Demographic assessment of the Dalmatian dog - effective population size, linkage disequilibrium and inbreeding coefficients

Background

The calculation of demographic measures is a useful tool for evaluating the genomic architecture of dog breeds and enables ranking dog breeds in terms of genetic diversity. To achieve this for the German Dalmatian dog population, 307 purebred animals of this breed were genotyped on the Illumina Canine high density BeadChip. The analysis of pedigree-based inbreeding was performed based on a pedigree with 25,761 dogs including the genotyped dogs.

Results

The effective population size derived from squared correlation coefficients between SNP alleles (r²) was 69. The maximum value of r² was 0.56, resulting in a 50% decay value of 0.28 at a marker distance of 37.5 kb. The effective population size calculated from pedigree data using individual increase in inbreeding over equivalent generations was 116. The pedigree inbreeding coefficient was 0.026. The genomic inbreeding coefficient based on the length of runs of homozygosity (ROH) was calculated for seven length categories of ROHs, and ranged from 0.08 to 0.28. The fixation coefficients F_{IS_PED} and F_{IS_GENO} were at 0.017 and 0.004. PANTHER statistical overrepresentation analysis of genes located in consensus ROHs revealed highly underrepresented biological processes in 50% of the investigated dogs. One of those is the 0.28 fold enriched “immune response”, which might be associated to the high prevalence of allergic dermatitis in the breed. Candidate genes for congenital sensorineural deafness (CCSD, a highly prevalent disease in the Dalmatian) were discovered in consensus ROHs.

Conclusions

The fast decay of r² and the moderate inbreeding coefficients indicate that the German Dalmatian dog population is rather diverse. Pedigree- and genomic-based inbreeding measures were highly correlated and therefore prove good reliability for the given population. Analyses of consensus ROHs with genes coding for deafness and other breed-defining traits, such as hyperuricosuria, indicate that those ROH became fixed in the Dalmatian population about 500 years ago. In case of the Dalmatian dog, a ROH of 40 SNPs length is enough to investigate signatures of selection (e.g. the ROH with the fixed hyperuricosuria mutation) as far back as the breed formation point approximately 500 years ago.

Clinical, cytogenetic and molecular genetic characterization of a tandem fusion translocation in a male Holstein cattle with congenital hypospadias and a ventricular septal defect

Hypospadias, disorder of sex development (DSD), is a sporadic congenital abnormality of the genital region in male ruminants, which is characterized by a non-fused urethra during fetal development. Detailed clinical examination classified the hypospadias phenotype of a male Holstein calf studied here as the perineal type. In combined use of cytogenetic analysis and whole genome sequencing, a non-mosaic, pseudo-monosomy 59, XY + tan(18;27) was detected. This chromosomal aberration had its origin in a tandem fusion translocation of the bovine autosomes (BTA) 18 and 27 with an accompanying loss of genomic sequences mainly in the distal end of BTA 18 and the proximal end of BTA 27. The resulting phenotype included hypospadias, growth retardation and ventricular septal defect.

Study of congenital Morgagnian cataracts in Holstein calves

Cataracts are focal to diffuse opacities of the eye lens causing impaired vision or complete blindness. For bilateral congenital cataracts in Red Holsteins a perfectly cosegregating mutation within the CPAMD8 gene (CPAMD8:g.5995966C>T) has been reported. We genotyped the CPAMD8:g.5995966C>T variant in Holstein calves affected by congenital bilateral congenital cataracts, their unaffected relatives and randomly selected herd mates. Ophthalmological examinations were performed in all affected individuals to confirm a congenital cataract. Whole genome sequencing was employed to screen variants in candidate genes for the Morgagnian cataract phenotype. In the present study, 3/35 cases were confirmed as homozygous mutated and 6/14 obligate carriers. Further 7/46 unaffected animals related with these cases were heterozygous mutated for the CPAMD8:g.5995966C>T variant. However 32 cases with a congenital cataract showed the wild type for the CPAMD8 variant. We did not identify variants in the candidate genes CPAMD8 and NID1 or in their close neighborhood as strongly associated with the congenital cataract phenotype in Holstein calves with the CPAMD8 wild type. In conclusion, the CPAMD8:g.5995966C>T variant is insufficient to explain the majority of Morgagnian congenital cataract phenotypes in Holsteins. It is very likely that congenital bilateral cataracts may be genetically heterogeneous and not yet known variants in genes other than CPAMD8 and NID1 are involved.

