جستجوی مقالات مرتبط با کلیدواژه "holstein cattle" در نشریات گروه "علوم دام"

The purpose of present study was to detection and comparison of molecular markers in BOLA gene were between pregnant and non-pregnant Holstein cows. The studied animals included Holstein Friesian cows and did not have any clinical diseases or history of reproductive problems. The number of studied samples included 8 pregnant and 11 non-pregnant cows. The data analyzed in the present research were the result of RNA sequencing. After quality control, the reads were aligned and located against the reference genome and the software provided in two packages, Picardtools and GATK were used to identify the considered variants. The interaction network of studied gene was drawn at the protein level using the STRING database. The results showed that there are 4 different transcripts and a total of 15 SNPs in the BOLA gene in non-pregnant cows compared to pregnant ones, and these polymorphisms were observed in the BOLA gene and its upstream regulatory region which is the binding site of microRNA bta-mir-11979 and specifically, it has only been observed in non-pregnant cows. Among the observed mutations, a mutation at the position of 28723238 base pairs leads to the substitution of adenine with cytosine nucleotide and creating a stop codon in the BOLA protein. No deletion/insertion variants were observed in the studied gene. Considering the missense and nonsense mutations observed in the BOLA gene, which probably leads to fundamental changes in its protein structure, the polymorphisms identified in this research can be used for selection in breeding programs.

The purpose of this research was to determine the population structure and effective population size of Najdi, Holstein and their hybrids in the herds of Khuzestan province. For this purpose, the genomic information of 329 cattle samples including 141, 60 and 128 samples from Holstein, mixed and Najdi breeds were used. The samples were genotyped with Illumina SNP30K genomic arrays. Population analysis was done using PCA and plotNJ, and in both methods the populations were somewhat separated. The range of r2 is from 0.150 ± 0.359 in chromosome 26 to 0.244 ± 0.450 in chromosome 20 for the Holstein breed and 0.130 ± 0.319 in chromosome 28 to 0.271 ± 0.462 in chromosome 20 in were mixed livestock, while the highest value of r2 was observed in the Najdi breed from the range of 0.120 ± 0.311 in chromosome 28 to 0.271 ± 0.483 in chromosome 20. The effective size of the populations in the fifth generation for the populations of this study was 45 Najdi heads, 101 mixed heads and 110 Holstein heads. These numbers for Najdi cattle are far from the recommended values for the protection of populations, and this indicates a serious risk of eliminating native Najdi cattle in the near future. Reducing the effective size will increase the sensitivity of this population to the upcoming environmental changes.

In this study, genomic data of 590 cattle were used including native breeds of Sarabi, Kermani, Kurdi, Talashi, Sistani, Najdi, Mazandarani and Pars, crossbred from northwest of Iran, Holstein populations from Iran, France and Ireland. Quality control and data filtration were performed using Plink 1.9 software. After this quality control, individuals and SNPs with call rate below 0.95%, SNP makers with minor allele frequency (MAF) > 0.01%, divergence from Hardy-Weinberg Equilibrium were excluded. This procedure yielded 509 individuals with 13512 SNP marker. Then filtered data were used to genetic diversity and clustering analysis. Identification of genetic groups were performed using PCA analysis data by GenABEL software. PCA and ADMIXTURE analysis showed that studied populations are in 4 separate categories including purebred Sarabi population in the first group, crossbred from northwest of Iran in the second group, purebred Holstein populations in the third group and native breeds of Iran were in the fourth group. Further details of demographic differentiation were identified by Weir and Cockerham's fixation index. The range of differentiation in the present study varied from 0.180 between Sistani and Kurdish breeds to 0.007 to 0.004 between the Iran Holstein breed and Ireland with France Holstein breeds. The results showed that the highest difference between indigenous and Holstein breeds related to Sistani breed that had the highest difference with different Holstein breeds (0.128 to 0.138). With slight differences from other Iranian indigenous breeds, the Kurdish and Mazandaran breeds had the smallest genetic differences with the studied Holstein populations.

