Evaluation of haplotypes associated with copper toxicosis in Bedlington Terriers in Australia

OBJECTIVE: To evaluate the haplotype distribution associated with the copper toxicosis gene and the segregation of the mutated allele in a Bedlington Terrier population in Australia. ANIMALS: 131 Bedlington Terriers. PROCEDURE: Samples of DNA and RNA were obtained from each dog. Genetic status of each dog was evaluated by use of the DNA markers C04107; single nucleotide polymorphism (SNP), which was adjacent to exon 2 of Murr1; and a deletion marker for exon 2. A subgroup of the study population was evaluated by use of biochemical and histologic techniques to elucidate the correlation between genotype and phenotype. RESULTS: We identified a recombination between the C04107 marker and Murr1 and a variation in a nucleotide in the splice site of exon 2 in our Bedlington Terrier cohort. Furthermore, we identified a novel haplotype associated with copper toxicosis in this cohort. CONCLUSIONS AND CLINICAL RELEVANCE: Our findings indicate that the deletion of exon 2 was not the sole cause of copper toxicosis, although only exon 2 deletion of Murr1 has been responsible for copper toxicosis in Bedlington Terriers. Although we failed to find a novel mutation in our cohort, we identified an affected dog family with an intact exon 2. Furthermore, we found that an SNP in the 5' splicing site of exon 2 may or may not be associated with a novel mutation of the Murr1 gene or other genes. Loss of linkage between the C04107 marker and the Murr1 gene was also identified in a certain family of dogs.     

von Willebrand disease phenotype and von Willebrand factor marker genotype in Doberman Pinschers

OBJECTIVE: To define the relationship between clinical expression of a type-1 von Willebrand disease phenotype and genotype at 2 von Willebrand factor marker loci in Doberman Pinschers. ANIMALS: 102 client-owned Doberman Pinschers. PROCEDURES: Dogs were recruited on the basis of plasma von Willebrand factor concentration, clinical history, and pedigree. Blood samples and response to a history questionnaire were obtained for each dog. Plasma von Willebrand factor concentration was measured by use of an ELISA, and genotyping was performed via polymerase chain reaction for 1 intragenic and 1 extragenic von Willebrand factor marker. Amplification product size was determined by use of polyacrylamide gel electrophoresis (intragenic marker) or automated sequence analysis (extragenic marker). Western blots were prepared from a subset of dogs with low plasma von Willebrand factor concentration to evaluate multimer distribution. RESULTS: Strong associations were detected between plasma von Willebrand factor concentration and von Willebrand factor marker genotype. Twenty-five dogs had substantial reduction in plasma von Willebrand factor concentration and multiple hemorrhagic events. All were homozygous for a 157-base-pair intragenic marker allele and homozygous or compound heterozygous for 1 of 4 extragenic marker alleles. These marker genotypes were exclusively detected in dogs with low plasma von Willebrand factor concentration, although some dogs with these genotypes did not have abnormal bleeding. CONCLUSIONS AND CLINICAL RELEVANCE: Type-1 von Willebrand disease in Doberman Pinschers is associated with the von Willebrand factor gene locus; however, the expression pattern in this breed appears more complex than that of a simple recessive trait.     

Copper toxicosis in the Bedlington terrier: a diagnostic dilemma

Diagnosis of copper toxicosis (CT) in Bedlington terriers by the quantitative and qualitative assessment of copper (Cu) in, and pathology of, biopsies has been largely superseded by a DNA-based assay which uses a microsatellite marker (C04107) linked to the CT disease allele. A retrospective study was conducted comprising 154 liver biopsies from Bedlington terriers with 22 matched DNA markers to compare the two methods in the diagnosis of CT. For the biopsy method, three categories (phenotypes) were identified based on analytical and morphological criteria: 'unaffected' in 83 samples (54 per cent), where Cu was much less than 400 microg/g, and there was an absence of visual Cu or liver damage; 'intermediate' in 18 samples (12 per cent), where Cu was less than 400 microg/g, and there was limited histochemical Cu and no/equivocal damage; and 'affected' in 53 samples (34 per cent), where Cu was greater than 400 microg/g, there was histochemical Cu and liver damage was poorly related to Cu content. In the DNA assay, which was used alone on unrelated individuals, the microsatellite marker failed to identify the CT status of any of the groups. Liver biopsy remains a reliable indicator of Cu accumulation and progressive liver disease in individual dogs. The microsatellite marker C04107 has a predictive value only when supported by a pedigree.     