Short communication: Lethal mutations in Vorderwald cattle through Montbéliarde incrossings

Vorderwald cattle are a dual-purpose cattle breed with high migrant contributions from Montbéliarde bulls in the recent past. Through the wide use of Montbéliarde bulls, undesirable alleles were also disseminated into the Vorderwald population. Haplotypes on bovine chromosome 19 (MH1) and 29 (MH2), supposed to harbor lethal mutations, were identified in Montbéliarde cattle. A study in French Montbéliarde cattle identified the PFAS:g.28511199C>T (rs455876205) variant as the most likely MH1 embryonic lethal mutation. The objective of the present study was to determine whether the PFAS:g.28511199C>T variant was introduced into Vorderwald cattle through Montbéliarde bulls and disseminated in this population. The present study expands on previous work on the deleterious SLC37A2 variant (ss2019324563) of the MH2 locus. Herein, we traced the ss2019324563 variant back to the Montbéliarde bull, which was the most likely source for this deleterious mutation in Vorderwald cattle. We genotyped 354 Vorderwald cattle for the PFAS variant, resulting in 41 heterozygous individuals and a T allele frequency of 0.058. An aborted fetus homozygous mutant for SLC37A2 from our previous study on the MH2 locus in Vorderwald cattle was wild type for the PFAS variant. Both lethal mutations were segregating independently of each other, and we found no indications of joint occurrence in a larger number of animals. Neither SLC37A2 nor PFAS double heterozygous mutants were lethal. The earliest animal with a heterozygous PFAS genotype was 1 of 5 migrant Montbéliarde bulls, and this bull was the most likely origin of the deleterious PFAS allele in Vorderwald cattle. All Vorderwald cattle under study born before introgression of this Montbéliarde bull were homozygous wild type. In addition, all 41 heterozygous Vorderwald cattle had genetic contributions from this Montbéliarde bull, whereas in 74 Vorderwald cattle without genes from Montbéliarde bulls, the PFAS T allele was not observed. In a sample of actual German Fleckvieh the PFAS T allele could be found at a very low frequency. Our study demonstrated the introgression of lethal variants through Montbéliarde bulls into a traditional cattle breed highly adapted to harsh local conditions. These findings underline the need to screen bulls for lethal mutations before their wide use in breeding, particularly in breeds with a focus on preservation of their genetic uniqueness.

Genome-wide association analysis for lethal brachycephalic-like facial dysmorphia in Labrador Retrievers

A GWAS was performed for inborn X-linked facial dysmorphia with severe growth retardation in Labrador Retrievers. This lethal condition was mapped on the X chromosome at 17-21 Mb and supported by eight SNPs in complete LD. Dams of affected male puppies were heterozygous for the significantly associated SNPs and male affected puppies carried the associated alleles hemizygously. In the near vicinity to the associated region, RPS6KA3 was identified as a candidate gene causing facial dysmorphia in humans and mice known as Coffin-Lowry syndrome. Haplotype analysis showed significant association with the phenotypes of all 18 animals under study. This haplotype was validated through normal male progeny from a dam with the not-associated haplotype on both X chromosomes but male affected full-sibs with the associated haplotype.

Genetic parameters and estimated breeding values for traits of raw and frozen-thawed semen in German Warmblood stallions