Today, reproductive problems are one of the major concerns in the dairy industry. The aim of this study was to detect the lack of function mutation of p.Q579X affecting spontaneous abortion and reproduction problems in APAF1 gene in Holstein cattle. In total, 200 blood samples were prepared and DNA was extracted with commercial kit. Then a specific pair of primers was designed to amplify a fragment with lengths of 456 bp from the exons 11 of the APAF1 gene and genotyping was performed by PCR-SSCP method. In APAF1 locus two alleles of A and B and two genotypes of AA and AB with frequencies of 96.76, 3.24 and 93.51 and 6.49 were observed, respectively. The BB genotype was not observed in the studied samples. After determining the genotype of the samples, two samples from each genotype were sequenced from both end and alignment of the obtained sequences and their comparison with the reference sequence from the gene bank to detect the mutation was carried out using BioEdit (version7.0.9.0) software. The results of bioinformatics analysis showed that the lack of function mutation of p.Q579X, which is one of the mutations affecting abortion in Holstein cattle, is present in the AB genotype of APAF1 gene in Holstein cattle in Iran. Given that this mutation causes abortion in cow in homozygous form, the results of this study can be directly used in breeding programs in order to identify the carriers of this mutation and culling them from Holstein dairy herd.

The aim of this study was to identify the lack of function mutation of p.R12X affecting reproductive problems and abortion in SLC37A2 gene by PCR-SSCP and sequencing methods in Holstein and Montbeliarde cows, For this purpose, 250 blood samples (150 Holstein and 100 samples of Montbeliarde) were prepared and DNA was extracted by kit. A pair of specific primers was designed with Oligo7 software to amplify a fragment with length of 208 bp from exon 2 of the SLC37A2 gene, which contains mutation. Genotyping was done by SSCP method and allelic and genotypic frequencies and population genetic indices were calculated by POPGEN software. In SLC37A2 locus, two AA and AB genotypes with frequencies of 98.7 and 1.3, and 86 and 14% were observed in Holstein and Montbeliarde breeds, respectively. Also, SLC37A2 allelic frequencies in both Holstein and Montbeliarde for alleles A and B were estimated to be 99.3, 0.7 and 93 and 7%, respectively. The Fischerchr('39')s exact and Chi-square tests for comparing allelic and genotypic frequencies between two populations showed that there was a significant difference in allelic and genotypic frequencies between Holstein and Montbeliarde population (P <0.05). After genotyping, a sample of each genotype was sequenced in both end and the bioinformatics of the sequences obtained were performed with BioEdit software. The results showed that in the AB genotype of SLC37A2 gene in Holstein and Montbeliarde cows there was a lack of function mutation (p.R12X). Considering the role of p.R12X mutation in reproductive defects and abortion in Montbeliarde cattle, the results of this study can be directly used in the breeding programs to identify carrier animals and culling them from commercial and rural herds.

This study was performed to determine the digital expression profile of different genes expressed in Holstein and Cholistani breeds as well as to evaluate the performance of predicted proteins derived from differentially expressed genes between these two breeds using RNA-Seq data. For this purpose, the whole mRNA sequence for a blood sample of American Holstein and Pakistani Cholistani cattle populations was obtained and by sequencing and locating RNA-Seq reads on the bovine reference genome and determining the digital expression profile, the differentially expressed genes were obtained. The results of this study showed that there were 24616 genes and 26716 isoforms on the transcriptome of these two breeds, out of which, 41 genes were identified with substantial and significant differential expression (P <0.000015). It was also found that approximately one-third of genes whose functions is altered accros two breeds, encode hydrolase enzymes, five of the predicted proteins, FOS Fos proto-oncogene proteins, AP-1 transcription factor subunit, the vhl-elonginc-elonginb structure, transcription factor FosB/ JunD bZIP domain, T yeast U2AF complex pseudomonas aeruginosa transcriptional regulator PA2196 and zif268 zinc finger-dna complex that are involved in transcriptional regulation and RNA editing. Investigation of network interactions between predicted proteins from differentially expressed genes showed that predicted proteins are involved in different pathways such as TNF signaling pathway, Salmonella infection, MAPK signaling pathway and rheumatoid arthritis. Overall, these two breeds were found to be well-adapted to environmental conditions due to different environmental conditions and evolutionary distance and this coordination at the molecular level of the expression of specific genes was found in this study. One of the reasons supporting this is the greater role of the immune system in the Cholistani breed due to its higher exposition to contamination than the Holstein breed that led the expression of bactericidal proteins (Cathelicidin 1) was up regulaged, as a result, the activity of the immune system might be improved. The study also found that the IL1B gene had the highest degree of gene-drug interaction with Canakinumab drug.The results of this study indicate that in breed comparisons, a close look at the activity of proteins produced by different genes could better explain breed differences at the molecular level.