Prevalence of Deafness in Dogs Heterozygous or Homozygous for the Merle Allele

Background: Deafness in dogs is frequently associated with the pigment genes piebald and merle. Little is known about the prevalence of deafness in dogs carrying the merle allele.
Objective: To determine the prevalence of deafness in dogs heterozygous and homozygous for the merle allele of the mouse Silver pigment locus homolog (SILV) gene.
Animals: One hundred and fifty-three privately owned merle dogs of different breeds and both sexes.
Methods: Hearing was tested by brainstem auditory-evoked response and classified as bilaterally hearing, unilaterally deaf, or bilaterally deaf. DNA from buccal cells was genotyped as either heterozygous or homozygous for the merle allele. Deafness association tests among merle genotype, eye color, and sex were performed by the χ² test.
Results: Deafness prevalence in merles overall was 4.6% unilaterally deaf and 4.6% bilaterally deaf. There was a significant association between hearing status and heterozygous versus homozygous merle genotype. For single merles ( Mm ), 2.7% were unilaterally deaf and 0.9% were bilaterally deaf. For double merles ( MM ), 10% were unilaterally deaf and 15% were bilaterally deaf. There was no significant association with eye color or sex.
Conclusions: Deafness prevalence in merle dogs was greater than that in some dog breeds homozygous for the piebald gene, such as the English Cocker Spaniel, but comparable to, or lower than, that in the Dalmatian and white Bull Terrier. Dogs homozygous for the merle allele were significantly more likely to be deaf than heterozygotes.     

Cosegregation of a factor VIII microsatellite marker with mild hemophilia A in Golden Retriever dogs

Mild hemophilia A (factor VIII deficiency) was diagnosed in Golden Retrievers and pedigree studies were undertaken to test the cosegregation of an intragenic factor VIII marker with the disease phenotype. The study population consisted of 30 client-owned dogs (22 males and 8 females). Hemophilic males (n = 12) typically demonstrated prolonged bleeding after trauma or surgery rather than spontaneous hemorrhagic events. The affected males had a proportionate reduction in factor VIII coagulant activity (mean FVIII:C = 4%) and factor VIII protein concentration (mean FVIII:Ag = 3%). Twenty-five dogs (10 affected males, 8 clear males, 2 obligate carrier dams, and 5 suspect carrier daughters) were genotyped for a factor VIII microsatellite marker, with allele size assigned by an automated capillary electrophoresis system. Five distinct marker alleles were present in the study pedigree and a 300-base pair allele was found to segregate with the hemophilia A phenotype. The inheritance of the hemophilia-associated allele defined carrier status for 5 suspect daughters of obligate carrier dams. The limitations inherent to linkage analyses (i.e., lack of access to key family members and homozygosity at the marker locus) did not preclude carrier detection in this pedigree. We conclude that genotype analysis for the intragenic factor VIII marker can aid in control of canine hemophilia A through enhanced carrier detection.     

Identification of a 6 base pair insertion in West Highland White Terriers with erythrocyte pyruvate kinase deficiency.

