The Estimation of Genetic Parameters for Chronic Progressive Lymphedema and Body Traits in the Rhenish German Draught Horse

Chronic progressive lymphedema (CPL) is a prevalent and progressive disease in Rhenish German draught horses. The objective of our follow-up study was to evaluate the heritability of this disease in Rhenish German draught horses using pedigree-based and genomic relationship matrices. We employed linear and threshold animal models. Models included the random animal effect and effects of breeding association, coat colour, sex, and age within sex, and farm-related factors, on CPL scores. In addition, we estimated heritabilities in models assuming censoring for data when horses were below an age of 1-15 years. The heritabilities of CPL scores across all ages were 0.595 ± 0.131 and 0.482 ± 0.105 in the threshold and linear animal model with pedigree-based relationship matrices, respectively. The restriction of data to horses with a minimum age at examination or accounting for censored data in younger animals showed an increase in heritabilities of CPL scores up to 0.788 ± 0.168 (threshold model) and 0.752 ± 0.153 (linear model) at an age of 7-8 years. Analyses including genomic relationship matrices yielded very similar estimates, but with smaller standard errors than pedigree-based analyses. Heritabilities in threshold models for CPL prevalence (CPL-bin-score) and the number of affected limbs (CPL-bin-sum) were 0.176-0.189 ± 0.061-0.064 and 0.375-0.433 ± 0.164-0.170, respectively. We were able to show moderately to highly positive genetic correlations between the CPL score and cannon bone circumference (0.529-0.825), height at withers (0.338-0.555), and skinfold thickness (0.241-0.517). Using the dichotomous trait for the CPL score and the genomic relationship matrix resulted in corresponding estimates of 0.868, 0.793, and 0.784, respectively. This study showed the great importance of additive genetic variation influencing the expression of chronic progressive lymphedema in Rhenish German draught horses. Therefore, further research is warranted to implement breeding programmes in a small breeding population that exploit the potential of additive genetic differences among animals for reducing the prevalence and severity of lesions of this incurable disease.

Genotyping KIF1C (c.608G>A) Mutant Reveals a Wide Distribution of Progressive Ataxia in German Charolais Cattle

Bovine progressive ataxia in Charolais cattle was first described in the 1970s; then, cases were reported in Charolais worldwide. A homozygous loss-of-function mutation within the KIF1C gene (c.608G>A) was found to be responsible for this neurodegenerative disease. The aim of this study was to determine whether the mutated KIF1C allele segregates in the German Charolais population and whether the estimated breeding values for growth and muscle conformation are associated with the mutated genotypes. Genetic test results of the KIF1C:c.608G>A variant were available for 1315 Charolais cattle from 35 herds located in Germany. In addition, 324 samples from eight other beef cattle breeds were tested for the mutated KIF1C allele. We were able to demonstrate that the KIF1C mutation is common, with a frequency of 11.75% in the German Charolais population. All but two of the eight (2/8 = 25%) homozygous mutated individuals showed clinical signs consistent with progressive ataxia. The estimated breeding values of muscle conformation in 200- and 365-day-old animals indicated a significant superiority for homozygous mutated animals when compared either with heterozygous or homozygous wild-type genotypes; this was also the case for heterozygous genotypes in comparison with homozygous wild-type genotypes. For the estimated breeding values of daily weight gain in 200- and 365-day-old animals, the significant differences between homozygous mutated and heterozygous or wild-type genotypes were in favour of the homozygous mutant animals. There were no differences in the estimated maternal breeding values among all three KIF1C genotypes. For the first time, two German Angus cattle carrying the KIF1C mutation heterozygous were detected. The breeders' survey highlighted that increased awareness would facilitate increased conviction among breeders of the need for genetic testing in order to eliminate the lethal KIF1C allele.

A Missense Mutation in the Collagen Triple Helix of EDA Is Associated with X-Linked Recessive Hypohidrotic Ectodermal Dysplasia in Fleckvieh Cattle

Mutations within the ectodysplasin A (EDA) gene have been associated with congenital hypotrichosis and anodontia (HAD/XHED) in humans, mice, dogs and cattle. We identified a three-generation family of Fleckvieh cattle with male calves exhibiting clinical and histopathological signs consistent with an X-linked recessive HAD (XHED). Whole genome and Sanger sequencing of cDNA showed a perfect association of the missense mutation g.85716041G>A (ss2019497443, rs1114816375) within the EDA gene with all three cases following an X-linked recessive inheritance, but normal EDAR and EDARADD. This mutation causes an exchange of glycine (G) with arginine (R) at amino acid position 227 (p.227G>R) in the second collagen triple helix repeat domain of EDA. The EDA variant was associated with a significant reduction and underdevelopment of hair follicles along with a reduced outgrowth of hairs, a complete loss of seromucous nasolabial and mucous tracheal and bronchial glands and a malformation of and reduction in number of teeth. Thermostability of EDA G227R was reduced, consistent with a relatively mild hair and tooth phenotype. However, incisors and canines were more severely affected in one of the calves, which correlated with the presence of a homozygous missense mutation of RNF111 (g.51306765T>G), a putative candidate gene possibly associated with tooth number in EDA-deficient Fleckvieh calves.