The aim of this study was the molecular and bioinformatics analysis of regulatory upstream region of leptin and SIGLEC5 genes in association with production and reproduction traits in Holstein cattle. For this purpose, 300 blood samples were collected randomly and DNA was extracted. Two fragments of 251 and 406 bp from regulatory upstream regions of leptin and SIGLEC5 genes were amplified by PCR and genotyping was done by SSCP method. One sample from each banding pattern was sequenced and bioinformatics analysis were done by BioEdit and DNASIS MAX softwares. The SIGLEC5 locus was monomorphic, whereas, four banding patterns of A, B, C and D with frequencies of 0.25, 0.36, 0.22 and 0.17 were observed in leptin locus, respectively. Statistical analysis showed that leptin gene polymorphism was significantly (P<0.05) associated with milk lipid and status of parturition, so that cows with banding pattern A had the highest milk fat and cows with banding pattern D showed lowest milk fat. Also, cows with banding pattern D had the best status of parturition (easy birth) (P<0.05). The bioinformatics analysis showed 14 and nine motifs in SIGLEC5 and leptin genes, respectively. Therefore, according to the results of this study, leptin gene can be suggested to improve production and reproduction traits. In addition, complementary studies on other regions of SIGLEC5 gene to find relations between production and reproduction traits in Holstein cattle are highly recommended.

Fatty acid synthase (FASN), a multifunctional protein that carries out the synthesis of fatty acids, is coded by FASN gene which is known as major candied gene and plays a central role in de novo lipogenesis in mammals. This study was conducted to detect single nucleotide polymorphisms (SNPs) of the FASN gene and explore their relationships with three economically important traits including milk production (M), calving interval (CI) and conception rate (CR) in Holstein cows of Kerman province. The whole blood samples corresponding to the 38 Holstein cows with high and low estimate breeding values were collected. Genomic DNA was extracted from blood samples of the cows using a genomic DNA kit according to the manufacturer’s instructions. The genetic material was used for polymerase chain reaction amplification of selected gene fragments (750bp length from exon 37 to 39). All of PCR products were subsequently used directly for sequencing. Analysis of the target sequence followed by multiple regression of average allele substitution effects on M, CI, and CR traits revealed 58 SNP markers, among which 8 SNPs were totally associated with productive and reproductive traits. (M), (CI) and (CR) were affected by three (g.16593A>G, g.16670C>A and g.16776C>T), three (g.16524G,C,T>A, g.16830G,C,T>A, g.16833A,T>G) and two (g.16594A,C>G and g.16811A,T>G) SNPs respectively (P<0.05). Association between polymorphism in FASN gene and traits could be used as molecular markers for determination of animal's genetic potential as well as breeding strategies in Holstein population.

