Identification of a mutation associated with factor XI deficiency in Holstein cattle

An autosomal recessive deficiency of blood coagulation factor XI (FXI) has been described in Holstein cattle. Current testing methods are unsuitable for accurately identifying carriers (heterozygotes) of the disease. To identify the molecular basis of this deficiency, a polymerase chain reaction (PCR)-based strategy was implemented to clone and sequence the bovine FXI gene (F11) from animals of different genotypes. Approximately 14 kb of genomic DNA sequence and 1.8 kb of cDNA sequence, corresponding to exon 3 through the 3'-UTR, of the bovine gene were obtained. Comparison of sequences derived from homozygous normal and deficient individuals revealed that FXI deficiency in Holsteins is associated with the insertion of a 76 bp segment [AT(A)(28)TAAAG(A)(26)GGAAATAATAATTCA] within exon 12. This insertion introduces a stop codon that results in a mature FXI protein lacking the functional protease domain encoded by exons 13, 14 and 15. Based on these data, a DNA-based diagnostic test has been developed for accurate genotyping. Using this method, the frequency of the mutated allele has been determined to be 1.2% in a contemporary population of the USA Holstein sires.     

Identification of carriers of the mutation causing coagulation factor XI deficiency in Polish Holstein-Friesian cattle

Factor XI (FXI) deficiency is a hereditary coagulation disorder observed in various mammalian species. The molecular basis of coagulopathy has been recognized in Holstein cattle as a 76-bp insertion in the coding region of theFXI gene. Because the disorder seems to have an impact on reproductive traits and udder health in cattle, we tested 103 randomly selected cows, 28 cows with repeat breeding, and 9 cows with recurrent mastitis for the presence of an abnormalFXI allele. Three related cows were diagnosed as carriers.     

Screening for bovine leukocyte adhesion deficiency,deficiency of uridine monophosphate synthase,complex vertebral malformation,bovine citrullinaemia,and factor XI deficiency in Holstein cows reared in Turkey

Background  

Bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), complex vertebral malformation (CVM), bovine citrullinaemia (BC) and factor XI deficiency (FXID) are autosomal recessive hereditary disorders, which have had significant economic impact on dairy cattle breeding worldwide. In this study, 350 Holstein cows reared in Turkey were screened for BLAD, DUMPS, CVM, BC and FXID genotypes to obtain an indication on the importance of these defects in Turkish Holsteins.     

Simulation of normal, carrier and affected controls for large-scale genotyping of cattle for factor XI deficiency

An insertion mutation within exon 12 of the factor XI gene has been described in Holstein cattle. This has opened the prospect for large-scale screening of cattle using the polymerase chain reaction (PCR) technique for the rapid identification of heterozygous animals. To facilitate such a screening process, the mutant and normal alleles of factor XI gene, represented by 244- and 320-bp PCR amplified fragments, were individually cloned in Escherichia coli using a multicopy plasmid cloning vehicle to generate pFXI-N and pFXI-M, respectively. The authenticity of the inserts was confirmed by nucleotide sequencing. A nested PCR method was developed, by which PCR amplicons generated from primers with annealing sites on the recombinant plasmids and by flanking the insert were used as templates for amplification of the diagnostic products using factor XI gene-specific primers. An equimolar mixture of both PCR amplicons, originating from pFXI-N and pFXI-M, constituted the carrier control while the individual amplicons were the affected and normal controls. The controls were used as references for in-gel comparison to screen a population of 307 cattle and 259 water buffaloes; the frequency of the mutant allele was found to be 0. No DNA size standards were required in this study. The simulated control DNA samples representing normal, carrier and affected cattle have the potential to help in large-scale screening of a cattle population for individuals that are carriers or affected by factor XI deficiency.     

An insertion mutation of the bovine F11 gene is responsible for factor XI deficiency in Japanese black cattle

Factor XI deficiency in Japanese black cattle is an hereditary mild bleeding disorder with an autosomal recessive mode of inheritance. To characterize the molecular lesion causing factor XI deficiency in cattle, we isolated an entire coding region of the bovine F11 gene, which comprises 15 exons and 14 introns, and determined its nucleotide sequences. Comparison of the nucleotide sequences of the F11 gene between affected and unaffected animals revealed an insertion of 15 nucleotides in exon 9 of the affected animals. The insertion results in a substitution of one amino acid with six amino acids in a highly conserved amino acid sequence in the fourth apple domain of factor XI protein. Genotyping of the F11 gene in 109 Japanese black cattle revealed that the insertion clearly corresponded to the factor XI activities of the animals. We therefore concluded that the insertion of 15 nucleotides in the F11 gene is the causative mutation for factor XI deficiency in Japanese black cattle. Genotyping of the F11gene by detecting the insertion will be an effective DNA-based diagnostic system to prevent incidence of the disease.     

