Mutation In Cattle Research Articles

Whole genome screening for deleterious alleles in Hanwoo cattle

Selective breeding of cattle increases the level of inbreeding and, as a result, the risk of transmitting deleterious recessive alleles in a population. Numerous genetic disorders have been identified in various breeds of cattle. Although these disorders occur sporadically, the widespread use of semen from carrier sires can increase their prevalence in a population. In this regard, routine testing and elimination of carrier bulls is essential. The availability of a large amount of genomic data enables the screening and identification of causal alleles in the absence of phenotypes. This study aimed to investigate the presence of candidate variants of genetic disorders in Hanwoo cattle using whole genome data. 16,970 cattle were genotyped using the 50K Illumina Bovine chip and imputed to the whole genome sequence level using reference data from 203 bulls. Genetic coordinates of previously reported mutations in cattle were obtained from the OMIA online database. The information was then used to screen for harmful alleles in Hanwoo cattle. Fortunately, we did not identify any candidate variants in the tested population. However, this study was limited to a small sample. Moreover, the reliability of the results could have been affected by low imputation accuracy and genotype liftover errors. In this regard, we recommend regular screening of the breeding cattle to minimize the prevalence of genetic disorders in Hanwoo cattle.

White coat color of a Black Angus calf attributed to an occurrence of the delR217 variant of MITF.

A white calf, with minimal pigmented markings, was born to two registered Black Angus parents. Given the possibility of an unknown recessive or de novo dominant mutation, whole-genome sequencing was conducted on the trio of individuals. A 3-bp in-frame deletion in MITF was identified; this mutation was unique to the calf but identical to the delR217 variant reported in both humans and murine models of Waardenburg syndrome type 2A and Tietz syndrome. Given the coat color phenotype and identity of the mutation, our data support that this calf represents the first instance of this recurring MITF mutation in cattle.

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

BackgroundBovine 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.ResultsThe 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.ConclusionsWe 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.

Short communication: A splice site mutation in CENPU is associated with recessive embryonic lethality in Holstein cattle

A genome scan for homozygous haplotype deficiency coupled with whole-genome sequence data analysis is a very effective method to identify embryonic lethal mutations in cattle. Among other factors, the power of the approach depends on the availability of a greater amount of genotyping and sequencing data. In the present study, we analyzed the largest known panel of Illumina BovineSNP50 (Illumina Inc., San Diego, CA) genotypes, comprising 401,896 Holstein animals, and we report the mapping of a new embryonic lethal haplotype on chromosome 27, called HH7. We fine mapped the locus in a 2.0-Mb interval using an identical-by-descent approach and analyzed genome sequence data from 4 carrier and 143 noncarrier Holstein bulls to identify the causative mutation. We detected a strong candidate variant in the gene encoding centromere protein U (CENPU), a centromere component essential for proper chromosome segregation during mitosis. The mutant allele is a deletion of 4 nucleotides located at position +3 to +6 bp after the splicing donor site of exon 11. Cross-species nucleotide alignment revealed that the nucleotide at position +3 is entirely conserved among vertebrates, suggesting that it plays an important role in the regulation of CENPU splicing. For verification, we genotyped the candidate variant in 232,775 Holstein individuals and did not observe any homozygotes, whereas 16 were expected (Poisson P-value = 1.1 × 10-7; allele frequency = 0.8%). In addition, genotyping of 250,602 animals from 19 additional breeds revealed that the mutant allele is restricted to animals of Holstein descent. Finally, we estimated the effect of the candidate variant on 2 fertility traits in at-risk mating (i.e., between carrier bulls and daughters of carrier bulls) versus non-risk mating. In agreement with a recessive lethal inheritance pattern, we observed a marked reduction in both conception rate and 56-d nonreturn rate in heifers and cows. The effect on 56-d nonreturn rate suggests that a substantial proportion of homozygous mutants die before 35 d after insemination, which is consistent with the early embryonic death previously reported in CENPU-/- mouse embryos. In conclusion, we demonstrate that with more than 400,000 genotypes, we can map very rare recessive lethal mutations segregating at a frequency below 1% in the population. We recommend performing new analyses regularly as data are accumulating.