The objective of the present study was the genetic evaluation of retained placenta (RP), metritis (MET), number of inseminations to conception (INS), and days open (DO) in Holstein cows using standard (SMMs) and recursive (RMMs) mixed models. Data on 50230 first-lactation Holstein dairy cattle, collected during 2008 to 2017 in 17 large dairy herds were used. The data was analyzed using four-variate animal Threshold-Gaussian models under SMMs and RMMs. The existence of causal effects from RP on MET, INS and DO, from MET on INS and DO and from INS to DO were considered in RMMs. The causal effects of RP and MET on INS were 0.19 and 0.09 services, respectively; and those on DO were 4.74 and 5.38 days, respectively. Also, causal effect of INS on DO was obtained as 33 days. The considered causal relationships except that of RP on MET, phenotypic and residual correlations among the disorders and fertility traits were statistically significant and different under two models. Posterior means of heritability for RP, MET, INS and DO were 0.15, 0.17, 0.07 and 0.09 under SMMs, respectively; and 0.16, 0.17, 0.07 and 0.1 under RMMs, respectively. The difference between the corresponding heritability estimates under SMMs and RMMs were not statistically significant. Therefore; RMMs may be an alternative for SMMs in genetic evaluation of studied traits in first -lactation Holstein cows.

Abstract Introduction With the advent of high throughput genotyping technologies, interest has grown in using genomic information to estimate breeding values. Genomic selection, in which genetic markers across the whole genome are used to estimate breeding values of individuals, is routinely applied in dairy cattle breeding programs. In dairy cattle, genomic selection has resulted in a substantial increase in the rate of genetic gain compared to traditional selection. This has been achieved mainly by reducing the generation interval, which became possible because of the higher accuracies of genomic breeding values (GEBV) estimated early in life compared to parent averages. Since single nucleotide polymorphism (SNP) genotypes are bi-allelic and, therefore, their information content is not high, so SNP-based methods may not effectively capture the linkage disequilibrium (LD) between SNPs and multi-allelic quantitative trait loci (QTLs). Haplotypes are in general “multi-allelic” and compared to individual SNPs may better capture LD with multi-allelic QTL. Furthermore, most of the SNPs in the chips are old mutations. This may imply that SNP-based relationship matrix traces very old relationships from distant relatives and, therefore, may not trace changes due to recent selection accurately. It has also been hypothesized that using similarity between haplotypes to model the covariance between genomic effects can result in better predictive ability than modeling covariance based on SNP genotypes. So the objective of this study was to investigate the accuracy and bias of GEBV using genomic best linear unbiased prediction (GBLUP) with alternate genomic relationship matrices (G) based on SNPs and haplotypes information. Materials and Methods The North American Holstein genotype data was provided by the Canadian Dairy Network (CDN). The Holstein bulls with official domestic proofs were genotyped using the Illumina Bovine SNP 50 TM Chip. The genotyped Holstein bulls were classified as estimation group and prediction group. All bulls in prediction group were those bulls who were born from 2007 to 2011 and had official proof in 2015. De-regressed EBV (dEBV) based on the 2015 genetic evaluation (dEBV2015) were used for validation purposes. The estimation group included bulls born mainly between 1960 to 2007. The analyzed traits were fat yield, milk yield, somatic cell score, conformation, and days open. The GEBVs for mentioned traits were estimated based on GBLUP models using SNP1101 software. Three G matrices were built: 1) SNP genotype based relationship matrix (GSNP), 2) haplotype based relationship matrix (GHAP), and 3) hybrid matrix composing of SNP genotype and haplotype based relationship matrices (GSNP, HAP). Accuracy of prediction was calculated as Pearson’s correlation between estimated GEBV and dEBV2015 for prediction group. Bias of prediction was also calculated as regression coefficient of dEBV2015 on GEBV for prediction group. Results and Discussion Observed differences between alternate G matrices were larger in prediction bias than in prediction accuracy. Accuracy of genomic predictions based on GHAP were 0.73, 0.71, 0.62, 0.54, and 0.50 for fat yield, milk yield, somatic cell score, conformation, and days open, respectively. Accuracy of genomic predictions based on GSNP also were 0.72, 0.70, 0.61, 0.56, and 0.49, respectively. Although using GHAP instead of GSNP did not significantly improve the accuracy of prediction, it resulted in estimates with 6 (conformation) to 15% (days open) less bias and closer to one over the different traits. Genomic selection based on GHAP instead of GSNP seems to improve bias of prediction for traits under recent selection, such as days open. This might also be due to the fact that this trait is lowly heritable. Although accuracy of genomic predictions based on GSNP, HAP were similar to GSNP, using GSNP, HAP resulted in higher biases than GHAP or GSNP. Conclusion Based on these findings, GHAP might be an alternative approach to reduce bias of genomic predictions in routine genomic evaluations. Genomic selection based on GHAP instead of GSNP improved bias of prediction especially for low heritable traits under recent selection, such as days open. Small gain achieved with GHAP compared to GSNP may imply that the correlation between IBS and IBD in GHAP is not optimal for maximization of prediction accuracy. Based on current results further research is needed to investigate the use of haplotype length and allele frequency of markers in haplotype segments in the definition of haplotype similarity. In addition, this study suggests further research to assess the effect of recent selection, heritability and genetic architecture of the traits on the performance of haplotype based relationship matrix.