Identification of complex vertebral malformation carriers in Holstein cattle in south China

Complex vertebral malformation (CVM) is a recently described monogenic autosomal recessive hereditary defect of Holstein dairy cattle that causes premature birth, aborted fetuses and stillborn calves. Guanine is substituted by thymine (G>T) in the solute carrier family 35 member A3 gene (SLC35A3). A valine is changed to a phenylalanine at position 180 of uridine 5'-diphosphate-N-acetyl-glucosamine transporter protein. CVM is expected to occur in many countries due to the widespread use of sire semen. We developed a created restriction site PCR (CRS-PCR) method to diagnose CVM in dairy cows. This was tested on 217 cows and 125 bulls selected randomly from a Holstein cattle population in south China. Five Holstein cows and five Holstein bulls were identified to be CVM carriers; the percentages of CVM carriers were estimated to be 2.3, 4.0 and 2.9% in the cows, bulls and entire Holstein cattle sample, respectively.     

Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

Background

Inbreeding reduces the fitness of individuals by increasing the frequency of homozygous deleterious recessive alleles. Some insight into the genetic architecture of fitness, and other complex traits, can be gained by using single nucleotide polymorphism (SNP) data to identify regions of the genome which lead to reduction in performance when identical by descent (IBD). Here, we compared the effect of genome-wide and location-specific homozygosity on fertility and milk production traits in dairy cattle.

Methods

Genotype data from more than 43 000 SNPs were available for 8853 Holstein and 4138 Jersey dairy cows that were part of a much larger dataset that had pedigree records (338 696 Holstein and 64 049 Jersey animals). Measures of inbreeding were based on: (1) pedigree data; (2) genotypes to determine the realised proportion of the genome that is IBD; (3) the proportion of the total genome that is homozygous and (4) runs of homozygosity (ROH) which are stretches of the genome that are homozygous.

Results

A 1% increase in inbreeding based either on pedigree or genomic data was associated with a decrease in milk, fat and protein yields of around 0.4 to 0.6% of the phenotypic mean, and an increase in calving interval (i.e. a deterioration in fertility) of 0.02 to 0.05% of the phenotypic mean. A genome-wide association study using ROH of more than 50 SNPs revealed genomic regions that resulted in depression of up to 12.5 d and 260 L for calving interval and milk yield, respectively, when completely homozygous.

Conclusions

Genomic measures can be used instead of pedigree-based inbreeding to estimate inbreeding depression. Both the diagonal elements of the genomic relationship matrix and the proportion of homozygous SNPs can be used to measure inbreeding. Longer ROH (>3 Mb) were found to be associated with a reduction in milk yield and captured recent inbreeding independently and in addition to overall homozygosity. Inbreeding depression can be reduced by minimizing overall inbreeding but maybe also by avoiding the production of offspring that are homozygous for deleterious alleles at specific genomic regions that are associated with inbreeding depression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0071-7) contains supplementary material, which is available to authorized users.     

APOB‐associated cholesterol deficiency in Holstein cattle is not a simple recessive disease

In 2015, cholesterol deficiency (CD) was reported for the first time as a new recessive defect in Holstein cattle. After GWAS mapping and identification of a disease‐associated haplotype, a causative loss‐of‐function variant in APOB was identified. CD‐clinically affected APOB homozygotes showed poor development, intermittent diarrhea and hypocholesterolemia and, consequently, a limited life expectation. Herein, we present a collection of 18 cases clinically diagnosed as CD‐affected APOB heterozygotes. CD‐clinically affected heterozygotes show reduced cholesterol and triglyceride blood concentrations. The differences in total blood cholesterol and triglycerides between nine CD‐clinically affected and 36 non‐affected heterozygotes were significant. As only some APOB heterozygotes show the clinical CD phenotype, we assume that the penetrance is reduced in heterozygotes compared to the fully penetrant effect observed in homozygotes. We conclude that APOB‐associated CD represents most likely an incomplete dominant inherited metabolic disease with incomplete penetrance in heterozygotes.     