Two detrimental mutations in cattle mitogenome indicate the presence of Leber's hereditary optic neuropathy

While mitochondriopathies, mitochondrial diseases, caused by mutations in mitochondrial DNA (mtDNA), are well documented in humans, single pathogenic mtDNA mutation or disorders are unknown in livestock populations. In a survey of 799 complete cattle mtDNAs belonging to more than 120 breeds two mutations, one in ND1 (C4171T) and the other in ND4L (T10663C) gene were identified, that are confirmed to be pathogenic in humans causing Leber's hereditary optic neuropathy (LHON). In one Cika cow with T10663C mutation, which was in humans reported to cause an acute onset of visual loss or/and many other LHON associated clinical manifestations, an exophthalmia of the right eye that might fit to the pathogenesis of LHON was observed. This work supports the existence of potentially detrimental mtDNA mutations in cattle, while aetiology and pathogenesis need to be further documented.

Sequence variation of necdin gene in Bovidae

BackgroundNecdin (NDN), a member of the melanoma antigen family showing imprinted pattern of expression, has been implicated as causing Prader-Willi symptoms, and known to participate in cellular growth, cellular migration and differentiation. The region where NDN is located has been associated to QTLs affecting reproduction and early growth in cattle, but location and functional analysis of the molecular mechanisms have not been established.MethodsHere we report the sequence variation of the entire coding sequence from 72 samples of cattle, yak, buffalo, goat and sheep, and discuss its variation in Bovidae. Median-joining network analysis was used to analyze the variation found in the species. Synonymous and non-synonymous substitution rates were determined for the analysis of all the polymorphic sites. Phylogenetic analysis were carried out among the species of Bovidae to reconstruct their relationships.ResultsFrom the phylogenetic analysis with the consensus sequences of the studied Bovidae species, we found that only 11 of the 26 nucleotide changes that differentiate them produced amino acid changes. All the SNPs found in the cattle breeds were novel and showed similar percentages of nucleotides with non-synonymous substitutions at the N-terminal, MHD and C-terminal (12.3, 12.8 and 12.5%, respectively), and were much higher than the percentage of synonymous substitutions (2.5, 2.6 and 4.9%, respectively). Three mutations in cattle and one in sheep, detected in heterozygous individuals were predicted to be deleterious. Additionally, the analysis of the biochemical characteristics in the most common form of the proteins in each species show very little difference in molecular weight, pI, net charge, instability index, aliphatic index and GRAVY (Table 4) in the Bovidae species, except for sheep, which had a higher molecular weight, instability index and GRAVY.ConclusionsThere is sufficient variation in this gene within and among the studied species, and because NDN carry key functions in the organism, it can have effects in economically important traits in the production of these species. NDN sequence is phylogenetically informative in this group, thus we propose this gene as a phylogenetic marker to study the evolution and conservation in Bovidae.

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species

In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci. Moreover, we demonstrate that the emergence of recessive genetic defects can be monitored by detecting de novo deleterious mutations in the genome of bulls used for artificial insemination. These results demonstrate the attractiveness of cattle as a model species in the post genomic era, particularly to confirm the genetic aetiology of isolated clinical case reports in humans.

The effect of mislabeled phenotypic status on the identification of mutation-carriers from SNP genotypes in dairy cattle

BackgroundStatistical and machine learning applications are increasingly popular in animal breeding and genetics, especially to compute genomic predictions for phenotypes of interest. Noise (errors) in the data may have a negative impact on the accuracy of predictions. The effects of noisy data have been investigated in genome-wide association studies for case–control experiments, and in genomic predictions for binary traits in plants. No studies have been published yet on the impact of noisy data in animal genomics. In this work, the susceptibility to noise of five classification models (Lasso-penalised logistic regression—Lasso, K-nearest neighbours—KNN, random forest—RF, support vector machines with linear—SVML—or radial—SVMR—kernel) was tested. As illustration, the identification of carriers of a recessive mutation in cattle (Bos taurus) was used. A population of 3116 Fleckvieh animals with SNP genotypes on the same chromosome as the mutation locus (BTA 19) was available. The carrier status (0/1 phenotype) was randomly sampled to generate noise. Increasing proportions of noise—up to 20%— were introduced in the data.ResultsSVMR and Lasso were relatively more robust to noise in the data, with total accuracy still above 0.975 and TPR (true positive rate; accuracy in the minority class) in the range 0.5–0.80 also with 17.5–20% mislabeled observations. The performance of SVML and RF decreased monotonically with increasing noise in the data, while KNN constantly failed to identify mutation carriers (observations in the minority class). The computation time increased with noise in the data, especially for the two support vector machines classifiers.Conclusions This work was the first to assess the impact of phenotyping errors on the accuracy of genomic predictions in animal genetics. The choice of the classification method can influence results in terms of higher or lower susceptibility to noise. In the presented problem, SVM with radial kernel performed relatively well even when the proportion of errors in the data reached 12.5%. Lasso was the second best method, while SVML, RF and KNN were very sensitive to noise. Taking into account both accuracy and computation time, Lasso provided the best combination.