OBJECTIVE: To define the disease-causing mutation in West Highland White Terriers (WHWT) with erythrocyte pyruvate kinase (R-PK) deficiency and to design a genetic test capable of recognizing affected (homozygous) and carrier (heterozygous) dogs. ANIMALS: 3 anemic WHWT littermates and 1 unaffected littermate; 16 dogs from the same kennel, including 4 unrelated, phenotypically normal dogs (control dogs), and 12 for which PK activity was not known; 2 PK-deficient Basenjis; 2 PK-deficient Beagles; 4 unaffected English Springer Spaniels; and 1 mixed-breed dog. PROCEDURES: cDNA was cloned and sequenced, and cDNA sequences were compared with the published sequence for canine R-PK cDNA to identify the putative disease-causing mutation. Genomic DNA spanning the affected region was cloned and sequenced to verify the mutation. Subsequently, polymerase chain reaction primers were designed to amplify the section of the gene containing the mutation from DNA in blood or buccal swab samples. Gel electrophoresis allowed assignment of genotypes on the basis of allele separation. RESULTS: 4 single base polymorphisms attributable to sequencing errors in the published sequence were identified, along with a 6 base pair (bp) insertion in exon 10 that was recognized as a putative disease-causing mutation. An identical insertion was found in genomic DNA. Amplification of genomic DNA yielded a 117 bp product for genotypically normal dogs and a 123 bp product for WHWT homozygous for PK deficiency. Carriers had 1 copy of each allele and variable heteroduplex structures. CONCLUSIONS AND CLINICAL RELEVANCE: A 6 bp insertion in the C domain of R-PK was identified in WHWT with PK deficiency. Affected and carrier dogs could be distinguished with a genetic test.     

Inheritance of von Willebrand's disease in a colony of Doberman Pinschers

OBJECTIVE: To determine the mode of inheritance of von Willebrand's disease (vWD) and perform linkage analysis between vWD and coat color or narcolepsy in a colony of Doberman Pinschers. ANIMALS: 159 Doberman Pinschers. PROCEDURE: von Willebrand factor antigen (vWF:Ag) concentration was measured by use of ELISA, and results were used to classify dogs as having low (< 20%), intermediate (20 to 65%), or high (> 65%) vWF:Ag concentration, compared with results of analysis of standard pooled plasma. Buccal bleeding time was measured, and mode of inheritance of vWD was assessed by pedigree analysis. RESULTS: von Willebrand's disease was transmitted as a single autosomal gene defect. Results suggested that 27.04% of dogs were homozygous for vWD, 62.26% were heterozygous, and 10.69% did not have the defect. Most homozygous and some heterozygous dogs had prolonged bleeding times. Dogs with diluted coat colors (blue and fawn) were significantly overrepresented in the homozygous group, compared with black and red dogs, but a significant link between vWD and coat color was not detected. CONCLUSIONS AND CLINICAL RELEVANCE: von Willebrand's disease is transmitted as an autosomal dominant trait with variable penetrance; most dogs in this colony (89.3%) were carriers of vWD. Homozygosity for vWD is not likely to be lethal. Some heterozygous dogs have prolonged bleeding times. An association between diluted coat colors and vWD may exist.     

Comparison of polymerase chain reaction-restriction fragment length polymorphism assay and enzyme assay for diagnosis of G(M1)-gangliosidosis in Shiba dogs.

In the present study, diagnostic methods for canine G(M1)-gangliosidosis were examined by comparing a DNA mutation assay with an enzyme assay. Sixty-two Shiba dogs of a pedigree with G(M1)-gangliosidosis were differentiated into 3 genotypes, i.e., normal, heterozygous, and homozygous affected dogs, using a DNA mutation assay, which consists of polymerase chain reaction amplification and the determination of restriction fragment length polymorphisms. The beta-galactosidase activity in leukocytes, umbilical cords, and plasma was measured using 4-methylumbelliferyl beta-D-galactoside and p-nitrophenyl beta-D-galactoside as artificial substrates and compared among the 3 genotypes. The results showed that it was possible to identify homozygous dogs with the enzyme assay using leukocytes and umbilical cords. When using leukocytes, heterozygous carriers could be differentiated from normal dogs in many cases. However, the use of the DNA mutation assay is essential for a complete determination of heterozygous carriers because of the overlap in the distribution of enzyme activity between these 2 groups. When umbilical cords were used, heterozygous carriers could not be differentiated from normal dogs because of no significant difference in enzyme activity between these 2 groups. The beta-galactosidase activity in plasma was not applicable to the diagnosis and genotyping of G(M1)-gangliosidosis in Shiba dogs.     