Objectives of the present study were to estimate genetic parameters for frozen-thawed semen traits of 271 fertile German Warmblood stallions and genetic correlations with raw semen quality traits. Semen samples were collected from stallions utilized for semen collection and artificial insemination (AI) on the Lower Saxon National Stud Celle and the North Rhine-Westphalian National Stud Warendorf. Semen quality variables were analyzed in 63,972 raw (gel-free volume, concentration, progressive motility, number of sperm) and 3681 frozen-thawed samples (motility, DNA fragmentation index (DFI), non-viable sperm). A multivariate linear animal model was used to estimate additive genetic and permanent environmental variances among stallions as well as estimated breeding values (EBVs) for all semen traits. Heritability estimates were greatest for DFI (h² = 0.45) and least for non-viable sperm counts ( h² = 0.11). Additive genetic correlations between progressive sperm motility in raw semen and DFI (r_g = -0.79) as well as non-viable sperm (r_g = -0.45) were negative. The EBVs for frozen-thawed semen traits ranged from 49 to 181 with mean reliabilities of 0.28 to 0.43. The EBVs for progressively motile sperm post-thawing and DFI were the most highly correlated traits with EBVs for stallion fertility (r = 0.38 and r = -0.17). Stallions with relatively greater EBVs for progressive motility in raw semen may be most suitable when freezing semen for storage and subsequently thawing it for AI. Using EBVs for semen traits in selection of stallions to AI mares appears as an option for genetic improvement to enhance fertility after AI.

Breed and stallion effects on frozen-thawed semen in warmblood, light and quarter horses

The objectives of the present study were to analyze systematic effects on semen quality traits from fresh and frozen-thawed semen collected in and outside season. A total of 4,681 reports on semen traits of 121 stallions representing Arabian, Thoroughbred, Quarter Horse and four warmblood breeds used for artificial insemination at the Lower Saxon National stud Celle were edited for analysis of gel-free volume, sperm concentration, total number of sperm and total number of motile sperm in fresh semen and in frozen-thawed semen progressive motility, DNA fragmentation index and non-viable sperm. Month, year, age, breed and stallions effects were analyzed with a linear mixed model procedure. Breed differences were significant for sperm concentration, total number of sperm, total motile sperm number and DNA fragmentation index. Hanoverian stallions showed significant higher least squares means for sperm concentration, total number of sperm and total motile sperm number in fresh semen, whereas Thoroughbred had significant higher least squares means for DNA fragmentation index. Stallions with an age of 2-6 years had significant lower least squares means in sperm concentration, total number of sperm and total motile sperm number and progressively motile sperm post-thawing than the other age groups. Month was significant for all semen traits but progressively motile sperm post-thawing. Month by age class interaction showed a significant influence. Inter-stallion variance accounted for 27-71% and the two-way stallion by month interaction for 2-7% of the total variance of semen quality traits. The largest proportion of inter-individual variance among stallions was obtained for the DNA fragmentation index.

Split spinal cord malformations in 4 Holstein Friesian calves

Background

The split spinal cord malformation (SSCM) is an uncommon congenital malformation of the vertebral canal in which parts of the spinal cord are longitudinally duplicated. In SSCM Type I, each spinal cord has its own dura tube. In the SSCM Type II, both parts of the spinal cord are surrounded by a common dura tube.

Cases presentation

During the clinical examination one calf showed ambulatory paresis and 3 calves non-ambulatory paraparesis. Calf 4 additionally had a congenital tremor. The examination of calf 4 using magnetic resonance imaging (MRI) showed a median hydrosyringomyelia at the level of the 4th lumbar vertebra. The caudal part of this liquid-filled cavity was split longitudinally through a thin septum. From there, the spinal cord structures duplicated with an incomplete division, so that the transverse section of the spinal cord appeared peanut-shaped and in each half a central canal could be observed. The pathological-anatomical examination after euthanasia showed a duplication of the spinal cord in the area of the lumbar vertebral column in all calves. The histopathological examination revealed two central lumbar vertebral column channels. The two spinal cord duplicates were each surrounded by two separate meninges in calf 2 (SSCM type I); in the other calves (1, 3, 4, and) the two central canals and the spinal cord were covered by a common meninx (SSCM type II). A pedigree analysis of calves 2, 3 and 4 showed a degree of relationship suggestive of a hereditary component. This supports the hypothesis of a possible recessive inheritance due to common ancestors, leading to partial genetic homozygosity.

Conclusions

The clinical appearance of SSCM can vary widely. In calves with congenital paralysis SSCM should always be considered as a differential diagnosis. A reliable diagnosis intra vitam is possible only with laborious imaging procedures such as MRI. Further studies on the heritability of this malformation are necessary to confirm a genetic cause of this disease.