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity.

Local breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350-year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high-density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62-90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r(2) = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.

Efficient generation of myostatin (MSTN) biallelic mutations in cattle using zinc finger nucleases.

Genetically engineered zinc-finger nucleases (ZFNs) are useful for marker-free gene targeting using a one-step approach. We used ZFNs to efficiently disrupt bovine myostatin (MSTN), which was identified previously as the gene responsible for double muscling in cattle. The mutation efficiency of bovine somatic cells was approximately 20%, and the biallelic mutation efficiency was 8.3%. To evaluate the function of the mutated MSTN locus before somatic cell nuclear transfer, MSTN mRNA and protein expression was examined in four mutant cell colonies. We generated marker-gene-free cloned cattle, in which the MSTN biallelic mutations consisted of a 6-bp deletion in one of the alleles and a 117-bp deletion and 9-bp insertion in the other allele, resulting in at least four distinct mRNA splice variants. In the MSTN mutant cattle, the total amount of MSTN protein with the C-terminal domain was reduced by approximately 50%, and hypertrophied muscle fibers of the quadriceps and the double-muscled phenotype appeared at one month of age. Our proof-of-concept study is the first to produce MSTN mutations in cattle, and may allow the development of genetically modified strains of double-muscled cattle.

Molecular analysis of solute carrier family 11 member a1 (Slc11a1) gene in ruminants and non-ruminants using computational method

Solute carrier family 11 member a1 gene (Slc11a1) previously known as natural resistance-associated macrophage protein 1 (Nramp1) is a gene of member of family of metal ion-transport protein. The cellular expression is restricted to phagocytic cells. Slc11a1 delivers bivalent metal cations from the cytosol into acidic endosomal and lysosomal compartments where Fenon and Haber-Weiss reaction generates toxic antimicrobial radicals for direct antimicrobial activity against harmful microorganisms. The present study was undertaken with the objective of analyzing Slc11a1 gene to gain insight into the evolutionary proximity and divergence as well as the polymorphism of this gene in ruminants and non-ruminants including the attendant effects of the genetic variants on the function of the Slc11a1 protein. Thirty Slc11a1 gene sequences of 6 mammalian species classified as ruminant (goat, sheep, cattle, Bubalus bubalis and Bubalus carabanensis) and non-ruminant (swine and horse) animals were investigated. The length of the Slc11a1 gene varied from 448-2,357. There was substantial genetic variation and polymorphism in the aligned sequences of Slc11a1 gene within and across species. Functional analysis of non-synonymous mutations in cattle revealed that twenty five of the amino acid substitutions at the peptide binding region could be beneficial, (E36G), (T52A), (N161S) and (V248I) were likely to be beneficial while only (Q312K) was harmful. In horse, two of the amino acid mutations were harmful, two were likely to be harmful, one was undecided, four were likely beneficial and the rest twenty were beneficial. The phylogenetic trees showed some form of proximity and differentiation in Slc11a1 sequences within and across species. The present information on the polymorphism of Slc11a1 gene might be exploited in the search for association with disease resistance in Nigerian livestock species.

Real-time PCR genotyping and frequency of the myostatin F94L mutation in beef cattle breeds

This research developed two real-time PCR assays, employing high-resolution melt and allele-specific analysis to accurately genotype the F94L mutation in cattle. This mutation (g.433C > A) in the growth differentiation factor 8 or myostatin gene has recently been shown to be functionally associated with increased muscle mass and carcass yield in cattle. The F94L mutation is not, like other myostatin mutations, associated with reduced fertility and dystocia. It is therefore a candidate for introgression into other breeds to improve retail beef yield and the development of a simple and accurate test to genotype this specific mutation is warranted. Variations in the efficiency of enzyme cleavage compromised the accuracy of genotyping by published methods, potentially resulting in an overestimation of the frequency of the mutant allele. The frequency of the F94L mutation was determined by real-time PCR in 1140 animals from 15 breeds of cattle in Australia. The mutation was present in Simmental (0.8%), Piedmontese (2%), Droughtmaster (4%) and Limousin (94.2%) but not found in Salers, Angus, Poll Hereford, Hereford, Gelbvieh, Charolais, Jersey, Brahman, Holstein, Shorthorn or Maine Anjou. The low prevalence of F94L in all beef breeds except Limousin indicates the significant potential for this mutation to improve retail yield in Australian beef cattle.

Quantitative trait mutations in cattle, sheep and pigs: a review.