Single Nucleotide Polymorphisms Associated with AA-Amyloidosis in Siamese and Oriental Shorthair Cats

AA-amyloidosis in Siamese and Oriental shorthair cats is a lethal condition in which amyloid deposits accumulate systemically, especially in the liver and the thyroid gland. The age at death of affected cats varies between one and seven years. A previous study indicated a complex mode of inheritance involving a major locus. In the present study, we performed a multi-locus genome-wide association study (GWAS) using five methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB and ISIS EM-BLASSO) to identify variants associated with AA-amyloidosis in Siamese/Oriental cats. We genotyped 20 affected mixed Siamese/Oriental cats from a cattery and 48 healthy controls from the same breeds using the Illumina Infinium Feline 63 K iSelect DNA array. The multi-locus GWAS revealed eight significantly associated single nucleotide polymorphisms (SNPs) on FCA A1, D1, D2 and D3. The genomic regions harboring these SNPs contain 55 genes, of which 3 are associated with amyloidosis in humans or mice. One of these genes is SAA1, which encodes for a member of the Serum Amyloid A family, the precursor protein of Amyloid A, and a mutation in the promotor of this gene causes hereditary AA-amyloidosis in humans. These results provide novel knowledge regarding the complex genetic background of hereditary AA-amyloidosis in Siamese/Oriental cats and, therefore, contribute to future genomic studies of this disease in cats.

Inbreeding Depression and Purging for Meat Performance Traits in German Sheep Breeds

This study provides estimates on genetic parameters, inbreeding depression and purging for meat performance measures from 25 German sheep breeds. All German meat, merino sheep breeds and breeds of other breeding directions with a sufficient number of pedigree and performance data were included in this study. Phenotypic traits retrieved from the national database OviCap were evaluated: daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness. We employed animal models to estimate heritability, variance and covariance components for these meat performance traits as well as inbreeding depression and purging. The heritabilities, on average, reached estimates of 0.55, 0.34, 0.53 and 0.61 for daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness, respectively. We estimated the linear regression slopes for the individual rate of inbreeding, new and ancestral inbreeding, as well as the inbreeding coefficient and its interaction with the inbreeding coefficient of Ballou, employing animal models with non-genetic effects and the additive genetic effect of the animal. Across all breeds, inbreeding was only significant for daily weight gain, whereas for all other traits, estimates were not significant. Within sheep breeds, we found significant inbreeding depression for daily weight gain in German Mutton Merino and German Blackheaded Mutton as well as for the meatiness score in German Whiteheaded Mutton. Significant effects for purging, based on ancestral inbreeding and the interaction effect of the classical inbreeding coefficient with the inbreeding coefficient of Ballou, were not obvious either across or within any sheep breed. A 1% increase in inbreeding significantly decreased the phenotypic trait median of daily weight gain across all sheep breeds by 0.50% and 0.70% of phenotypic and genetic standard deviation, respectively. Purging effects due to ancestral inbreeding were not significant in any breed or across breeds. The results of this study may indicate that inbreeding depression may be more harmful in traits under stronger selection than in traits that exert low selection pressure. The results of this study demonstrate the different effects that result in meat performance traits due to inbreeding. With increasing rates of inbreeding and critical effective population sizes, selection intensity for breeding objectives has to be critically reviewed for each sheep breed. Inbreeding depression and purging should be evaluated in order to prevent a decrease in trait means due to inbreeding and to determine whether detrimental alleles are eliminated.