The horse Y chromosome as an informative marker for tracing sire lines

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

A recessive lethal chondrodysplasia in a miniature zebu family results from an insertion affecting the chondroitin sulfat domain of aggrecan

Background

Congenital skeletal malformations represent a heterogeneous group of disorders affecting bone and cartilage development. In cattle, particular chondrodysplastic forms have been identified in several miniature breeds. In this study, a phenotypic characterization was performed of an affected Miniature Zebu calf using computed tomography, necropsy and histopathological examinations, whole genome sequencing of the case and its parents on an Illumina NextSeq 500 in 2 × 150 bp paired-end mode and validation using Sanger sequencing and a Kompetitive Allele Specific PCR assay. Samples from the family of an affected Miniature Zebu with bulldog syndrome including parents and siblings, 42 healthy Miniature Zebu not related with members of the herd and 88 individuals from eight different taurine cattle breeds were available for validation.

Results

A bulldog-like Miniature Zebu calf showing a large bulging head, a short and compressed body and extremely short and stocky limbs was delivered after a fetotomy. Computed tomography and necropsy revealed severe craniofacial abnormalities including a shortening of the ventral nasal conchae, a cleft hard palate, rotated limbs as well as malformed and fused vertebrae and ribs. Histopathologic examination showed a disorganization of the physeal cartilage with disorderly arranged chondrocytes in columns and a multifocal closed epiphyseal plate. Whole-genome sequencing of this malformed Miniature Zebu calf, its dam and sire and subsequent comparative sequence analysis revealed a one base pair insertion (ACAN:c.5686insC) located within the cartilage development gene aggrecan (ACAN) exclusively homozygous in the affected calf and heterozygous in its parents. This variant was predicted to cause a frameshift (p.Val1898fsTer9) and thus a truncation of the chondroitin sulfate domain as well as a loss of the C-terminal globular domain of ACAN. It perfectly co-segregated with the lethal bulldog syndrome in Miniature Zebus.

Conclusions

We found a novel mutation in ACAN causing a recessive lethal chondrodysplasia in Miniature Zebu cattle. A diagnostic test for this mutation is now available for Miniature Zebu breeders preventing further cases of bulldog syndrome by targeted matings. To the authors’ best knowledge, this is the first case of a Miniature Zebu associated with an ACAN mutation.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0678-8) contains supplementary material, which is available to authorized users.

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Background

Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in “SweepFinder”, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F_ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F₂ individuals from a cross of Goettingen Minipigs and large pigs.

Results

Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F₂ cross-breds.

Conclusion

The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5009-y) contains supplementary material, which is available to authorized users.

Genome data uncover four synergistic key regulators for extremely small body size in horses

Background

Miniature size in horses represents an extreme reduction of withers height that originated after domestication. In some breeds, it is a highly desired trait representing a breed- or subtype-specific feature. The genomic changes that emerged due to strong-targeted selection towards this distinct type remain unclear.

Results

Comparisons of whole-genome sequencing data from two Miniature Shetland ponies and one standard-sized Shetland pony, performed to elucidate genetic determinants for miniature size, revealed four synergistic variants, limiting withers height to 34.25 in. (87 cm). Runs of homozygosity regions were detected spanning these four variants in both the Miniature Shetland ponies and the standard-sized Shetland pony. They were shown to be characteristic of the Shetland pony breed, resulting in a miniature type under specific genotypic combinations. These four genetic variants explained 72% of the size variation among Shetland ponies and related breeds. The length of the homozygous regions indicate that they arose over 1000 years ago. In addition, a copy number variant was identified in DIAPH3 harboring a loss exclusively in ponies and donkeys and thus representing a potential height-associated variant.

Conclusion

This study reveals main drivers for miniature size in horses identified in whole genome data and thus provides relevant candidate genes for extremely short stature in mammals.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4877-5) contains supplementary material, which is available to authorized users.

