Within these two clusters, the least (n = 3) and most popular (n = 3) breeds were then selected to explore any potential role of sex on success in the show ring. The popularity of breeds was determined using the numbers of dogs registered with the Australian National Kennel Council. Using results from dog shows (n = 18) from 2015 to 2016, data on 1,080 dogs were obtained. Within these 12 breeds for the 18 shows, there were 137 Best of Breed (BOB) titles awarded: Pug (n = 18), Toy Poodle (n = 18), Bullmastiff (n = 14), Rottweiler (n = 17), Fox Terrier (Smooth) (n = 18), Bloodhound (n = 3), Schnauzer (miniature) (n = 15), Great Dane (n = 17), Norfolk Terrier (n = 10), Norwich Terrier (n = 5), Central Asian Shepherd Dog (n = 2). Despite the near parity of male and female dogs being exhibited, of these 137 titles, 86 (62.8%) were awarded to male dogs (at least 41 individuals) and 51 (37.2%) to female dogs (at least 32 individuals) showing that male dogs are more likely to win BOB titles (χ2 = 9.4455, df = 1, p-value = 0.002117). Among the toy subset of breeds, this effect was higher (χ2 = 6.798, df = 1, p-value = 0.009126) than among the giant breed subset, for whom the advantage to male dogs did not reach statistical significance versus χ2 = 3.0967, df = 1, p-value = 0.07845). This suggests that judges find the male dogs more appealing, presumably because they are more aligned with breed standards.

Analysis of single nucleotide polymorphisms variation associated with important economic and computed tomography measured traits in Texel sheep

Sheep are an important part of the global agricultural economy. Growth and meat production traits are significant economic traits in sheep. The Texel breed is the most popular terminal sire breed in the UK, mainly selected for muscle growth and lean carcasses. This is a study based on a genome-wide association approach that investigates the links between some economically important traits, including computed tomography (CT) measurements, and molecular polymorphisms in UK Texel sheep. Our main aim was to identify single nucleotide polymorphisms (SNP) associated with growth, carcass, health and welfare traits of the Texel sheep breed. This study used data from 384 Texel rams. Data comprised ten traits, including two CT measured traits. The phenotypic data were placed in four categories: growth traits, carcass traits, health traits and welfare traits. De-regressed estimated breeding values (EBV) for these traits together with sire genotypes derived with the Ovine 50 K SNP array of Illumina were jointly analysed in a genome wide association analysis. Eight novel chromosome-wise significant associations were found for carcass, growth, health and welfare traits. Three significant markers were intronic variants and the remainder intergenic variants. This study is a first step to search for genomic regions controlling CT-based productivity traits related to body and carcass composition in a terminal sire sheep breed using a 50 K SNP genome-wide array. Results are important for the further development of strategies to identify causal variants associated with CT measures and other commercial traits in sheep. Independent studies are needed to confirm these results and identify candidate genes for the studied traits.

Trends in genetic diversity for all Kennel Club registered pedigree dog breeds.

BackgroundInbreeding is inevitable in closed populations with a finite number of ancestors and where there is selection. Therefore, management of the rate of inbreeding at sustainable levels is required to avoid the associated detrimental effects of inbreeding. Studies have shown some pedigree dog breeds to have high levels of inbreeding and a high burden of inherited disease unrelated to selection objectives, implying loss of genetic diversity may be a particular problem for pedigree dogs. Pedigree analysis of all 215 breeds currently recognised by the UK Kennel Club over the period 1980–2014 was undertaken to ascertain parameters describing the rate of loss of genetic diversity due to inbreeding, and the presence of any general trend across all breeds.ResultsThe trend over all breeds was for the rate of inbreeding to be highest in the 1980s and 1990s, tending to decline after 2000. The trend was comparable in very common and rarer breeds, although was more pronounced in rarer breeds. Rates of inbreeding over the entire period 1980–2014 were not correlated with census population size. The existence of popular sires was apparent in all breeds.ConclusionThe trends detected over 1980–2014 imply an initial excessive loss of genetic diversity which has latterly fallen to sustainable levels, even with modest restoration in some cases. The theory of genetic contributions, which demonstrates the fundamental relationship of inbreeding and selection, implies that popular sires are the major contributor to high rate of inbreeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s40575-015-0027-4) contains supplementary material, which is available to authorized users.

Genetic management of Dutch golden retriever dogs with a simulation tool.

Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each year. The five most popular sires sire approximately 25% of the litters in a year. Simulations show that the small number of popular sires and their high contribution to the next generation are the main determinants of the inbreeding rates. Restricting breeding to animals with a low average relatedness to all other animals in the population was the most effective measure and decreased the rate of inbreeding per generation from 0.41 to 0.12%. Minimizing co-ancestry of parents was not effective in the long run, but decreased variation in inbreeding rates. Restricting the number of litters per sire generally decreased the generation interval because sires were replaced more quickly, once they met their restriction. In some instances, this lead to an increase in inbreeding rates because the next generations were more related. The simulation tool proved to be a powerful and educational tool for deciding which breeding restrictions to apply, and can be effective in different breeds and species as well.

Progress in purebred dog health since the Bateson report of 2010

JUST occasionally, a landmark event triggers lasting animal welfare change. This was the case for farm animal welfare with a book called Animal Machines by Ruth Harrison (1964). The book...

Where Do the Cold Blood Breeds Come from and Where Does Polysaccharide Storage Myopathy Fit in?

IntroductionMyopathy associated with a gain‐of‐ function mutation in the GYS1 gene is known in Quarter Horses and cold blood breeds. The mutation occurred between the collapse of the Roman Empire (500 AD) and the upsurge of Carolinian Reign (800 AD). The aim of this review is to reconstruct the development of the cold blood (brachimorph) breeds in Europe using existing literature.MethodsLiterature reviewResultsAlthough archaeological evidence indicates the existence of a mesomorph horse (Cob) type in the early Iron Age, real cold blood breeding only started after 1750. The demand for draught power in the early Industrial Revolution resulted in a large population of cold bloods from 1850 onwards. In Roman times, the huge ugly horses from Thrace were known as “easy keepers” and Ardennes might have been the first land races carrying the GYS1 mutation. Hunnish horses might have contributed to the prototype cold bloods as well. With mtDNA, Y‐chromosome polymorphism, satellite markers and SNP genotyping some indication from where ancestors of particular breeds originate was obtained. Most phylogenetic trees place cold blood breeds, including Fell ponies, Haflinger and Friesian in a clearly different cluster than ponies, saddle horses and Thoroughbreds. Fjords and Mongolian horses are in neighbouring clusters. Since the last 200 years, genetic bottlenecks and the popular sire phenomenon could have caused high GYS1 H allele frequencies in many continental cold blood breeds.ConclusionsCold blood breeds and the GYS1 mutation likely trace back to the mesomorph tough, easily satisfied horse types from Eastern Europe and central Asia.Ethical Animal ResearchNo animals were used in the study. Sources of funding: none. Competing interests: none.

Prediction of expected genetic variation within groups of offspring for innovative mating schemes

BackgroundExperience from progeny-testing indicates that the mating of popular bull sires that have high estimated breeding values with excellent dams does not guarantee the production of offspring with superior breeding values. This is explained partly by differences in the standard deviation of gamete breeding values (SDGBV) between animals at the haplotype level. The SDGBV depends on the variance of the true effects of single nucleotide polymorphisms (SNPs) and the degree of heterozygosity. Haplotypes of 58 035 Holstein animals were used to predict and investigate expected SDGBV for fat yield, protein yield, somatic cell score and the direct genetic effect for stillbirth.ResultsDifferences in SDGBV between animals were detected, which means that the groups of offspring of parents with low SDGBV will be more homogeneous than those of parents with high SDGBV, although the expected mean breeding values of the progeny will be the same. SDGBV was negatively correlated with genomic and pedigree inbreeding coefficients and a small loss of SDGBV over time was observed. Sires that had relatively low mean gamete breeding values but high SDGBV had a higher probability of producing extremely positive offspring than sires that had a high mean gamete breeding value and low SDGBV.ConclusionsAn animal’s SDGBV can be estimated based on genomic information and used to design specific genomic mating plans. Estimated SDGBV are an additional tool for mating programs, which allows breeders to identify and match mating partners using specific haplotype information.

The American Quarter Horse: population structure and relationship to the thoroughbred.

A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred's influence on QH diversity. Results showed significant population structure among all QH performance groups excepting the comparison between the cutting and working cow horses; divergence was greatest between the cutting and racing QHs, the latter of which had a large contribution of Thoroughbred ancestry. Significant coancestry and the potential for inbreeding exist within performance groups, especially when considering the elite performers. Relatedness within performance groups is increasing with popular sires contributing disproportionate levels of variation to each discipline. Expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses suggest these QHs can be broadly classified into 3 categories: stock, racing, and pleasure/halter. Although the QH breed as a whole contains substantial genetic diversity, current breeding practices have resulted in this variation being sequestered into subpopulations.