Identification of loci associated with tolerance to Johne’s disease in Holstein cattle

Johne’s disease, caused by Mycobacterium avium subspecies paratuberculosis (Map), is a fatal disease in cattle. The objective of this study was to identify loci associated with tolerance in cows infected with Map. Tolerance was defined as a cow’s fitness at a given level of Map infection intensity. Fitness was measured by Map faecal cultures, and Map infection intensity was measured by culturing four gut tissues. The quantitative phenotype of tolerance was defined by numerical indexes of cultures of peak (peak tolerance, PT) and average (average tolerance, AT) faecal and tissue Map from 245 Holstein cows. The categorical phenotype was defined as: ≥100 cfu Map tissue infection, and faecal shedding ≥75 cfu (intolerant) or <10 cfu (tolerant cows). In 94 cows, Map was identified in ≥1 tissue, including 44 cows with ≥100 Map tissue cfu and 36 with ≥1 faecal cfu. A genome‐wide association analysis was performed after filtering, leaving genotypes for 45 789 SNPs in 90 animals for the quantitative phenotype and 16 cases and 25 controls for the categorical analysis of tolerance. rs41748405:A>C (BTA15) was associated with PT (P = 1.12 × 10^?7) and AT (P = 2.17 × 10^?6). Associations were identified with PT and adjacent SNPs ss61512613:A>G and ss61530518:A>G (BTA6) (P < 3.0 × 10^?5), and with AT for ss61469568:A>G (BTA 2) (P = 3.3 × 10^?5) and ss86284768:A>G (BTA1) (P = 3.31 × 10^?5). For the categorical phenotype, an association was found with ss8632653:A>G (BTA6) (P < 5.0 × 10^?5). This is the first study to identify loci associated with tolerance to Johne’s disease.     

Serologically detected lymphocyte antigens in Holstein cattle

Lymphocytes from 103 Holstein cattle were tested with 11 antilymphocytotoxic sera. Four of these sera were produced by whole blood immunization; these generally yielded lymphocytotoxicity against a large number of animals in each test panel. The majority of the sera were collected from parous cows which had never been immunized. Observations about this latter group of sera are (1) lymphocyte antibodies, may occur by alloimmunization in foetal-maternal interaction, (2) normal sera from non-immunized parous cows generally had a narrower specificity of antibodies than from parous cows immunized with blood from unrelated animals and in some cases these antisera may be monospecific, and (3) these sera from parous cows are easy to obtain without the need for laborious immunizations. Analysis of these lymphocytotoxic sera indicate several reagents were obtained which possessed different antibodies; these were useful in detecting polymorphism of cattle lymphocyte antigens. Using these 11 sera, an analysis of the reactions patterns among 103 Holsteins, including parent-offspring data resulted in the postulation of several alleles. These data suggest that cattle lymphocyte antigens are very polymorphic and inherited.     

Identification of amino acids in the factor XI apple 3 domain required for activation of factor IX

Activated coagulation factor XI (factor XIa) proteolytically cleaves its substrate, factor IX, in an interaction requiring the factor XI A3 domain (Sun, Y., and Gailani, D. (1996) J. Biol. Chem. 271, 29023-29028). To identify key amino acids involved in factor IX activation, recombinant factor XIa proteins containing alanine substitutions for wild-type sequence were expressed in 293 fibroblasts and tested in a plasma clotting assay. Substitutions for Ile(183)-Val(191) and Ser(195)-Ile(197) at the N terminus and for Ser(258)-Ser(264) at the C terminus of the A3 domain markedly decreased factor XI coagulant activity. The plasma protease prekallikrein is structurally homologous to factor XI, but activated factor IX poorly. A chimeric factor XIa molecule with the A3 domain replaced with A3 from prekallikrein (FXI/PKA3) activated factor IX with a K(m) 35-fold greater than that of wild-type factor XI. FXI/PKA3 was used as a template for a series of proteins in which prekallikrein A3 sequence was replaced with factor XI sequence to restore factor IX activation. Clotting and kinetics studies using these chimeras confirmed the results obtained with alanine mutants. Amino acids between Ile(183) and Val(191) are necessary for proper factor IX activation, but additional sequence between Ser(195) and Ile(197) or between Phe(260) and Ser(265) is required for complete restoration of activation.     

A novel factor XI missense mutation (Val371Ile) in the activation loop is responsible for a case of mild type II factor XI deficiency

Coagulation factor XI (FXI) is the zymogen of a serine protease that, when converted to its active form, contributes to blood coagulation through proteolytic activation of factor IX. FXI deficiency is typically an autosomal recessive disorder, characterized by bleeding symptoms mainly associated with injury or surgery. Of the more than 100 FXI gene mutations reported in FXI-deficient patients, most are associated with a proportional decrease in FXI functional and immunologic levels (type I defects), whereas only a few mutations leading to the presence of dysfunctional molecules in plasma have been molecularly analyzed to date (type II deficiencies). We report the functional and molecular characterization of a missense mutation (Val371Ile) identified, in the heterozygous state, in a 25-year-old Italian male with mild FXI deficiency. Laboratory analysis revealed reduced functional FXI levels (34%), but normal antigen levels (102%), distinctive of a type II defect. Given the proximity of Val371 to the FXI activation site, a possible interference with zymogen activation was postulated. Expression experiments of the FXI-Val371Ile recombinant protein, followed by activation assays, showed both a different time course in FXI activation and a slight delay in factor IX activation by thrombin-activated FXI.     

