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.     

牛脊柱畸形综合征检测方法的建立与应用

牛脊柱畸形综合征(Complex vertebral malformation, CVM)是近年来新发现的致死性牛常染色体隐性遗传缺陷病。由于编码UDP-N-乙酰葡糖胺载体的SLC35A3基因发生G→T的突变而引起本病的发生, 可引起胎牛死胎、流产、早产。为了解我国正常的荷斯坦牛(黑白花奶牛)的CVM携带和发生情况, 建立、应用创造酶切位点PCR(Created restriction site PCR, CRS-PCR)、等位基因特异性PCR(Allele-specific polymerase chain reaction, AS-PCR)检测方法检测了表型正常的436头荷斯坦母牛和93头荷斯坦公牛, 检测到3头CVM携带者, 其中杂合母牛1头, 杂合公牛2头, 携带率分别为0.60%、2.20%。此方法简便、可靠, 为奶牛CVM有害基因的分型和筛选提供了新的方法和思路, 为我国奶牛的分子选育提供了可靠的理论依据。     

No incidence of DUMPS carriers in Polish dairy cattle

DUMPS (Deficiency of Uridine Monophosphate Synthase) is a hereditary recessive disorder in Holstein cattle causing early embryo mortality during its implantation in the uterus. The only way to avoid the economic losses is early detection of DUMPS carriers. Because American Holstein semen has been intensively imported to Poland since 1970, there was a risk that DUMPS could have spread in Polish dairy cattle. In our study, 2209 dairy cattle of the Polish Holstein breed have been screened by the DNA test. The dominant group was young bulls entering the testing program (1171) and proven bulls (781). They represented all sires entering Polish breeding programs between 1999 and 2003. Also, 257 sire dams were included in the screening program. No DUMPS carrier has been found. Our results then indicate that the population of dairy cattle reared in Poland is free from DUMPS. Because of the economical significance of the DUMPS mutation and its recessive mode of inheritance, attention has to be paid to any case of a bull having in his origin any known DUMPS carrier. Such a bull should be tested and if positive eliminated from the active population. Also, young bulls (testing bulls) should be screened for DUMPS if in their progeny a high incidence of embryo mortality is observed and their genealogy cannot exclude their relatedness to any DUMPS carriers.     

Polymorphisms of the prion protein gene (PRNP) in Hanwoo (Bos taurus coreanae) and Holstein cattle

Polymorphisms in the prion protein gene (PRNP) in humans and sheep correlate with susceptibility to transmissible spongiform encephalopathies (TSEs). Bovine spongiform encephalopathy (BSE) has been reported in British and Japanese cattle; it has occurred thus far in Holstein cattle. BSE in Hanwoo (Bos taurus coreanae) cattle has not been diagnosed up to now. To characterize the bovine PRNP polymorphisms in Korean cattle, we analyzed the open reading frame (ORF) of PRNP in 120 Hanwoo (beef) cattle and 53 Holstein (dairy) cattle. Three polymorphisms were found, the third position of codon 78 (G-->A), the third position of codon 192 (C-->T), and the deletion of a single octa-repeat. An analysis of codon 78 revealed no difference in the genotype (P = 0.2026) or allele (P = 0.7180) frequencies between Hanwoo and Holstein animals. However, there were significant differences in the genotype (P < 0.0001) and allele (P < 0.0001) frequencies at PRNP codon 192 between Hanwoo and Holstein animals. The rate of Holstein animals with deletion of a single octa-repeat was 91.5% undeleted homozygotes, 8.5% heterozygotes (with R3 deletion), and 0% deleted homozygotes. However, none of the 120 Hanwoo animals had any octa-repeat deletions. The genotype (P < 0.0001) and allele (P < 0.0001) frequencies of a single octa-repeat-deletion were also significantly different between Hanwoo and Holstein animals.     

Influence of Diet Composition on Cattle Rumen Methanogenesis: A Comparative Metagenomic Analysis in Indian and Exotic Cattle

Comparative metagenomics approach has been used in this study to discriminate colonization of methanogenic population in different breeds of cattle. We compared two Indian cattle breeds (Gir and Kankrej) and two exotic cattle (Holstein and Jersey) breeds. Using a defined dietary plan for selected Indian varieties, the diet dependent shifts in microbial community and abundance of the enzymes associated with methanogenesis were studied. This data has been compared with the available rumen metagenome data from Holstein and Jersey dairy cattle. The abundance of genes for methanogenesis in Holstein and Jersey cattle came from Methanobacteriales order whereas, majority of the enzymes for methanogenesis in Gir and Kankrej cattle came from Methanomicrobiales order. The study suggested that by using slow/less digestible feed, the propionate levels could be controlled in rumen; and in turn, this would also help in further reducing the hydrogenotrophic production of methane. The study proposes that with the designed diet plan the overall methanogenic microbial pool or the individual methanogens could be targeted for development of methane mitigation strategies.     