Determinants of gestation length in Thoroughbred mares on German stud farms

The aim of the present study was to analyze the effects of stallion and mare, their ages, and maternal lineage on the gestation length (GL) in Thoroughbreds. In addition, additive genetic effects of the dam, stallion and fetus were analyzed. Data were taken from 1993 through 2009, and included 16,226 pregnancies from 5959 Th oroughbred mares mated with 290 different stallions. All analyses were performed using linear mixed models. The GL ranged from 306 to 390 days, with a mean length of 347.0 ± 14.4 days. Mating of mares with stallions aged 17 years and older resulted in a significantly longer GL compared to younger stallions. Furthermore, the GL significantly increased with the increasing age of the mares, and the GL was longer with male foals. The month and year of breeding, as well as the mare´s breeding history (parity and reproductive status) also affected GL. The mare and stallion themselves explained 18% and 4% of the variance in GL. Coefficients of inbreeding of mares and foals had no significant effect on GL. The heritability for the GL was 0.17 for the dam and 0.006 for the fetus, whereas an additive genetic paternal effect was not estimable. The relative proportions among the additive genetic and permanent environmental contributions of the dam were 76.5% and 23.5%. A maternal lineage effect was not obvious.

Functional variants in the sucrase-isomaltase gene associate with increased risk of irritable bowel syndrome

OBJECTIVE

IBS is a common gut disorder of uncertain pathogenesis. Among other factors, genetics and certain foods are proposed to contribute. Congenital sucrase-isomaltase deficiency (CSID) is a rare genetic form of disaccharide malabsorption characterised by diarrhoea, abdominal pain and bloating, which are features common to IBS. We tested sucrase-isomaltase (SI) gene variants for their potential relevance in IBS.

DESIGN

We sequenced SI exons in seven familial cases, and screened four CSID mutations (p.Val557Gly, p.Gly1073Asp, p.Arg1124Ter and p.Phe1745Cys) and a common SI coding polymorphism (p.Val15Phe) in a multicentre cohort of 1887 cases and controls. We studied the effect of the 15Val to 15Phe substitution on SI function in vitro. We analysed p.Val15Phe genotype in relation to IBS status, stool frequency and faecal microbiota composition in 250 individuals from the general population.

RESULTS

CSID mutations were more common in patients than asymptomatic controls (p=0.074; OR=1.84) and Exome Aggregation Consortium reference sequenced individuals (p=0.020; OR=1.57). 15Phe was detected in 6/7 sequenced familial cases, and increased IBS risk in case-control and population-based cohorts, with best evidence for diarrhoea phenotypes (combined p=0.00012; OR=1.36). In the population-based sample, 15Phe allele dosage correlated with stool frequency (p=0.026) and Parabacteroides faecal microbiota abundance (p=0.0024). The SI protein with 15Phe exhibited 35% reduced enzymatic activity in vitro compared with 15Val (p<0.05).

CONCLUSIONS

SI gene variants coding for disaccharidases with defective or reduced enzymatic activity predispose to IBS. This may help the identification of individuals at risk, and contribute to personalising treatment options in a subset of patients.

Intersexualität beim Pferd – Pseudohermaphroditismus masculinus bei einer Bayerischen Warmblutstute

Bei einer sechsjährigen Bayerischen Warmblutstute konnte hengstartiges Verhalten beobachtet werden. Das äußere Erscheinungsbild der Geschlechtsorgane wies keine Auffälligkeiten auf. Das innere Genitale bestand aus einer blind endenden Vagina, die über ein strangartiges Gebilde mit intraabdominal liegenden Hoden in Verbindung stand. Der Testosteronwert des Pferdes lag im hengsttypischen Bereich. Durch eine zytogenetische Untersuchung konnte ein XY-Genotyp und mittels einer PCR das geschlechtsdeterminierende SRY-Gen nachgewiesen werden. Anhand dieser Befunde wurde ein Pseudohermaphroditismus masculinus diagnostiziert. Um die reiterliche Nutzung auch weiterhin zu gewährleisten, erfolgte eine bilaterale Gonadektomie via Flankenschnitt von der linken Seite.