Abstract Most economically important traits in farm animals, such as daily gain, muscularity, meat quality, milk production, reproduction and others, are complex multifactorial traits that are controlled by an unknown number of genes combined with environmental factors. Since these traits show a continuous distribution rather than discrete values as monogenic or qualitative traits do, they are called quantitative traits and a polymorphism that affects such a quantitative trait is called a quantitative trait mutation (QTM). During the last few decades, several QTMs for different economically important quantitative traits in farm animals, such as muscularity, meat quality and milk production, were discovered. Also, for various congenital disorders, causal polymorphisms could be found or are under investigation. However, for other quantitative traits, no such QTMs have been revealed so far. An explanation for this discrepancy lies in the extent of the effect of the different polymorphisms that underlie a certain quantitative trait since this effect can vary from very small to quite large (up to 25-30% of the total phenotypic variance of a particular trait). Although new, emerging cost-effective genome-wide single-nucleotide polymorphism (SNP) genotyping techniques have become available, only QTMs that explain a large portion of the phenotypic variation are worth unravelling, especially in the light of genome-wide selection. In this review, the research for QTMs is positioned against these contemporary techniques. Moreover, an overview is given of, past and present, research efforts in identifying QTMs in farm animals and the incorporation of these polymorphisms in modern animal breeding.

Additions and corrections: Prion protein gene sequence of Canada's first non-imported case of bovine spongiform encephalopathy (BSE)

On page 1006 of the above-cited article, reference is made to a 2001 report by Horn et al. (Horn, G., Bobrow, M., Bruce, M., Goedert, M., McLean, A., and Webster, J. 2001. Review of the origin of BSE: report to United Kingdom Government. http://147.46.94.112/BSE/bse0927.pdf), with the intention of directing the reader to the most recently published broad discussion of various questions surrounding the origins of BSE, including but not limited to the occurrence of a spontaneous mutation in cattle. Unfortunately, the single reference might suggest incorrectly that it was in this report that the hypothesis of the origin of BSE via spontaneous mutation in cattle was first advanced. In fact, it was in the Report of the BSE Inquiry (http://www.bseinquiry.gov.uk; see Vol. 2, paragraph 7.3) that the idea was first fully articulated. The reader is directed to the Report to obtain a more complete background discussion on the novel-mutation hypothesis, in addition to detailed consideration of alternative hypotheses.

Bovine spongiform encephalopathy.

Early epidemiological studies identified bovine spongiform encephalopathy as a feed-borne infection associated with infected meat-and-bone meal in animal feed. The infection may have derived from scrapie in sheep, a spontaneous genetic mutation in cattle, or a transmissible spongiform encephalopathy in another mammalian species. Experimental work on the risk of transmission has necessarily tried to identify risk materials and their infectivity levels, the nature and size of species barriers, the infectious dose, the route of infection, the strain of the agent and the genotype of the animals at risk. The identification of levels of infection in cattle tissues has aided the removal of risk materials from the human and animal food chains. Maternally associated transmission is unlikely to maintain an outbreak, but the offspring of clinical cases appear to be at greater risk when the rate of food-borne exposure is high. Studies of embryo transfer have not shown infection to be transmitted by this means. While the control measures appeared to be straightforward, compliance has at times proved difficult to enforce and quantify. This has necessitated more extensive prohibitions, aggressive enforcement and thorough auditing of compliance levels.

Autosomal dominant distal renal tubular acidosis and the AE1 gene.

Autosomal dominant distal renal tubular acidosis and the AE1 gene.

Cloning of bovine muscle glycogen phosphorylase cDNA and identification of a mutation in cattle with myophosphorylase deficiency, an animal model for McArdle's disease

Genetic defects of myophosphorylase in humans cause a metabolic myopathy (McArdle's disease) characterized by exercise intolerance, cramps, and recurrent myoglobinuria. Recently, a breed of cattle with myophosphorylase deficiency has been identified: this is the first animal model of McArdle's disease. To define the molecular genetic error in the cattle, we cloned and sequenced the wild-type bovine myophosphorylase cDNA. Homology to human cDNA is 95.8% for the amino acid sequence, and 92.0% for the nucleotide sequence. Sequence homology to rabbit cDNA is 97.3% in amino acid, 90.8% in nucleotide. In the cDNA fragments amplified by RT-PCR from muscle RNA of the cattle with myophosphorylase deficiency, we identified a C-to-T substitution, changing an encoded arginine (CGG) to tryptophan (TGG) at codon 489. The mutant residue is adjacent to pyridoxal phosphate binding sites and to an active site residue, and the sequence around this mutation is highly conserved in different species.