Linkage disequilibrium in the North American Holstein population

Linkage disequilibrium was estimated using 7119 single nucleotide polymorphism markers across the genome and 200 animals from the North American Holstein cattle population. The analysis of maternally inherited haplotypes revealed strong linkage disequilibrium ( r ²   >   0.8) in genomic regions of ∼50 kb or less. While linkage disequilibrium decays as a function of genomic distance, genomic regions within genes showed greater linkage disequilibrium and greater variation in linkage disequilibrium compared with intergenic regions. Identification of haplotype blocks could characterize the most common haplotypes. Although maximum haplotype block size was over 1 Mb, mean block size was 26–113 kb by various definitions, which was larger than that observed in humans (∼10 kb). Effective population size of the dairy cattle population was estimated from linkage disequilibrium between single nucleotide polymorphism marker pairs in various haplotype ranges. Rapid reduction of effective population size of dairy cattle was inferred from linkage disequilibrium in recent generations. This result implies a loss of genetic diversity because of the high rate of inbreeding and high selection intensity in dairy cattle. The pattern observed in this study indicated linkage disequilibrium in the current dairy cattle population could be exploited to refine mapping resolution. Changes in effective population size during past generations imply a necessity of plans to maintain polymorphism in the Holstein population.     

Seroprevalence of Toxoplasma gondii infection in cattle,horses, pigs and chickens in Japan

The presence of antibodies to Toxoplasma gondii in livestock and poultry was investigated by latex agglutination tests; samples that agglutinated at dilutions of 1:64 or higher were regarded as positive. Sera were collected from fattening beef cattle (102 Japanese black, 105 crossbreeds and 114 castrated Holstein), culled dairy cattle (101 Holstein), 100 horses, 115 fattening pigs and 235 chickens (163 free-range and 72 broilers) at abattoirs in Gifu Prefecture, Japan, from August 2012 to August 2013. Antibodies to T. gondii were found in 7.3% (31/422) in cattle, 5.2% (8/155) in pigs, but not in horses or chickens. These results suggest that toxoplasmosis may be transmitted to humans via consumption of T. gondii-infected raw beef in Japan.     

中国荷斯坦牛白细胞黏附缺陷症PCR-RFLP检测方法的研究

本试验根据已知牛染色体上CD18编码基因序列设计引物,提取牛血液和精液DNA,可扩增出338bp的DNA片段,将PCR产物克隆到pMD18-T载体中,对阳性重组质粒进行测序,确定为牛的CD18基因。由于CD18基因的383位碱基由A变为G,而引起牛白细胞黏附缺陷症(BLAD),通过对济南市11个奶牛场356头奶牛及53头荷斯坦种公牛进行了BLAD的PCR-RFLP检测,共检出3头杂合母牛(携带者),占检测母牛群的0.84%,在荷斯坦公牛中只检测到一种基因型,没有发现隐性突变基因的携带者。     

SNPs of CXCR1 gene and its associations with somatic cell score in Chinese Holstein cattle

Mastitis is one of the most prevalent diseases in dairy cattle; CXCR1 plays a key role in mastitis resistance via IL8 signaling pathway, with the CXCR1 SNPs showing a different degree of mastitis resistance. To investigate the situation of CXCR1 polymorphisms in Chinese Holstein cattle and determine the relationship between the CXCR1 SNPs and mastitis resistance, the CXCR1 SNPs in 610 Chinese Holstein cattle of 30 families were investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique. The results showed that four SNPs, -1830A > G, -1768T > A, -344T > C, and 783C > A were detected at 5' upstream and coding region. The correlation analysis demonstrated that -1830AA, -1768TT, and -344TT correlated significantly with the lowest SCS for each site, respectively. Haplotype analysis revealed Haplo2 (ATTA) correlated significantly with the lowest SCS. These findings indicated a prospect genetic marker of mastitis resistance in dairy cattle.     