Einflussfaktoren auf die Trächtigkeitsrate in der deutschen Vollblutzucht

Ziel der Untersuchungen war, Einflussfaktoren auf die Trächtigkeitsrate in der deutschen Vollblutzucht zu analysieren und insbesondere Maßnahmen zur Optimierung der Fruchtbarkeit des alternden Zuchthengstes herauszustellen. Material und Methoden: Es erfolgte eine Auswertung der Stammdaten und Deckdaten der deutschen Vollblutzucht aus den Jahren 1996–2009. Daten von 319 Deckhengsten, 6622 Zuchtstuten mit insgesamt 21 372 Trächtigkeiten am Ende der Zuchtsaison wurden einbezogen. Ergebnisse: Das Trächtigkeitsergebnis war signifikant beeinflusst durch das Hengst- und Stutenalter und den Monat der Bedeckung. Signifikante Interaktionen des Hengstalters mit der Anzahl gedeckter Stuten pro Decksaison und des Hengstalters mit dem Monat der Bedeckung wurden festgestellt. Sowohl mit zunehmendem Alter der Stuten und Hengste als auch mit fortschreitender Decksaison fällt die Trächtigkeitsrate ab. Alte Hengste (> 16 Jahre) erzielen signifikant höhere Trächtigkeitsraten, wenn sie hohe Belegungszahlen ( 12 Stuten) pro Decksaison erreichen. Im Ablauf der Decksaison sinken die von Hengsten über 16 Jahren erreichten Trächtigkeitsraten besonders deutlich am Ende der Zuchtsaison. Schlussfolgerung und klinische Relevanz: Um bei alten Hengsten hohe Trächtigkeitsraten zu erzielen, sollten die zu deckenden Stuten dem Hengst so früh wie möglich in der Decksaison zugeführt werden und Hengste über 16 Jahre sollten auch mit einer ausreichend hohen Anzahl Stuten in der Zucht eingesetzt werden.

Nierenfunktionsuntersuchungen an Milchkälbern – Referenzwerte und Einfluss der bovinen neonatalen Panzytopenie (BNP)

Gegenstand und Ziel: An 38 klinisch gesunden Holstein-Kälbern im Alter von 14–35 Tagen, darunter sieben Kälber, die eine bovine neonatale Panzytopenie (BNP) überlebt hatten, wurden Nierenfunktionsanalysen durchgeführt. Primäres Ziel war die Etablierung von Referenzwerten für die renale fraktionelle Exkretion (FE) von Natrium (Na), Kalium (K), Kalzium (Ca) und Phosphat (P) bei Kälbern im Alter von unter 5 Wochen, die mit Milchaustauscher getränkt werden. Zusätzlich sollte geklärt werden, ob Kälber im Verlauf einer BNP bleibende Nierenschädigungen davontragen. Material und Methoden: Die FE wurde auf der Basis der Analysen einer simultan gewonnenen Harn- und Blutprobe mit nasschemischen Methoden bestimmt und auf der Grundlage der endogenen Kreatininexkretion berechnet. Ergebnisse: Zwischen gesunden Kälbern und Kälbern, die eine BNP überlebt hatten, ergaben sich keine Unterschiede in den Nierenfunktionsparametern. Auf der Basis der ermittelten Werte aller 38 Kälber wurden Referenzwerte für die oben genannten fraktionellen Exkretionen sowie für die Aktivität der γ-Glutamyl-Transferase (GGT) im Harn in Bezug zur Konzentration von Kreatinin im Harn als Maß für die Schädigung von Tubulusepithelzellen ermittelt. Schlussfolgerungen: Für Nierenfunktionswerte bei Rindern sind alters- und fütterungsspezifische Referenzwerte notwendig. Bei Nierenfunktionsanalysen bei Kälbern muss die Elektrolytversorgung über die Nahrung beachtet werden, um die alimentär bedingte Beeinflussung der Elektrolytexkretion von Nierenfunktionsstörungen unterscheiden zu können. Auf der Basis der erarbeiteten Referenzwerte für Milchkälber lassen sich Nierenfunktionsstörungen sensitiv ermitteln und eventuell weiter differenzieren.