Serologically detected lymphocyte antigens in Holstein cattle1

Lymphocytes from 103 Holstein cattle were tested with 11 antilymphocytotoxic sera. Four of these sera were produced by whole blood immunization; these generally yielded lymphocytotoxicity against a large number of animals in each test panel. The majority of the sera were collected from parous cows which had never been immunized. Observations about this latter group of sera are (1) lymphocyte antibodies may occur by alloimmunization in foetal-maternal interaction, (2) normal sera from non-immunized parous cows generally had a narrower specificity of antibodies than from parous cows immunized with blood from unrelated animals and in some cases these antisera may be monospecific, and (3) these sera from parous cows are easy to obtain without the need for laborious immunizations. Analysis of these lymphocytotoxic sera indicate several reagents were obtained which possessed different antibodies; these were useful in detecting polymorphism of cattle lymphocyte antigens. Using these 11 sera, an analysis of the reactions patterns among 103 Holsteins, including parent-offspring data resulted in the postulation of several alleles. These data suggest that cattle lymphocyte antigens are very polymorphic and inherited.     

荷斯坦奶牛脊柱畸形综合征的研究进展

荷斯坦奶牛脊柱畸形综合征是近年新发现的一种常染色体隐性遗传病,该病对纯合子胎儿是致死性的。当荷斯坦牛的育种核心群中携带者达到一定比例,脊柱畸形综合征就会对奶业造成巨大损失。文章综述了脊柱畸形综合征的主要症状和影响、致病基因及检测方法的研究进展以及我国潜在的荷斯坦奶牛脊柱畸形综合征携带者的状况。     

Management of summer infertility in Texas Holstein dairy cattle

The objectives of this study were to describe the impact of season on pregnancy odds and the effect of specific herd management practices to modify seasonal effects. Pregnancy odds were significantly associated with herd, season, days in milk, and milk production, and with 3 interactions: milk production-by-days in milk, milk production-by-parity, and season-by-days in milk. The estimate of relative risk for summer insemination resulting in pregnancy was 0.66 at 60 d post calving and 0.53 at 160 d post calving. Shade in the lounging area, holding pen or dry cow areas, and fans in the lounging area had positive effects on summer pregnancy odds. Fans in the dry cow area were associated with a reduced odds of pregnancy. Sprinklers did not significantly modify the effect of season on pregnancy odds. The strong seasonal decrease in pregnancy odds was less severe on farms that provided shade in the lounging areas, holding pens and dry cow areas and fans in lounging areas. Insemination strategies can also be adapted to increase the pregnancy odds.     

The pattern of linkage disequilibrium in German Holstein cattle

This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein–Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein–Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r² statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r² = 0.30 ± 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 ± 0.24 at 50–75 kb, which is nearly the average inter‐marker space in this study. The proportion of SNPs in useful LD (r² ≥ 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance ≤100 kb than previously thought. Analysis revealed 712 haplo‐blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 ± 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r². It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r² estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N_e = 103 up to ～4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed.     

Observed frequency of monozygotic twinning in Holstein dairy cattle

Bonnier's equation is used to mathematically estimate the frequency of monozygotic (MZ) twinning in epidemiologic studies of twinning in dairy cattle; however, no empirical determination of MZ twinning has been reported in the literature. Our objectives were to empirically determine the frequency of MZ twinning in lactating Holstein cows and to compare this result with published estimates predicted using Bonnier's equation. Ear biopsies were collected from 107 sets of Holstein twins from six Wisconsin dairies resulting in 40 opposite-sex twins, 29 same-sex male twins, and 38 same-sex female twins. To empirically determine the frequency of MZ twinning, DNA extracted from ear biopsies collected from the 67 same-sex twins was PCR amplified using primers for a minimum of 5 polymorphic microsatellite DNA markers. Opposite-sex twins were classified as dizygotic (DZ) as well as same-sex twins differing in at least one microsatellite DNA marker. Same-sex twins were classified as MZ when all genotypes for a minimum of five markers were identical. Of the 67 same-sex twins, 62 were classified as DZ and 5 MZ resulting in a MZ twinning frequency of 7.5% of same-sex twins and 4.7% of all twins. The estimated frequency of MZ twinning in this population of twin calves using Bonnier's equation was 39.5% of same-sex twins and 24.7% of all twins. We concluded that MZ twinning occurred infrequently in Holstein cattle and perhaps less frequently than that reported in studies using Bonnier's equation to estimate MZ twinning.