Detection of benzimidazole resistance in Haemonchus contortus using RFLP-PCR technique

Benzimidazole (BZ) resistance in Haemonchus contortus is linked primarily with the mutation in the beta-tubulin isotype 1 gene that substitute phenylalanine (Phe) to tyrosine (Tyr) at 200 codon of the gene. In the present study, a new restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) technique has been developed for detection of BZ resistance in the beta-tubulin isotype 1 gene of H. contortus. The technique utilizes two primers viz. AvikaF and AvikaR to amplify the region containing mutation in the beta-tubulin gene followed by restriction digestion. After digestion, the 'rr' individuals (homozygous resistant) revealed 257 and 48 bp bands, the 'rS' individuals (heterozygous) showed 305, 257 and 48 bp bands, while 'SS' individuals (homozygous susceptible) revealed uncut 305 bp band. A total of 162 adult male H. contortus collected from Avikanagar, Jaipur and Bikaner regions (54 from each region) were genotyped for analyzing BZ resistance in the beta-tubulin gene. Out of which, 130 adults were 'rr' types, 20 'rS' types and 12 'SS' types. The results showed that genotypic frequencies of different genotypes (rr, rS and SS) were highly significant difference among the three regions (P<0.001). The 'rr' individuals were higher (98%) in Jaipur followed by Avikanagar (93%) and Bikaner (50%) regions. Overall, the prevalence of BZ resistant allele (r) was higher (86%) as compared to BZ susceptible allele (S) (14%). The technique was also found suitable for genotyping of larvae of H. contortus and yielded reproducible results. The study indicated that RFLP-PCR is an easy, reproducible and less expensive than allele specific PCR. This technique will be helpful in establishing the prevalence rate of BZ resistance in H. contortus and can also be utilized for existing worm control programme.     

Frequency of the mutant MDR1 allele associated with multidrug sensitivity in a sample of collies from France

A study was performed to determine the frequency of the mutant MDR1 allele associated with ivermectin sensitivity in a sample of collies living in France. Buccal swab samples were collected from approximately 83 collies for determination of MDR1 genotype. DNA was extracted and the polymerase chain reaction was performed to amplify a 148 bp (wildtype MDR1 genotype) or 144 bp (mutant MDR1 genotype) amplicon containing the MDR1 mutation. Sequence analysis was performed to determine the genotype of each dog. Adequate quantities of DNA for unequivocal genotyping were obtained from only 25 of 83 swabs. Twenty percent (5/25) of the collies studied were homozygous for the normal allele (normal), 32% (8/25) were heterozygous (carrier), and 48% (12/25) were homozygous for the mutant allele (affected). The results of this study indicate that a high percentage of collies presenting to veterinarians in France harbor the MDR1 mutation, thus impacting some therapeutic decisions.     

Development and use of a polymerase chain reaction-based diagnostic test for the causal mutation of progressive retinal atrophy in Cardigan Welsh Corgis

OBJECTIVE: To develop an allele-specific polymerase chain reaction (ASPCR)-based diagnostic test for the mutation in the cyclic guanosine monophosphate phosphodiesterase alpha subunit gene (PDE6A) that causes the rcd3 form of progressive retinal atrophy (PRA) in Cardigan Welsh Corgis. ANIMALS: 1 affected homozygote, 1 unaffected carrier, 1 genotypically normal dog, and 500 unknown-PRA status Cardigan Welsh Corgis. PROCEDURE: Control blood samples were collected from Cardigan Welsh Corgis of known PRA status (ie, affected homozygote, unaffected carrier, and a genotypically normal dog) for test development. Test blood samples were collected from 500 Cardigan Welsh Corgis of unknown PRA status. Genomic DNA was used as a template in ASPCR. One pair of primers was designed to specifically amplify only the mutant allele, and another set to amplify only the wildtype allele. The PCR conditions were adjusted to ensure each reaction was 100% specific. RESULTS: The PCR conditions were identified so that each ASPCR only amplified the allele it was designed to amplify. Of the 500 Cardigan Welsh Corgis tested using the newly developed ASPCR, 457 were homozygous for the normal allele (genotypically normal), 43 were heterozygous (phenotypically normal carriers), and none were homozygous for the mutant allele. CONCLUSION AND CLINICAL RELEVANCE: A rapid, ASPCR diagnostic test able to detect the PDE6A gene mutation responsible for the rcd3 form of PRA in Cardigan Welsh Corgis was developed. The test provides a useful service for Cardigan Welsh Corgi breeders and will enable them to prevent the birth of homozygote mutant dogs.     

A von Willebrand's factor genomic nucleotide variant and polymerase chain reaction diagnostic test associated with inheritable type-2 von Willebrand's disease in a line of german shorthaired pointer dogs

Heritable, type-2 von Willebrand's disease (vWD) was studied in a line of German Shorthaired Pointers (GSPs) in which some members had a nucleotide variant in exon 28 of the von Willebrand factor (VWF) gene. A polymerase chain reaction (PCR) diagnostic test for the nucleotide variant was developed to establish the disorder's mode of inheritance and to eliminate it from the line. Thirty-six of the 49 GSPs in the line, 14 unrelated GSP controls, and 71 unrelated dogs of various breeds were tested for the presence of the variant nucleotide. All the dogs with a vWF antigen deficiency (<70% of normal) were either homozygous or heterozygous for the nucleotide variant. The variant was not located in any tested dog in the line or outside of the line with a vWF antigen value greater than 68%. Of the GSPs in the line tested, two were homozygous for the variant, 15 were heterozygous, and 19 were variant free. The collective evidence of this and other studies is consistent with the variant nucleotide being the cause of the type-2 vWD in this line of GSPs and German Wirehaired Pointers. The PCR diagnostic test for the variant nucleotide was successfully used to select and produce progeny that were variant free and vWD free. This test should be effective in the subsequent elimination of this same variant from other lines of dogs.     

Polymorphisms in the canine glucocorticoid receptor alpha gene (NR3C1α)

Corticosteroids are one of the most extensively used class of therapeutic agents in dogs. In human patients, response to corticosteroid therapy has been correlated with the presence of certain polymorphisms of the glucocorticoid receptor gene (NR3C1). Depending on the polymorphism present, patients may show either increased sensitivity to glucocorticoid‐induced adverse effects or resistance to their therapeutic effects. Because response to corticosteroid therapy in dogs can also be variable and unpredictable, we hypothesized that genetic variability exists in the canine NR3C1 gene. The aim of this study was to sequence the coding regions of the canine NR3C1 gene in a representative sample of dogs. Samples from 97 dogs from four previously identified genetic groupings of domestic breeds (Asian/Ancient, Herding, Hunting, and Mastiff) were sequenced and evaluated. Four exons contained polymorphisms and four exons showed no variation from the reference sequence. A total of six single nucleotide polymorphisms (SNPs) were identified including four synonymous SNPs and two nonsynonymous SNPs (c.811A>T and c.2111T>C). No dogs were homozygous for either variant allele, while 23 dogs were heterozygous for the c.811A>T allele and 2 were heterozygous for c.2111T>C allele. The amino acid changes caused by c.811A>T (serine to cysteine) and c.2111T>C (isoleucine to threonine) were both predicted by in silico analysis to be ‘probably damaging’ to structure and function of the resulting protein. We conclude that NR3C1 polymorphisms occur in dogs and may cause individual variation in response to corticosteroid therapy.     

Candidate gene markers for litter size in different German pig lines.