A genome-wide association study for left-sided displacement of the abomasum using a high-density single nucleotide polymorphism array

Left-sided displacement of the abomasum (LDA) is a frequent disease in dairy cattle causing significant financial losses for dairy farmers. Heritability (h²) of this complex disease was estimated at up to 0.5 in German Holstein (GH) cattle. Using the Bovine High Density BeadChip (Illumina Inc., San Diego, CA) comprising 588,753 single nucleotide polymorphisms (SNP) after quality control for 126 LDA cases and 280 population-based controls, we used a mixed linear model analysis in a genome-wide association study (GWAS). We identified 6 genomic regions for LDA on bovine chromosomes 2, 8, 13, 20, 24, and X that were significantly associated with LDA. Each of these regions was covered by 4 to 12 LDA-associated SNP. Single SNP within these regions explained up to 7.3% of the phenotypic variance. An independent sample of 1,554 GH cows, including 539 controls and 1,015 cases, were genotyped for 8 SNP highly associated with LDA on Bos taurus autosomes (BTA) 2, 8, 13, and 24, as well as 6 SNP located in previously identified LDA regions on BTA1, 5, 11, and 27 using competitive allele-specific PCR genotyping technology (KASP). The analysis using the KASP genotypes confirmed LDA-associated loci on BTA2, 8, 13, and 27. These genomic regions may contribute to the susceptibility to LDA in Holstein cows and may harbor functional variants for LDA.

Complex segregation analysis of craniomandibular osteopathy in Deutsch Drahthaar dogs

This study investigated familial relationships among Deutsch Drahthaar dogs with craniomandibular osteopathy and examined the most likely mode of inheritance. Sixteen Deutsch Drahthaar dogs with craniomandibular osteopathy were diagnosed using clinical findings, radiography or computed tomography. All 16 dogs with craniomandibular osteopathy had one common ancestor. Complex segregation analyses rejected models explaining the segregation of craniomandibular osteopathy through random environmental variation, monogenic inheritance or an additive sex effect. Polygenic and mixed major gene models sufficiently explained the segregation of craniomandibular osteopathy in the pedigree analysis and offered the most likely hypotheses. The SLC37A2:c.1332C>T variant was not found in a sample of Deutsch Drahthaar dogs with craniomandibular osteopathy, nor in healthy controls. Craniomandibular osteopathy is an inherited condition in Deutsch Drahthaar dogs and the inheritance seems to be more complex than a simple Mendelian model.

Effects of inbreeding and other systematic effects on fertility of Black Forest Draught horses in Germany

Background

The Black Forest Draught horse (BFDH) is an endangered German coldblood breed with its origin in the area of the Black Forest in South Germany. In this retrospective study, the influence of the inbreeding coefficient on foaling rates was investigated using records from ten breeding seasons. Due to the small population size of BFDH, the level of inbreeding is increasing and may have an effect on foaling rates.The data of the present study included all coverings reported for 1024 BFDH mares in the years 2001–2009. These mares were covered by 32 BFDH stallions from the State Stud Marbach. Data from 4534 estrus cycles was used to calculate per cycle foaling rate (CFR). Pedigree data contained all studbook data up to the foundation of the breed as early as 1836. The level of inbreeding of the mare, stallion and expected foal along with other systematic effects on CFR were analysed using a generalized linear mixed model approach. Stallion was employed as a random effect. Systematic fixed effects were month of mating, mating type, age of the mare and stallion, reproductive status of the mare and stallion line of the mare. Inbreeding coefficients of the stallion, mare and expected foal were modelled as linear covariates.

Results

The average CFR was 40.9%. The mean inbreeding coefficients of the mares, stallions and expected foals were 7.46, 7.70 and 9.66%. Mating type, age of the mare, reproductive status of the mare and stallion line of the mare had a significant effect.

Conclusions

The results showed that the mating type, stallion line of the mare, sire, age and reproductive status of the mare exerted the largest influences on CFR in BFDH. Inbreeding coefficients of the stallion, mare and expected foal were not significantly related with CFR.

Electronic supplementary material

The online version of this article (doi:10.1186/s13028-017-0338-4) contains supplementary material, which is available to authorized users.