Historic Horse Family Displaying Malformations of the Cervicothoracic Junction and Their Connection to Modern German Warmblood Horses

Malformations of the equine cervicothoracic junction affect the C6 and C7 cervical vertebrae, the T1 thoracic vertebra and in variable extent the first and second sternal ribs. To date, the clinical impact of this malformation, its prevalence and mode of inheritance in equine populations are not yet determined. We examined five skeletons for signs of malformation of the cervicothoracic junction, including three skeletons from widely used Thoroughbred stallions affected with the malformation and two skeletons serving as a comparison. The three affected historical horses were the Thoroughbred stallions Der Loewe XX, Birkhahn XX and their common great grandsire Dark Ronald XX. Malformations of C6 and C7 showed a large variation between the three stallions, as Dark Ronald XX, Der Loewe XX and Birkhahn XX were affected uni-laterally at C6 and C7, uni-laterally at C6 and bi-laterally at C6 and C7, respectively, with varying grades. In order to evaluate whether or not these malformations are incidental, we took a random sample of 20 living German Warmblood horses, which are distant descendants of these stallions. This sample consisted of ten controls and ten horses with malformations of C6/C7. Blood proportions of the historical sires in the modern Warmblood horses ranged from 0.10 to 6.25%. The contribution to inbreeding in each individual horse of our selected horse group by those sires was expressed as a percentage of the total inbreeding coefficient and ranged from 0.01 to 17.96%, demonstrating their influence on the modern Warmblood. In the present study, we were able to describe the variability of the malformation of C6/C7 within a horse family including historic and modern horses. Additionally, we detected variations appearing in connection with malformations of the cervicothoracic junction that have not been described in the literature yet. This is the first time that the malformations of C6 and C7 have been described within a familial context, providing hints on inheritance in Thoroughbreds and Warmbloods. It is worthwhile to carry out further studies in a larger setting to gain more comprehensive insights into the inheritance of the malformation and the role of important ancestors.

Effect of Individual Rate of Inbreeding, Recent and Ancestral Inbreeding on Wool Quality, Muscling Conformation and Exterior in German Sheep Breeds

This study provides comprehensive results on the current status of inbreeding depression for traits upon which sheep are selected for the herdbook in Germany. A total of 30 sheep breeds from the OviCap national database met the inclusion criteria for the present analysis regarding the depth and completeness of pedigrees and the number of animals with phenotypic data. We analyzed heritabilities and inbreeding depression for the three breeding objective traits of wool quality, muscling conformation and exterior. Heritabilities were across all breeds of moderate size, with estimates of 0.18 for wool quality and muscling conformation and of 0.14 for exterior. The models employed to estimate linear regression slopes for individual and ancestral inbreeding rates also account for non-genetic effects and the additive genetic effect of the animal. Inbreeding depression was obvious for all three traits when we averaged the estimates across all 30 sheep breeds. Inbreeding depression was significant for wool quality for only a few breeds, whereas for muscling conformation, 14/30 breeds achieved significant estimates. A 1% increase in inbreeding decreased the mean of all three traits across all sheep breeds by 0.33% of their standard deviation. Positive effects due to ancestral inbreeding were only significant in very few breeds in the different traits. Across all 30 sheep breeds, there were indications that purging effects (a reduction in negative effects of inbreeding depression due to selection for heterozygotes) may play a role for the exterior. The results of this study should help for reviewing breeding programs, particularly for sheep breeds with critical effective population sizes and increasing rates of inbreeding, with regard to the selection policy and selection intensity applied.

Impact of Inbreeding and Ancestral Inbreeding on Longevity Traits in German Brown Cows

A recent study on the population structure of the German Brown population found increasing levels of classical and ancestral inbreeding coefficients. Thus, the aim of this study was to determine the effects of inbreeding depression and purging on longevity traits using classical and ancestral inbreeding coefficients according to Kalinowski (2002) (Fa_Kal, FNew), Ballou (1997) (Fa_Bal), and Baumung (2015) (Ahc). For this purpose, uncensored data of 480,440 cows born between 1990 and 2001 were available. We analyzed 17 longevity traits, including herd life, length of productive life, number of calvings, lifetime and effective lifetime production for milk, fat, and protein yield, the survival to the 2nd, 4th, 6th, 8th, and 10th lactation number, and the culling frequencies due to infertility, or udder and foot and leg problems. Inbreeding depression was significant and negative for all traits but for culling due to udder and to foot and leg problems. When expressed in percentages of genetic standard deviations, inbreeding depression per 1% increase in inbreeding was -3.61 to -10.98%, -2.42 to -2.99%, -2.21 to -4.58%, and 5.13% for lifetime production traits, lifetime traits, survival rates, and culling due to infertility, respectively. Heterosis and recombination effects due to US Brown Swiss genes were positive and counteracted inbreeding depression. The effects of FNew were not significantly different from zero, while Fa_Kal had negative effects on lifetime and lifetime production traits. Similarly, the interaction of F with Fa_Bal was significantly negative. Thus, purging effects could not be shown for longevity traits in German Brown. A possible explanation may be seen in the breed history of the German Brown, that through the introgression of US Brown Swiss bulls ancestral inbreeding increased and longevity decreased. Our results show, that reducing a further increase in inbreeding in mating plans is advisable to prevent a further decline in longevity due to inbreeding depression, as purging effects were very unlikely in this population.

SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses

Before the genomics era, heritability estimates were performed using pedigree data. Data collection for pedigree analysis is time consuming and holds the risk of incorrect or incomplete data. With the availability of SNP-based arrays, heritability can now be estimated based on genotyping data. We used SNP array and 1.6 million imputed genotype data with different minor allele frequency restrictions to estimate heritabilities for osteochondrosis dissecans in the fetlock, hock and stifle joints of 446 Hanoverian warmblood horses. SNP-based heritabilities were estimated using a genomic restricted maximum likelihood (GREML) method and accounting for patterns of regional linkage disequilibrium in the equine genome. In addition, we employed GREML for family data to account for different degrees of relatedness in the study population. Our results indicate that we were able to capture a larger proportion of additive genetic variance compared to pedigree-based estimates in the same population of Hanoverian horses. Heritability estimates on the linear scale for fetlock-, hock- and stifle-osteochondrosis dissecans were 0.41-0.43, 0.62-0.63, and 0.23-0.25, respectively, with standard errors of 0.11-0.14. Accounting for linkage disequilibrium patterns had an upward effect on the imputed data and a downward impact on the SNP array genotype data. GREML for family data resulted in higher heritability estimates for fetlock-osteochondrosis dissecans and slightly higher estimates for hock-osteochondrosis dissecans, but had no effect on stifle-osteochondrosis dissecans. The largest and most consistent heritability estimates were obtained when we employed GREML for family data with genomic relationship matrices weighted through patterns of regional linkage disequilibrium. Estimation of SNP-based heritability should be recommended for traits that can only be phenotyped in smaller samples or are cost-effective.

Prevalence of Chronic Progressive Lymphedema in the Rhenish German Draught Horse

Chronic progressive lymphedema (CPL) is a common disease in Rhenisch German draught horses. The objective of our study was to evaluate the prevalence of this disease and its progression with age in 493 Rhenish German draught horses from different regions in Germany. We employed generalized linear models with binomial, multinomial, and normal distributions to analyse the effects of breeding association, coat colour, sex and age within sex, time of examination, limb on which CPL was recorded, and farm-related factors on disease scores. The occurrence and severity of CPL were significantly influenced by breeding area, sex, coat colour, and interaction of age by sex. Males had significantly higher CPL-scores than geldings (1.92-fold) and females (5.02-fold) as well as a faster (1.85-fold) disease progression per year of life than females (1.44-fold) and geldings (1.25-fold). Regression on age within sex was still significant when age was restricted to a minimum of 7 years in the analysis. Bay horses exhibited 1.77-fold and 2.19-fold higher CPL-scores than chestnut and black horses. Keeping horses on pasture and keeping bedding clean reduced CPL-scores, whereas feeding of hay silage and concentrates during winter increased CPL-scores. Our analysis revealed significant regression coefficients of cannon bone circumference on CPL-scores. Relationships with hoof measures and skinfold diameter at the neck were not found. In conclusion, differences among breeding districts and sexes by age had the largest impact on CPL prevalence and scores. Disease progression was evident up to a mean age of 16 years in males and 20 years in females. The identification of risk factors and their effects on CPL should help to reduce the occurrence and progression of CPL.

Tracking footprints of artificial and natural selection signatures in breeding and non-breeding cats

Stray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for aesthetic traits. Runs of homozygosity (ROH) and demographic measures are useful tools to discover chromosomal regions of recent selection and to characterize genetic diversity in domestic cat populations. To achieve this, we genotyped 150 stray and 26 household non-breeding cats (household) on the Illumina feline 63 K SNP BeadChip and compared them to SIAM and OSH. The 50% decay value of squared correlation coefficients (r²) in stray (0.23), household (0.25), OSH (0.24) and SIAM (0.25) corresponded to a mean marker distance of 1.12 Kb, 4.55 Kb, 62.50 Kb and 175.07 Kb, respectively. The effective population size (N_e) decreased in the current generation to 55 in stray, 11 in household, 9 in OSH and 7 in SIAM. In the recent generation, the increase in inbreeding per generation (ΔF) reached its maximum values of 0.0090, 0.0443, 0.0561 and 0.0710 in stray, household, OSH and SIAM, respectively. The genomic inbreeding coefficient (F_ROH) based on ROH was calculated for three length categories. The F_ROH was between 0.014 (F_ROH60) and 0.020 (F_ROH5) for stray, between 0.018 (F_ROH60) and 0.024 (F_ROH5) for household, between 0.048 (F_ROH60) and 0.069 (F_ROH5) for OSH and between 0.053 (F_ROH60) and 0.073 (F_ROH5) for SIAM. We identified nine unique selective regions for stray through genome-wide analyses for regions with reduced heterozygosity based on F_ST statistics. Genes in these regions have previously been associated with reproduction (BUB1B), motor/neurological behavior (GPHN, GABRB3), cold-induced thermogenesis (DIO2, TSHR), immune system development (TSHR), viral carcinogenesis (GTF2A1), host immune response against bacteria, viruses, chemoattractant and cancer cells (PLCB2, BAHD1, TIGAR), and lifespan and aging (BUB1B, FGF23). In addition, we identified twelve unique selective regions for OSH containing candidate genes for a wide range of coat colors and patterns (ADAMTS20, KITLG, TYR, TYRO3-a MITF regulator, GPNMB, FGF7, RAB38) as well as congenital heart defects (PDE4D, PKP2) and gastrointestinal disorders (NLGN1, ALDH1B1). Genes in stray that represent unique selective events indicate, at least in part, natural selection for environmental adaptation and resistance to infectious disease, and should be the subject of future research. Stray cats represent an important genetic resource and have the potential to become a research model for disease resistance and longevity, which is why we recommend preserving semen before neutering.

A comparison of strategies for generating artificial replicates in RNA-seq experiments

Due to the overall high costs, technical replicates are usually omitted in RNA-seq experiments, but several methods exist to generate them artificially. Bootstrapping reads from FASTQ-files has recently been used in the context of other NGS analyses and can be used to generate artificial technical replicates. Bootstrapping samples from the columns of the expression matrix has already been used for DNA microarray data and generates a new artificial replicate of the whole experiment. Mixing data of individual samples has been used for data augmentation in machine learning. The aim of this comparison is to evaluate which of these strategies are best suited to study the reproducibility of differential expression and gene-set enrichment analysis in an RNA-seq experiment. To study the approaches under controlled conditions, we performed a new RNA-seq experiment on gene expression changes upon virus infection compared to untreated control samples. In order to compare the approaches for artificial replicates, each of the samples was sequenced twice, i.e. as true technical replicates, and differential expression analysis and GO term enrichment analysis was conducted separately for the two resulting data sets. Although we observed a high correlation between the results from the two replicates, there are still many genes and GO terms that would be selected from one replicate but not from the other. Cluster analyses showed that artificial replicates generated by bootstrapping reads produce it p values and fold changes that are close to those obtained from the true data sets. Results generated from artificial replicates with the approaches of column bootstrap or mixing observations were less similar to the results from the true replicates. Furthermore, the overlap of results among replicates generated by column bootstrap or mixing observations was much stronger than among the true replicates. Artificial technical replicates generated by bootstrapping sequencing reads from FASTQ-files are better suited to study the reproducibility of results from differential expression and GO term enrichment analysis in RNA-seq experiments than column bootstrap or mixing observations. However, FASTQ-bootstrapping is computationally more expensive than the other two approaches. The FASTQ-bootstrapping may be applicable to other applications of high-throughput sequencing.

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

Simple Summary

Deutsch Drahthaar (DD) is the most popular hunting dog in Germany, fulfilling all aspects of hunting including searching for trails. This breed was newly created at the beginning of the 20th century from a large number existing versatile hunting dog breeds. The aim of the breed was, and still is, to achieve the best performance in all aspects of hunting. We analyzed pedigrees of DD using demographic measures to quantify genetic diversity such as probabilities of gene origin and degrees of ancestral and individual inbreeding. A large number of genetically diverse founder dogs should open up the opportunity of creating a breed with a high genetic diversity and a low increase of inbreeding per generation. On the other hand, intense use of top sires and dams from a limited number of breeding lines may accelerate breeding progress in hunting abilities but reduce genetic diversity. Monitoring genetic diversity should help to maintain a high diversity of breeding populations. Our analysis of pedigree data from 101,887 DD dogs revealed inbreeding measures (coefficient of inbreeding F = 0.042, individual rate of inbreeding ΔF_i = 0.00551) and effective population size (Ne = 92) in the mean range compared to a wide range of other dog breeds. Ancestral inbreeding had a strong increasing trend, whereas trends in individual inbreeding and rate of individual inbreeding were slightly negative.

Abstract

Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔF_i) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔF_i. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.

AA-amyloidosis in captive northern tree shrews (Tupaia belangeri)

A high prevalence of AA-amyloidosis was identified in a breeding colony of northern tree shrews (Tupaia belangeri) in a retrospective analysis, with amyloid deposits in different organs being found in 26/36 individuals (72%). Amyloid deposits, confirmed by Congo red staining, were detected in kidneys, intestines, skin, and lymph nodes, characteristic of systemic amyloidosis. Immunohistochemically, the deposited amyloid was intensely positive with anti-AA-antibody (clone mc4), suggesting AA-amyloidosis. The kidneys were predominantly affected (80%), where amyloid deposits ranged from mild to severe and was predominantly located in the renal medulla. In addition, many kidneys contained numerous cysts with atrophy of the renal parenchyma. There was no significant association between concurrent neoplastic or inflammatory processes and amyloidosis. The lack of distinctive predisposing factors suggests a general susceptibility of captive T. belangeri to develop amyloidosis. Clinical and laboratory findings of a female individual with pronounced kidney alterations were indicative of renal failure. The observed tissue tropism with pronounced kidney alterations, corresponding renal dysfunction, and an overall high prevalence suggests amyloidosis as an important disease in captive tree shrews.

An FGA Frameshift Variant Associated with Afibrinogenemia in Dachshunds

Congenital fibrinogen disorders are very rare in dogs. Cases of afibrinogenemia have been reported in Bernese Mountain, Bichon Frise, Cocker Spaniel, Collie, Lhasa Apso, Viszla, and St. Bernard dogs. In the present study, we examined four miniature wire-haired Dachshunds with afibrinogenemia and ascertained their pedigree. Homozygosity mapping and a genome-wide association study identified a candidate genomic region at 50,188,932–64,187,680 bp on CFA15 harboring FGB (fibrinogen beta chain), FGA (fibrinogen alpha chain), and FGG (fibrinogen gamma-B chain). Sanger sequencing of all three fibrinogen genes in two cases and validation of the FGA-associated mutation (FGA:g.6296delT, NC_006597.3:g.52240694delA, rs1152388481) in pedigree members showed a perfect co-segregation with afibrinogenemia-affected phenotypes, obligate carriers, and healthy animals. In addition, the rs1152388481 variant was validated in 393 Dachshunds and samples from 33 other dog breeds. The rs1152388481 variant is predicted to modify the protein sequence of both FGA transcripts (FGA201:p.Ile486Met and FGA-202:p.Ile555Met) leading to proteins truncated by 306 amino acids. The present data provide evidence for a novel FGA truncating frameshift mutation that is very likely to explain the cases of severe bleeding due to afibrinogenemia in a Dachshund family. This mutation has already been spread in Dachshunds through carriers before cases were ascertained. Genetic testing allows selective breeding to prevent afibrinogenemia-affected puppies in the future.

De novo ZIC2 frameshift variant associated with frontonasal dysplasia in a Limousin calf

Background

Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examinations and whole genome sequencing on an Illumina NextSeq500 were performed to characterize a stillborn Limousin calf with frontonasal dysplasia. In order to identify private genetic and structural variants, we screened whole genome sequencing data of the affected calf and unaffected relatives including parents, a maternal and paternal halfsibling.

Results

The stillborn calf exhibited severe craniofacial malformations. Nose and maxilla were absent, mandibles were upwardly curved and a median cleft palate was evident. Eyes, optic nerve and orbital cavities were not developed and the rudimentary orbita showed hypotelorism. A defect centrally in the front skull covered with a membrane extended into the intracranial cavity. Aprosencephaly affected telencephalic and diencephalic structures and cerebellum. In addition, a shortened tail was seen. Filtering whole genome sequencing data revealed a private frameshift variant within the candidate gene ZIC2 in the affected calf. This variant was heterozygous mutant in this case and homozygous wild type in parents, half-siblings and controls.

Conclusions

We found a novel ZIC2 frameshift mutation in an aprosencephalic Limousin calf. The origin of this variant is most likely due to a de novo mutation in the germline of one parent or during very early embryonic development. To the authors’ best knowledge, this is the first identified mutation in cattle associated with bovine frontonasal dysplasia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07350-y.

Urogenital Hypoplasia and X Chromosome Monosomy in a Draft Horse Filly

A 5-month-old draft horse filly was presented with incontinence and severe perivulvar dermatitis, which developed during the previous 2 months. Left-sided ectopic ureter entering in the caudal vaginal lumen, signs of cervix hypoplasia, and urine accumulation in the uterus were found during initial vaginal endoscopy. Therefore, a left ureter-nephrectomy was conducted under general anesthesia. Additionally, a cytogenetic examination was performed, which showed a XO monosomy with a 63,X/64,XX mosaic. This is the first case report presenting a chromosome abnormality in a draft horse filly combined with a left-sided ectopic ureter. Cytogenetic evaluation is recommended in any female horse with developmental abnormalities of the cervix, uterus, ovaries, or with irregularities of estrus.

BAFF 60-mer, and Differential BAFF 60-mer Dissociating Activities in Human Serum, Cord Blood and Cerebrospinal Fluid

B cell activation factor of the TNF family (BAFF/BLyS), an essential B cell survival factor of which circulating levels are elevated in several autoimmune disorders, is targeted in the clinic for the treatment of systemic lupus erythematosus (SLE). The soluble form of BAFF can exist as 3-mer, or as 60-mer that results from the ordered assembly of twenty 3-mers and that can be obtained from naturally cleaved membrane-bound BAFF or made as a recombinant protein. However, which forms of soluble BAFF exist and act in humans is unclear. In this study, BAFF 3-mer and 60-mer in biological fluids were characterized for size, activity and response to specific stimulators or inhibitors of BAFF. Human cerebrospinal fluids (CSF) from patients with multiple sclerosis and adult human sera contained exclusively BAFF 3-mer in these assays, also when BAFF concentrations were moderately SLE or highly (BAFFR-deficient individual) increased. Human sera, but not CSF, contained a high molecular weight, saturable activity that dissociated preformed recombinant BAFF 60-mer into 3-mer. This activity was lower in cord blood. Cord blood displayed BAFF levels 10-fold higher than in adults and consistently contained a fair proportion of active high molecular weight BAFF able to dissociate into 3-mer but not endowed with all properties of recombinant BAFF 60-mer. If BAFF 60-mer is produced in humans, it is dissociated, or at least attenuated in the circulation.

Complex segregation analysis of familial amyloidosis in Oriental shorthair cats

Amyloidosis in Siamese/Oriental cats is a lethal condition with variable age of clinical onset. There is no sex predisposition and clinical signs of disease usually become apparent by 1-7 years of age. In the terminal stages, the liver is enlarged and pale, and contains parenchymal hemorrhages. In the present study, pedigree data from 17 cats with clinical signs consistent with amyloidosis underwent genetic analysis. Necropsy and histopathological data were available for 10 of the 17 cats. Necropsy findings included pale, fragile and enlarged livers with capsular ruptures and parenchymal hemorrhages, and sanguineous effusions in the abdominal cavity. Congo red staining with birefringence confirmed systemic amyloidosis mostly involving the liver and thyroid gland. In four of the 10 cases, protein deposits were classified as amyloid A protein (AA-amyloid) by immunostaining. Pedigree data for all 17 affected cats indicated a familial trait. Animal threshold model analysis demonstrated that the heritability for amyloidosis was 0.56 ± 0.09 (standard error). Complex segregation analysis was used for statistical comparisons among models to determine environmental or sex dependent effects, and Mendelian, polygenic, or mixed Mendelian and polygenic inheritance patterns. A mixed model with a Mendelian and polygenic component provided the best fit to the data and thus was most likely. All other models of inheritance were rejected due to their insufficient ability to explain segregation of amyloidosis. In conclusion, we found evidence for a complex genetic basis for amyloidosis in Oriental shorthair cats.

A structural UGDH variant associated with standard Munchkin cats

Background

Munchkin cats were founded on a naturally occurring mutation segregating into long-legged and short-legged types. Short-legged cats showed disproportionate dwarfism (chondrodysplasia) in which all four legs are short and are referred as standard Munchkin cats. Long-legged animals are referred as non-standard Munchkin cats. A previous study using genome-wide single nucleotide polymorphisms (SNPs) for genome-wide association analysis identified a significantly associated region at 168–184 Mb on feline chromosome (FCA) B1.

Results

In this study, we validated the critical region on FCA B1 using a case-control study with 89 cats and 14 FCA B1-SNPs. A structural variant within UGDH (NC_018726.2:g.173294289_173297592delins108, Felis catus 8.0, equivalent to NC_018726.3:g.174882895_174886198delins108, Felis catus 9.0) on FCA B1 was perfectly associated with the phenotype of short-legged standard Munchkin cats.

Conclusion

This UGDH structural variant very likely causes the chondrodysplastic (standard) phenotype in Munchkin cats. The lack of homozygous mutant phenotypes and reduced litter sizes in standard Munchkin cats suggest an autosomal recessive lethal trait in the homozygote state. We propose an autosomal dominant mode of inheritance for the chondrodysplastic condition in Munchkin cats.