Three diallelic RFLP markers at candidate gene loci for litter size, the estrogen receptor (ESR) gene, the prolactin receptor (PRLR) gene, and the retinol-binding protein 4 (RBP4) gene, were evaluated for their association with the number of piglets born alive in different German pig lines. Genotyping was performed on boars and sows belonging to three different genetic groups from a single farm. Information on 8,336 litter records from 2,159 sows (German Landrace, n = 1,672; Duroc, n = 214; and a synthetic line, n = 273) was used in the analyses with respect to litter size. Growth performance traits were only analyzed for the synthetic line. The ESR locus showed no polymorphism in the tested boars of the German Landrace and Duroc lines. In the synthetic line, the frequency for the A allele was 0.90 and no homozygous BB animal was detected. No significant associations of ESR alleles with number of piglets born alive, backfat thickness, or average daily gain were observed. A new PCR-RFLP was developed for testing the PRLR polymorphism. The frequencies of PRLR allele A were 0.40 in the German Landrace, 0.49 in the synthetic, and 0.82 in the Duroc line. In the Duroc line, a small additive effect of the allele B on litter size was observed. The allelic substitution effect was 0.71 piglets born alive across all parities (P = 0.05). No significant associations of the PRLR locus with litter and growth performance traits were detected. The frequencies of RBP4 allele A ranged from 0.62 in the synthetic line to 0.67 in the German Landrace to 0.85 in the Duroc line. For the genotyped sows of the synthetic line, there was no indication of a favorable effect of the A allele with respect to litter size. Results of this study demonstrate that allele effects differ between lines or populations. This may be due to possible different linkage phases between the marker alleles and the causal mutations in the different lines. The results may also be explained by many minor genes affecting litter size. A selection strategy should be designed for each line separately and should always consider possible pleiotropic effects.     

Detection of linkage between genetic markers and genes that affect growth and carcass traits in pigs.

Segregation of paternal marker alleles in the progeny of a single boar was used to estimate linkage between the marker genes and associations of these genes with quantitative trait loci (QTL). The sire was heterozygous at four polymorphic marker loci, haptoglobin (HP), glucosephosphate isomerase (GPI), phosphogluconate dehydrogenase (PGD), and esterase D (ESD), and sired 30 litters during an 8-mo period. Glucosephosphate isomerase and PGD were linked (theta = .09; P less than .005). The phase of these two loci in the sire was determined to be GPI A-PGD B, GPI B - PGD A. NO other linkages were detected. Growth (135 less than or equal to n less than or equal to 172) and carcass data (70 less than or equal to n less than or equal to 80) were analyzed assuming a fixed linear model. Least squares means were compared for differences in growth and carcass traits between pigs that inherited alternative paternal marker alleles. Pigs that inherited the GPI A allele from the sire had a 22-g higher daily live weight gain postweaning and reached 103 kg live weight in 2.6 fewer days than did pigs that inherited the GPI B allele (P less than .05), indicative of the presence of gene(s) that affect rate of gain linked to the GPI locus. Pigs that inherited the PGD B allele had a .14 unit higher score for muscle firmness (score ranged from 1 to 3 units) than pigs that inherited the PGD A allele (P less than .05). Pigs that inherited the HP 3 allele had a .06-kg higher weaning weight and a .11 lower ham muscle mass score than did pigs that inherited the HP 2 allele from the sire (P less than .05). No associations with quantitative traits were detected for ESD.     

Evidence of a new leukemia inhibitory factor-associated genetic marker for litter size in a synthetic pig line

The association of a diallelic polymorphism in the leukemia inhibitory factor (LIF) gene with reproductive, growth, and carcass traits was studied in a German synthetic pig line. The diallelic SNP has been located in the 3'-untranslated region of the third exon of the porcine LIF gene. Information on 955 litter records from 273 genotyped sows was used in the analyses with respect to the number of piglets born alive. To identify possible pleiotropic marker effects, the growth and carcass traits ADG and backfat thickness were tested for associations with the SNP within the LIF gene in this population. At the LIF locus, the allele frequencies were 0.27 for the A allele and 0.73 for the B allele. There was an indication of an additive effect on the number of piglets born alive, and a significant dominance effect of the B allele was observed for first, second, and third to 10th parities (P = 0.044). The dominance effect for the first parity amounted to -0.73 +/- 0.36 (P = 0.047). No associations were detected between the marker alleles and the growth and carcass traits.     

Accuracy of imputation of single nucleotide polymorphism marker genotypes from low‐density panels in Japanese Black cattle

Using target and reference fattened steer populations, the performance of genotype imputation using lower‐density marker panels in Japanese Black cattle was evaluated. Population imputation was performed using BEAGLE software. Genotype information for approximately 40 000 single nucleotide polymorphism (SNP) markers by Illumina BovineSNP50 BeadChip was available, and imputation accuracy was assessed based on the average concordance rates of the genotypes, varying equally spaced SNP densities, and the number of individuals in the reference population. Two additional statistics were also calculated as indicators of imputation performance. The concordance rates tended to be lower for SNPs with greater minor allele frequencies, or those located near the ends of the chromosomes. Longer autosomes yielded greater imputation accuracies than shorter ones. When SNPs were selected based on linkage disequilibrium information, relative imputation accuracy was slightly improved. When 3000 and 10 000 equally spaced SNPs were used, the imputation accuracies were greater than 90% and approximately 97%, respectively. These results indicate that combining genotyping using a lower‐density SNP chip with genotype imputation based on a population of individuals genotyped using a higher‐density SNP chip is a cost‐effective and valid approach for genomic prediction.     

新疆褐牛核心群母牛蜘蛛腿综合征的遗传检测

以173头新疆褐牛核心群母牛血样为基础,采用荧光引物PCR产物毛细管电泳法结合PCR产物直接测序法检测蜘蛛腿综合征隐性基因。结果显示,荧光引物PCR产物毛细管电泳法检测的173份血样DNA片段均在246～250bp出现单一信号峰。其中,21份PCR产物直接测序未出现牛蜘蛛腿综合征SUOX基因致病突变G碱基插入导致的叠峰现象,序列比对显示测序检测未发现突变的杂合子个体,22种方法检测结果一致。结果表明,2种检测方法所检测的新疆褐牛核心群母牛个体均为纯合基因型,没有发现牛蜘蛛腿综合征SUOX致病等位基因的存在或携带该致病基因的个体,说明该研究群体不存在传播牛蜘蛛腿综合征的风险。     

Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: development of a low-density single nucleotide polymorphism map

As genetic markers, SNP are well suited for the development of genetic tests for production traits in livestock. They are stable through many generations and can provide direct assessment of individual animal's genetic merit if they are in linkage disequilibrium and phase with functional genetic variation. Bovine chromosome 5 has been shown to harbor genetic variation affecting production traits in multiple cattle populations; thus, this chromosome was targeted for SNP-based marker development and subsequent association analysis with carcass and growth phenotypes. Discovery of SNP was performed in a panel of 16 sires representing two sires from each of seven beef breeds and two Holstein sires by PCR amplification and sequencing using primers designed from genomic sequence obtained by low-coverage sequencing of bacterial artificial chromosome (BAC) clones. From 550 SNP, 296 (54%) were tentatively identified as having a minor allele frequency >10%. Forty-five SNP derived from 15 BAC were chosen based on minor allele frequency and were genotyped in 564 steers and their sires. Production and carcass data were collected on the steers as a part of the Germplasm Evaluation (GPE), Cycle VII Project at the U.S. Meat Animal Research Center (Clay Center, NE), which involves of the evaluation of sires from seven of the most popular U.S. breeds. Haplotypes based on seven SNP derived from a BAC containing the bovine genes HEM1 and PDE1B were associated with traits related to carcass fat. Steers homozygous for the major haplotype had 0.15 +/- 0.04 cm less subcutaneous fat, 0.57 +/- 0.18 kg less rib fat, 0.18 +/- 0.07 lower yield grade, 1.11 +/- 0.35% less predicted fat yield, and 0.79 +/- 0.3% greater predicted retail product yield than heterozygotes. The frequency of the major haplotype was 0.70 in the steers, and it ranged from 0.44 (Limousin) to 0.98 (Simmental and Gelbvieh) in a panel consisting of an average of 20 purebred sires from each of the seven breeds. A second set of haplotypes based on four SNP derived from a BAC containing the genes NOL1 and CHD4 was associated with Warner-Bratzler shear force. Steers homozygous for the major haplotype had 0.27 +/- 0.11 kg greater shear force than those heterozygous for the major haplotype and one of two minor haplotypes. The frequency of the major haplotype was 0.59 in the steers and ranged from 0.27 (Hereford) to approximately 0.95 (Angus and Red Angus) in the panel of purebred sires. These results demonstrate the feasibility of targeting QTL regions for SNP-based marker development and that a low level of coverage can identify markers associated with phenotypic traits.