Whole‐Genome association analysis of susceptibility to paratuberculosis in Holstein cattle

The objective of this study was to identify genetic markers and genomic regions associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (MAP) infection in Holstein cattle. Associated single nucleotide polymorphisms (SNPs) were identified by genotyping 521 MAP‐infected Holstein cows and comparing SNP allele frequencies of these infected cows with allele frequencies estimated from specific reference populations. Reference population allele frequency estimates used Holstein sire genotype data and were weighted estimates based on sire usage within the population in question. The 521 infected cows were 233 and 288 cows from two resource populations of approximately 5000 cows each, collected independently. Population 1 was comprised primarily of daughters of twelve Holstein artificial insemination sires used heavily within the US dairy cattle population. Samples were obtained from 300 co‐operating commercial dairy herds throughout the US and were tested by both MAP faecal culture and blood‐enzyme‐linked immunosorbent assay (ELISA). Population 2 consisted of dairy cattle from six co‐operating dairy herds in Wisconsin, with all animals in the herds tested by blood enzyme‐linked immunosorbent assay (ELISA) for MAP infection. Genotyping was performed with the Illumina Bovine SNP50 Bead Chip, providing genotypes for 35 772 informative SNPs. Data from the two resource populations were analysed both in separate and combined analyses. The most significant autosomal markers from the individual and combined analyses (n = 197, nominal P < 0.001) were used in a stepwise logistic regression analysis to identify a set of 51 SNPs that could be used as a predictor of genetics for Holstein cattle susceptibility to MAP infection.     

The slick hair coat locus maps to chromosome 20 in Senepol-derived cattle

The ability to maintain normal temperatures during heat stress is an important attribute for cattle in the subtropics and tropics. Previous studies have shown that Senepol cattle and their crosses with Holstein, Charolais and Angus animals are as heat tolerant as Brahman cattle. This has been attributed to the slick hair coat of Senepol cattle, which is thought to be controlled by a single dominant gene. In this study, a genome scan using a DNA-pooling strategy indicated that the slick locus is most likely on bovine chromosome 20 (BTA20). Interval mapping confirmed the BTA20 assignment and refined the location of the locus. In total, 14 microsatellite markers were individually genotyped in two pedigrees consisting of slick and normal-haired cattle (n = 36), representing both dairy and beef breeds. The maximum LOD score was 9.4 for a 4.4-cM support interval between markers DIK2416 and BM4107. By using additional microsatellite markers in this region, and genotyping in six more pedigrees (n = 86), the slick locus was further localized to the DIK4835 - DIK2930 interval.     

利用PCR-RFLP检测中国荷斯坦牛遗传缺陷——瓜氨酸血症

瓜氨酸血症(Citrullinemia)是荷斯坦牛尿素循环发生代谢紊乱的一种常染色体隐性遗传缺陷。精氨酸琥珀酸合成酶基因外显子5发生突变(C-T)对这一紊乱负责。本研究应用PCR-RFLP方法和DNA测序技术检测济南市周边120头荷斯坦母牛和山东奥克斯生物技术有限公司种公牛站50头荷斯坦公牛的精氨酸琥珀酸合成酶基因外显子5。结果发现,所检测的公牛未发现瓜氨酸血症突变基因携带者,母牛中有2头为携带者,携带频率为1.18%。     

Effects of calf breed on milk production and other economic traits of Holstein dams

Production of purebred or crossbred feeder calves for beef, especially HolsteinxJapanese-Black (HxJB) and Japanese-Black (JB), from dairy cattle using artificial insemination or embryo transfer have been used widely in Japan. However, dairy farmers feel uneasy about the effects of calf breed on the economic traits of dams. In this study, those effects were investigated in 798 Holstein heifers bearing Holstein, HxJB, JB or other breed calves. The results of the least-squares ANOVA indicated the effects of calf breed to be significant for gestation length (P<0.01) and calf birth weight (P<0.01) but not for milk yield, fat yield, protein yield, peak yield, day of peak, number of artificial inseminations per pregnancy or days open. Frequency of dystocia was lower in dams bearing HxJB calves than in those bearing Holstein calves (P<0.05). There were no significant differences for frequencies of still birth, retained placenta and subsequent pregnancy. The present data suggest that the effects of calf breed do not place a serious problem on the economic traits of Holstein dams. In conclusion, it is indicated that the production of JB and HxJB feeder calves from Holstein dams does not result in a decrease in dam productivity.     

Haplotype analysis of TLR4 gene and its effects on milk somatic cell score in Chinese commercial cattle

Bovine mastitis is a very complex and common disease of dairy cattle and a major source of economic losses to the dairy industry worldwide. In this study, the bovine TLR4 was taken as a candidate gene for mastitis resistance. This study aimed to analyze the associations of single nucleotide polymorphisms (SNP) or haplotype and somatic cell score (SCS) in 404 Chinese commercial dairy cattle including Chinese Holstein, Sanhe cattle and Chinese Simmental breeds. The polymerase chain reaction and sequencing methods were used for detecting genotype and allele frequency distribution of the two SNPs (rs8193062, rs8193064), statistical results showed that T allele at rs8193062 and C allele at rs8193064 were the predominate alleles. Moreover, six SNPs, including two SNPs (rs8193062, rs8193064) and four SNPs (rs8193060, rs8193069, rs29017188, rs8193046) which were chosen according the polymorphism level for the same cattle populations in previous studies, were used for haplotype analysis, the results revealed that twenty-one haplotypes were found in the mentioned animals, of which, Hap1 (30.5 %) and Hap2 (30.4 %) were the most common haplotypes. Hap2, Hap4 and Hap12 might negatively effect on milk SCS, whereas Hap13 might positively effect on milk SCS. The results in this study might assist in marker assisted selection and provided some reference to be implemented in breeding programs to improve the mastitis resistance of dairy cattle.     

Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART,SHBG and SLC37A2

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10⁻⁴) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.     

Effect of BMP15 and/or AMH during in vitro maturation of oocytes from involuntarily culled dairy cows

The high metabolic activity to which the dairy cattle are exposed to maintain milk production altered steroid metabolism that affects reproductive physiology and reduce oocyte competence. Our aims were (a) to characterize the competence of immature oocytes collected from dairy cattle based on the expression of genes in cumulus cells (CCs) and (b) to improve oocyte competence to support preimplantation embryo development by the supplementation of maturation medium with bone morphogenetic protein 15 (BMP15) and/or anti‐mullerian hormone (AMH). Oocyte donors were identified at the moment of ovary collection and grouped by involuntarily culled dairy cows (Holstein breed) or beef cattle. The embryo development speed to blastocyst of the cull dairy cattle versus beef cattle (control group) was lower. Besides, <10% of oocytes (with CC biopsies) derived from dairy cattle were able to develop to the blastocyst stage. In addition, a higher level of expression and a positive correlation were observed in the expression of most of the genes evaluated (LUM, KRT18, KRT8, CLIC3, BMPR1B, and SLC38A3) in the cumulus–oocyte complexes that produced blastocysts versus those which did not develop correctly (arrested development). Further, use of BMP15 in the maturation of oocytes from dairy cattle seems to increase competence, modulating the expression of OCT4, SOX2, CDX2, GATA6, and TP1 in resulting blastocysts.     

Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

Background

Genomic selection is increasingly widely practised, particularly in dairy cattle. However, the accuracy of current predictions using GBLUP (genomic best linear unbiased prediction) decays rapidly across generations, and also as selection candidates become less related to the reference population. This is likely caused by the effects of causative mutations being dispersed across many SNPs (single nucleotide polymorphisms) that span large genomic intervals. In this paper, we hypothesise that the use of a nonlinear method (BayesR), combined with a multi-breed (Holstein/Jersey) reference population will map causative mutations with more precision than GBLUP and this, in turn, will increase the accuracy of genomic predictions for selection candidates that are less related to the reference animals.

Results

BayesR improved the across-breed prediction accuracy for Australian Red dairy cattle for five milk yield and composition traits by an average of 7% over the GBLUP approach (Australian Red animals were not included in the reference population). Using the multi-breed reference population with BayesR improved accuracy of prediction in Australian Red cattle by 2 – 5% compared to using BayesR with a single breed reference population. Inclusion of 8478 Holstein and 3917 Jersey cows in the reference population improved accuracy of predictions for these breeds by 4 and 5%. However, predictions for Holstein and Jersey cattle were similar using within-breed and multi-breed reference populations. We propose that the improvement in across-breed prediction achieved by BayesR with the multi-breed reference population is due to more precise mapping of quantitative trait loci (QTL), which was demonstrated for several regions. New candidate genes with functional links to milk synthesis were identified using differential gene expression in the mammary gland.

Conclusions

QTL detection and genomic prediction are usually considered independently but persistence of genomic prediction accuracies across breeds requires accurate estimation of QTL effects. We show that accuracy of across-breed genomic predictions was higher with BayesR than with GBLUP and that BayesR mapped QTL more precisely. Further improvements of across-breed accuracy of genomic predictions and QTL mapping could be achieved by increasing the size of the reference population, including more breeds, and possibly by exploiting pleiotropic effects to improve mapping efficiency for QTL with small effects.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0074-4) contains supplementary material, which is available to authorized users.     

正交优化法建立奶牛基因组DNA RAPD-PCR最佳反应体系

从 36头荷斯坦奶牛血样中提取基因组DNA ,以相同DNA浓度混成DNA池。以其为模板 ,通过正交设计试验 ,建立了RAPD PCR最佳反应体系。