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The herd of van der Veen family consists of about 40 cattle with the color-sided pattern and the rare diluted and roan color. Rare colors and pattern that are brought together through years of targeted breeding and conservation. The exclusive herd of small size therefore has unique combinations of rare alleles and genotypes. Because there are no registration papers present, the genetic make-up of this herd was investigated through DNA analysis. The herd of van der Veen family does not cluster with any one of the local Dutch cattle breeds and therefore consists of unique combinations of breeds and genetic diversity. The observed rare colors were verified through DNA analysis. The DNA, expect for one individual, matched the observed color for red/black and the absence or presence of the diluted color. F or the color-sided pattern, and the spotted and roan color no conclusions could be made as the mutation itself was not genotyped. Based on DNA all known mother-offspring relationships were verified and DNA also provided insights concerning other relationships between the individuals. The herd consists of unique combinations of rare colors and pattern and the animals are genetically unique. It is therefore important to conserve the genetic diversity within this herd., De veestapel van familie van der Veen bestaat uit ongeveer 40 runderen met de witrik aftekening en de zeldzame kleuren vaal en blauw. Zeldzame kleuren en aftekening die door jarenlange gerichte fokkerij bij elkaar zijn gebracht én in stand zijn gehouden. De bijzondere veestapel van beperkte omvang heeft daarmee unieke combinaties van zeldzame allelen en genotypes. Omdat er geen stamboekgegevens van de runderen zijn, is de genetische achtergrond van de runderen met behulp van DNA onderzoek in kaart gebracht. De veestapel van familie van der Veen clustert niet samen met een enkel oorspronkelijk Nederlands ras en omvat unieke combinaties van rassen en genetische diversiteit. De geobserveerde zeldzame kleuren werden middels DNA onderzoek geverifieerd. Het DNA kwam, op één rund na, overeen met de geobserveerde kleur voor de basiskleur rood/zwart en de aan- of afwezigheid van de vaal kleur. Voor de aftekening witrik en de kleuren blauw en bont konden geen harde uitspraken gedaan worden omdat de daadwerkelijke mutatie niet gegenotypeerd was. Op basis van DNA zijn alle bekende moeder-nakomeling relaties geverifieerd en relaties op basis van DNA inzichtelijk gemaakt. D e veestapel bevat unieke combinaties van zeldzame kleuren en aftekeningen en de runderen zijn genetisch uniek. Het is daarom van belang dat de genetische diversiteit van deze veestapel behouden blijft.

The Black blazed sheep breed is a rare, native Dutch breed of sheep. In order to maintain such a small population it is of great importance to monitor the population size, the rate of inbreeding and kinship in the population. Pedigree data of the current population within the two studbooks, the Dutch Black blazed Studbook (Nederlands Zwartbles Stamboek, NZS) and the Black blazed breeders group (Zwartbles Fokkersgroep, FG) was analyzed. The population was analyzed in terms of number of animals, number of offspring and rate of inbreeding per generation. In addition, simulations were carried out, where the effect of exchange of animals between the two studbooks on the rate of inbreeding was predicted for the next 50 years. Currently 95% of NZS animals have NZS parents and about 5% of NZS animals come from parents of the FG studbook. Conversely, about 35% of the animals in the FG studbook have parental animals registered at the NZS and about 65% of the FG animals stay within this studbook. The analysis of 93,634 sheep in total (1987 - 2018) showed that the rate of inbreeding per generation was especially high in the last period from 2015 to 2018 (0.82%). This is well above the FAO standard of 0.5% per generation. The current exchange between the studbooks should certainly be maintained for the purpose of inbreeding management, and especially for the FG population it is necessary to use breeding animals from the NZS population, Het Zwartbles schaap is een zeldzaam Nederlands schapenras. Voor de instandhouding van zeldzame rassen is het van groot belang om de populatiegrootte en de toename in inteelt en verwantschap in de populatie te monitoren. De huidige populatie is geanalyseerd op basis van alle afstammingsgegevens van het Nederlands Zwartbles Stamboek (NZS) én de Zwartbles Fokkersgroep (FG) gezamenlijk. Er is onderzocht hoe de huidige populatie ervoor staat qua aantal dieren, geboortes en inteelttoename. Daarnaast zijn er simulaties uitgevoerd, waarbij er werd gekeken naar de invloed van het wel of niet uitwisselen van dieren tussen beide stamboeken op het inteeltniveau. De huidige uitwisseling houdt in dat ongeveer 95% van de NZS dieren geboren worden uit NZS ouderdieren en ongeveer 5% van NZS dieren afkomstig zijn uit ouderdieren van het FG stamboek. Andersom heeft ongeveer 35% van de dieren in het FG stamboek, ouderdieren uit het NZS en blijft ongeveer 65% van de FG dieren binnen dit stamboek. De analyse van de in totaal 93.634 schapen (1987 – 2018) liet zien dat er in de periode van 2015 – 2018 sprake was van een hoge inteelttoename (0,82%). Dit ligt ruim boven de door FAO gestelde norm van 0,5% per generatie. Om de inteelttoename beperkt te houden wordt aanbevolen om de huidige uitwisseling tussen de stamboeken in stand houden. Zeker voor de FG is het noodzakelijk om ook fokdieren uit het NZS stamboek in te zetten.

Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.

The Dutch Draught horse is a rare Dutch horse breed. To conserve rare breeds, it is of great importance to monitor population size and increase in inbreeding and kinship in a population. When screening the Dutch Draught horse population, it turned out that inbreeding (and potential consequences) should be controlled by the studbook (KVTH) with participation of breeders. During the most recent generation (2010-2017) fewer foals were born annually compared to the generation before. Also, the percentage of foals that is used in breeding at a later age decreased steadily. At the same time there is a considerable increase in the kinship between horses that are used in breeding. The increase in inbreeding passes the FAO threshold of 0.5% per generation. In light of the increase in kinship, we expect that the increase in inbreeding will even be higher in the future. Screening the population clearly showed that genetic management is needed to be able to better control inbreeding (and potential accompanying consequences). It is possible to drastically reduce the inbreeding increase through genetic management., Het Nederlandse Trekpaard is een zeldzaam Nederlands paardenras. Voor de instandhouding van zeldzame rassen is het van groot belang om de populatiegrootte en de toename in inteelt en verwantschap in de populatie te monitoren. Uit het doorlichten van de Nederlandse Trekpaardenpopulatie bleek dat inteelt (en eventuele bijbehorende gevolgen) beter moeten worden beheerst door het stamboek (KVTH) én met medewerking van fokkers. In de meest recente generatie (2010-2017) werden minder veulens geboren dan in de generatie ervoor, er werden verhoudingsgewijs ook minder Trekpaarden ingezet voor de fokkerij terwijl de verwantschap tussen de paarden aanzienlijk toenam. De berekende inteelttoename bevindt zich ruim boven de door de FAO gestelde norm van maximaal 0,5% per generatie. Door aangepast genetisch beheer is het mogelijk de inteelttoename drastisch terug te dringen.

Background: Inbreeding and population bottlenecks in the ancestry of Friesian horses has led to health issues such as dwarfism. The limbs of dwarfs are short and the ribs are protruding inwards at the costochondral junction, while the head and back appear normal. A striking feature of the condition is the flexor tendon laxity that leads to hyperextension of the fetlock joints. The growth plates of dwarfs display disorganized and thickened chondrocyte columns. The aim of this study was to identify the gene defect that causes the recessively inherited trait in Friesian horses to understand the disease process at the molecular level. Results: We have localized the genetic cause of the dwarfism phenotype by a genome wide approach to a 3 Mb region on the p-arm of equine chromosome 14. The DNA of two dwarfs and one control Friesian horse was sequenced completely and we identified the missense mutation ECA14:g.4535550C > T that cosegregated with the phenotype in all Friesians analyzed. The mutation leads to the amino acid substitution p.(Arg17Lys) of xylosylprotein beta 1,4-galactosyltransferase 7 encoded by B4GALT7. The protein is one of the enzymes that synthesize the tetrasaccharide linker between protein and glycosaminoglycan moieties of proteoglycans of the extracellular matrix. The mutation not only affects a conserved arginine codon but also the last nucleotide of the first exon of the gene and we show that it impedes splicing of the primary transcript in cultured fibroblasts from a heterozygous horse. As a result, the level of B4GALT7 mRNA in fibroblasts from a dwarf is only 2 % compared to normal levels. Mutations in B4GALT7 in humans are associated with Ehlers-Danlos syndrome progeroid type 1 and Larsen of Reunion Island syndrome. Growth retardation and ligamentous laxity are common manifestations of these syndromes. Conclusions: We suggest that the identified mutation of equine B4GALT7 leads to the typical dwarfism phenotype in Friesian horses due to deficient s

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity