A de novo germline mutation of KIT in a white-spotted Brown Swiss cow.

White-spotting coat colour phenotypes in cattle are either fixed characteristics of specific cattle breeds or occur sporadically owing to germline genetic variation of solid-coloured parents. A Brown Swiss cow showing a piebald pattern resembling colour-sidedness was referred for genetic evaluation. Both parents were normal solid-brown-coloured cattle. The cow was tested negative for the three known DNA variants in KIT, MITF and TWIST2 associated with different depigmentation phenotypes in Brown Swiss cattle. Whole-genome sequencing of the cow was performed and a heterozygous variant affecting the coding sequence of the bovine KIT gene was identified on chromosome 6. The variant is a 40 bp deletion in exon 9, NM_001166484.1:c.1390_1429del, and leads to a frameshift that is predicted to produce a novel 50 amino acid-long C-terminus replacing almost 50% of the wt KIT protein, including the functionally important intracellular tyrosine kinase domain (NP_001159956.1:p.(Asn464AlafsTer50)). Interestingly, among three available offspring, two solid-coloured daughters were genotyped as homozygous wt whereas a single son showing a slightly milder but still obvious depigmentation phenotype inherited a copy of the novel variant allele. The genetic findings provide strong evidence that the identified loss-of-function KIT variant most likely represents a de novo germline mutation that is causative owing to haploinsufficiency.

A non-coding regulatory variant in the 5'-region of the MITF gene is associated with white-spotted coat in Brown Swiss cattle.

Recently, the Swiss breeding association reported an increasing number of white-spotted cattle in the Brown Swiss breed, which is normally solid brown coloured. A total of 60 Brown Swiss cattle with variably sized white abdominal spots, facial markings and depigmented claws were collected for this study. A genome-wide association study using 40k SNP genotypes of 20 cases and 1619 controls enabled us to identify an associated genome region on chromosome 22 containing the MITF gene, encoding the melanogenesis associated transcription factor. Variants at the MITF locus have been reported before to be associated with white or white-spotted phenotypes in other species such as horses, dogs and mice. Whole-genome sequencing of a single white-spotted cow and subsequent genotyping of 172 Brown Swiss cattle revealed two significantly associated completely linked single nucleotide variants (rs722765315 and rs719139527). Both variants are located in the 5'-regulatory region of the bovine MITF gene, and comparative sequence analysis showed that the variant rs722765315, located 139 kb upstream of the transcription start site of the bovine melanocyte-specific MITF transcript, is situated in a multi-species conserved sequence element which is supposed to be regulatory important. Therefore, we hypothesize that rs722765315 represents the most likely causative variant for the white-spotting phenotype observed in Brown Swiss cattle. Presence of the mutant allele in a heterozygous or homozygous state supports a dominant mode of inheritance with incomplete penetrance and results in a variable extent of coat colour depigmentation.

Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls.

Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.

Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed.

The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus-specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.

[Fanconi-Bickel-Syndrom: a novel genetic disease in Original Braunvieh]. / Fanconi-Bickel-Syndrom: eine bislang unerkannte Erbkrankheit beim Braunvieh.

INTRODUCTION: This case report describes a new genetic disease of the Braunvieh breed in Switzerland. The bovine disorder also occurs in German Fleckvieh, and corresponds to human Fanconi-Bickel syndrome which is an inherited glycogen storage disease caused by mutations of the SLC2A2 gene encoding the glucose transporter GLUT2. This case report describes a single affected Original Braunvieh calf genotyped as homozygous for the FH2-associated SLC2A2 frame shift mutation. The clinical examination showed stunted growth, polyuria and polydipsia, as well as poor claw horn and coat quality. Necropsy revealed a pale cortex of the kidneys and a unilateral renal hypoplasia. Histology showed tubulonephrosis of the proximal tubules with protein- and glucose-rich contents. Glycogen accumulation was not evident in any organ. This finding is different from the reported lesions in two previously described GLUT2-deficient Fleckvieh heifers. In the presented case, growth retardation mainly seems to be associated with renal dysfunction. A direct gene test is available to eliminate the mutant allele from the population.

Accuracy of direct genomic values for functional traits in Brown Swiss cattle.

In this study, direct genomic values for the functional traits general temperament, milking temperament, aggressiveness, rank order in herd, milking speed, udder depth, position of labia, and days to first heat in Brown Swiss dairy cattle were estimated based on ~777,000 (777 K) single nucleotide polymorphism (SNP) information from 1,126 animals. Accuracy of direct genomic values was assessed by a 5-fold cross-validation with 10 replicates. Correlations between deregressed proofs and direct genomic values were 0.63 for general temperament, 0.73 for milking temperament, 0.69 for aggressiveness, 0.65 for rank order in herd, 0.69 for milking speed, 0.71 for udder depth, 0.66 for position of labia, and 0.74 for days to first heat. Using the information of ~54,000 (54K) SNP led to only marginal deviations in the observed accuracy. Trying to predict the 20% youngest bulls led to correlations of 0.55, 0.77, 0.73, 0.55, 0.64, 0.59, 0.67, and 0.77, respectively, for the traits listed above. Using a novel method to estimate the accuracy of a direct genomic value (defined as correlation between direct genomic value and true breeding value and accounting for the correlation between direct genomic values and conventional breeding values) revealed accuracies of 0.37, 0.20, 0.19, 0.27, 0.48, 0.45, 0.36, and 0.12, respectively, for the traits listed above. These values are much smaller but probably also more realistic than accuracies based on correlations, given the heritabilities and samples sizes in this study. Annotation of the largest estimated SNP effects revealed 2 candidate genes affecting the traits general temperament and days to first heat.

[BLIRD - a new genetic disease in Holstein cattle in Switzerland]. / BLIRD ­ eine neue genetische Erkrankung beim Holsteinrind in der Schweiz.

INTRODUCTION: Recently, a new hereditary disease, bovine lymphocyte intestinal retention defect (BLIRD), was discovered in Holstein cattle in France and is caused by a variant in the Integrin subunit beta 7 (ITGB7) gene. The altered cell adhesion molecule resulting from this point mutation is responsible for an impaired tissue of CD4 T lymphocytes from the blood to intestinal tissue. The aim of this study was to assess the allelic frequency of this deleterious variant in the local Holstein population and to clinically examine ten BLIRD-affected Holstein cattle from Switzerland in order to characterise the phenotype of this new hereditary disease, which is still unknown to the veterinary community. BLIRD was associated with severely impaired animal health in the rearing phase and significantly reduced animal welfare due to weakened immune defences, below-average development and recurrent diarrhoea. Further examinations revealed increased leucocyte values and a slightly increased average age at first calving. Affected homozygous animals are labelled internationally as BLIRD-carrier homozygous (LRS), BLIRD-carrier heterozygous (LRC) and BLIRD-free (LRF). An obvious inbreeding practice was clearly demonstrated by the pedigree analysis of the ten animals, which all trace back to the potential founder bull. Herein, BLIRD has been detected and described in Switzerland for the first time. The ITGB7 variant allele has a frequency of 2,1 % in the current Swiss Holstein population, which is below the level of the cholesterol deficiency (CD)-associated apolipoprotein B (APOB) variant allele with a frequency of 3,9 %. Although relatively rare, attention should be paid to the BLIRD genotype when mating in order to exclude further affected animals. In cattle with clinically suspected BLIRD, the diagnosis should be confirmed by genetic testing.

INTRODUCTION: Récemment, une nouvelle maladie héréditaire récessive, le défaut de rétention intestinale des lymphocytes bovins (bovine lymphocyte intestinal retention defect BLIRD), a été découverte chez les bovins Holstein en France. Elle est causée par une variante du gène Integrin subunit beta 7 (ITGB7). L'altération de la molécule d'adhésion cellulaire résultant de cette mutation ponctuelle est responsable de l'altération du transfert des lymphocytes T CD4 du sang vers le tissu intestinal. L'objectif de cette étude était d'évaluer la fréquence allélique de cette variante délétère dans la population Holstein locale et d'examiner cliniquement dix bovins Holstein suisses atteints de BLIRD afin de caractériser le phénotype de cette nouvelle maladie héréditaire, qui est encore inconnue de la communauté vétérinaire. La BLIRD a été associée à une grave détérioration de la santé des animaux pendant la phase d'élevage et à une réduction significative de leur bien-être en raison de l'affaiblissement des défenses immunitaires, d'un développement inférieur à la moyenne et de diarrhées récurrentes. Des examens complémentaires ont révélé une augmentation des valeurs leucocytaires et une légère augmentation de l'âge moyen au premier vêlage. Les animaux homozygotes affectés sont étiquetés au niveau international comme homozygotes porteurs de BLIRD (LRS), hétérozygotes porteurs de BLIRD (LRC) et exempts de BLIRD (LRF). Une pratique de consanguinité évidente a été clairement démontrée par l'analyse généalogique des dix animaux, qui remontent tous au taureau fondateur potentiel. La BLIRD a été ainsi détectée et décrite pour la première fois en Suisse. La allèle délétère ITGB7 a une fréquence de 2,1 % dans la population Holstein suisse actuelle, ce qui est inférieur au niveau de la allèle délétère de l'apolipoprotéine B (APOB) associée à la déficience en cholestérol (CD), dont la fréquence est de 3,9 %. Bien que relativement rare, il convient de prêter attention au génotype BLIRD lors de l'accouplement afin d'exclure de la reproduction d'autres animaux affectés.

[Grey, curly and short-haired Swiss Holstein cattle show genetic traces of the Simmental breed]. / Graue, kraus- und kurzhaarige Schweizer Holstein Rinder weisen genetische ­Spuren der Rasse Simmental auf.

INTRODUCTION: Occasionally black-and-white spotted calves appear in Switzerland, which show a special fur only in the pigmented area. Otherwise these animals are normally developed. The white hairs are normal, but they appear relatively long and smooth, because the pigmented hairs are curly and thus appear shortened. In addition, the affected animals show a variable intensity of coat colour in the pigmented area. At birth affected calves often appear black, whereas older cattle show bright colours from reddish brown to grey. This is associated with a variable hair loss that increases during growth and is limited to the pigmented area of the coat. In adult cattle the coloured hairs appear rather smooth, but they are considerably shorter. This phenomenon of pigmentation-associated hypotrichosis was previously described internationally in various beef cattle populations. The affected cattle are often solid black and show only small white spots. Therefore, the loss of hair at the pigmented fur and most visibly at the pigmented tail is called rat-tail syndrome. Another name used is also crossbreeding-related congenital hypotrichosis. Molecular genetic investigations showed that the affected animals are heterozygous carriers for two variants in two different genes associated with pigmentation. The same genotype constellation was found in the 33 similarly affected cattle from Switzerland presented here. On one hand, they each carry a copy of the MC1R gene gain-of-function variant causing dominant black, as well as a copy of the recessively inherited red factor loss-of-function variant in the MC1R gene. On the other hand, all cases are heterozygous carriers for a variant in the PMEL gene that is associated with a semi-dominantly inherited form of colour dilution (dun or silver) in Simmental, Hereford and Highland Cattle. The introgression of Holstein cattle into the Original Simmental breed, which has been practised for decades, explains the occasional occurrence of this phenomenon in Swiss cattle breeding.

INTRODUCTION: En Suisse, on peut parfois observer des veaux tachetés noirs et blancs présentant un pelage spécial uniquement dans la zone pigmentée des poils. Ces animaux sont normalement développés; les poils blancs sont normaux mais semblent relativement longs et lisses, alors que les poils pigmentés sont bouclés et raccourcis. En outre, les animaux atteints présentent une intensité variable de la couleur du pelage dans la zone pigmentée. À la naissance, ces veaux apparaissent souvent noirs, alors qu'en grandissant ils présentent une couleur plus claire allant du brun rougeâtre au gris. Chez les bovins adultes, les poils colorés semblent plutôt lisses mais sont nettement raccourcis. Ceci est associé à une diminution de la pilosité variable augmentant pendant la croissance et se limitant à la zone pigmentée du pelage. Ce phénomène d'hypotrichose associée à la pigmentation a déjà été décrit au niveau international dans diverses races à viande bovines. Ces bovins sont souvent d'un noir uniforme et ne présentent que de petites taches blanches. En raison de la perte de poils dans le pelage pigmenté et plus visiblement au niveau de la queue pigmentée, on appelle ce syndrome syndrome de la queue de rat (rat-tail syndrom), également appelé hypotrichose congénitale liée au croisement. Les études de génétique moléculaire ont montré que les animaux affectés sont porteurs hétérozygotes de deux variantes de deux gènes différents associés à la pigmentation. La même constellation génotypique a été retrouvée chez les 33 bovins suisses présentés ici. D'une part, ces derniers portent chacun une copie de la variante du gène dominant MC1R causant le noir, ainsi qu'une copie de la variante récessive du facteur rouge dans le gène MC1R. D'autre part, tous les cas sont porteurs hétérozygotes d'une variante du gène PMEL associée à une forme de dilution de couleur semi-dominante héréditaire (dun ou argent) chez les races Simmental, Hereford et Highland Cattle. Le croisement des bovins Holstein avec la race Simmental originale, pratiquée depuis des décennies, explique la présence occasionnelle de ce phénomène dans l'élevage bovin suisse.