Genetics of Equine Orthopedic Disease

Orthopedic diseases are a common cause for limited exercise capacity in the horse. They often underlie genetic risk factors, which can affect bone, articular cartilage, tendons, ligaments, and adnexal structures among others. The genetic effects can directly interfere with tissue development and skeletal growth or can trigger degenerative or inflammatory processes. Many of these diseases of the locomotor system like osteochondrosis are complex and can be affected by multifactorial influences. For this reason, it is important for those performing diagnostic procedures to have a comprehensive knowledge of orthopedic diseases, their prevalence within breeds, and genetic background.

Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy

Kinesin-2 enables ciliary assembly and maintenance as an anterograde intraflagellar transport (IFT) motor. Molecular motor activity is driven by a heterotrimeric complex comprised of KIF3A and KIF3B or KIF3C plus one non-motor subunit, KIFAP3. Using exome sequencing, we identified heterozygous KIF3B variants in two unrelated families with hallmark ciliopathy phenotypes. In the first family, the proband presents with hepatic fibrosis, retinitis pigmentosa, and postaxial polydactyly; he harbors a de novo c.748G>C (p.Glu250Gln) variant affecting the kinesin motor domain encoded by KIF3B. The second family is a six-generation pedigree affected predominantly by retinitis pigmentosa. Affected individuals carry a heterozygous c.1568T>C (p.Leu523Pro) KIF3B variant segregating in an autosomal-dominant pattern. We observed a significant increase in primary cilia length in vitro in the context of either of the two mutations while variant KIF3B proteins retained stability indistinguishable from wild type. Furthermore, we tested the effects of KIF3B mutant mRNA expression in the developing zebrafish retina. In the presence of either missense variant, rhodopsin was sequestered to the photoreceptor rod inner segment layer with a concomitant increase in photoreceptor cilia length. Notably, impaired rhodopsin trafficking is also characteristic of recessive KIF3B models as exemplified by an early-onset, autosomal-recessive, progressive retinal degeneration in Bengal cats; we identified a c.1000G>A (p.Ala334Thr) KIF3B variant by genome-wide association study and whole-genome sequencing. Together, our genetic, cell-based, and in vivo modeling data delineate an autosomal-dominant syndromic retinal ciliopathy in humans and suggest that multiple KIF3B pathomechanisms can impair kinesin-driven ciliary transport in the photoreceptor.

Hanoverian F/W-line contributes to segregation of Warmblood fragile foal syndrome type 1 variant PLOD1:c.2032G>A in Warmblood horses

BACKGROUND

Warmblood fragile foal syndrome (WFFS) is a lethal condition detected in Warmblood horses. Its origin and association with performance traits and fertility among horse populations is unknown.

OBJECTIVES

To validate the previously identified WFFS type 1 (WFFST1)-associated missense variant PLOD1:c.2032G>A and to investigate its distribution among various horses with particular focus on Hanoverian breed, as well as its pathomorphological picture. The study aimed at identifying the origin of the mutant allele and its correlation with performance and fertility traits in Warmblood horses.

STUDY DESIGN

Retrospective case-control and association study.

METHODS

WFFST1 variant was validated using whole genome sequencing (WGS) in 78 equids. In an affected foal with a homozygous mutant genotype, necropsy was performed. Skin samples were examined using histology and transmission electron microscopy. Pathway analysis was performed to trace back 81 genetic carriers to the most common recent ancestor. Furthermore, generalised linear model analysis was employed to test estimated breeding values (EBVs) for differences in performance and fertility traits among different genotypes in Hanoverian horses.

RESULTS

WFFST1 variant had the lowest minor allele frequency among all variants detected in WGS data in the region of PLOD1. Further genotyping of this variant revealed allele frequencies of 0.14 in Hanoverian horses. Histological investigations of the WFFST1-affected foal showed loosely arranged collagen fibres in the dermis. Ultrastructurally, multifocal areas with degraded collagen fibrils and fibrillar plaques were detected. Further pathway analysis revealed a stallion from the Hanoverian sire F/W line as the most common recent ancestor of all tested genetic carriers. Furthermore, WFFST1 variant was found to be correlated with EBVs for gait-related traits as well as conformation and dressage.

MAIN LIMITATIONS

Study evaluated carriers and cases only from Europe.

CONCLUSIONS

This study provides a comprehensive evaluation of WFFST1 variant and traces it back to its potential origin.

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.