Enhancing disease resistance in animal production can be achieved by genetic improvement programs. Candidate gene polymorphism is one of the potential approaches for search of association between SNP within this gene phenotype of animals, particularly in MAS for mastitis of large dairy cattle populations. Polymorphism of exon 9 of the BRCA1 gene was investigated by the PCR-RFLP method in 60 Iranian Holstein cattle. In this study, 3 different alleles were recognized. Polymerase chain reaction-restricted fragment length polymorphism method was used to amplify, digestion and electrophoresis for a 219 base pair of bovine BRCA1 gene. A polymorphism was revealed by G-A single nucleotide polymorphism in +46126 position of BRCA1 gene. Observe genotype frequencies for KK, KL, LL were 0.27, 0.43 and 0.30 respectively, and allele frequencies for observed K and L allele were 0.48 and 0.52 accordingly. For analysis of variance, normality test and transformation of raw data for SSC records was performed based on previous main reports and literature reviews. GLM and logistic regression methods was used for association study between genotype and collected phenotype. As a final message of the present report, KK genotype was showed significantly affect SCC data and has tendency for low SCC score than other two genotypes. The results of present study indicated BRCA1 gene as an effective candidate gene could be benefit for mastitis resistant in Marker Assisted Selection strategies in dairy cattle.

In this study, estimation of genetic parameters were performed for some reproductive disorders (retained placenta, repetitious abortion and infertility) and genetic and phenotypic correlations between these traits with milk, fat and protein yield. The obtained data were collected from 63403 Holstein cows on Animal Breeding Center of Iran (from 2001 to 2013). After editing the data, estimation of genetic parameters for traits was performed by univariate animal and Threshold models. Estimates of genetic and phenotypic correlations among mentioned traits and production traits were performed by bivariate animal model via using the ASREML Software. Results showed that heritability for retained placenta, repetitious abortion and infertility traits by animal model were 0.00012, 0.0085 and 0.051, respectively, on the other hand by using threshold model, there was not a reasonable estimation. Genetic correlations between retained placenta and persistency of milk, fat and protein yield were 0.4, 0.32 and 0.38, respectively; with repetitious abortion were 0.14, 0.25 and 0.1; and with infertility were 0.01, 0.09 and 0.02, respectively the phenotypic correlations among these reproductive disorder traits and production traits were relatively low.

The aim of this research was to investigate the calving season effect on some of the productive traits including milk production, fat percentage and some of reproductive traits including pregnancy period and calf birth weight and also estimation of genetic parameters of studied traits too. In this study the data of 22360 Holestein dairy cows form Tehran province’s 65 herds of between 2012 to 2016 was used that were collected by the country animal breeding center. The study of fixed effects (HYS) and comparison of means was carried out with GLM Procedure of SAS 9.2 software. Estimation of genetic parameters was done by ASReml 3.0 software. The effect of calving season on all traits was significant (p

In this study, estimation of genetic parameters of Lameness and genetic and phenotypic correlations between Lameness and milk, fat and protein yield were performed. The data obtained from 63403 Holstein cows were collected from the Animal Breeding Center of Iran between 2001 to 2013 Estimation of genetic parameters for lameness was performed by univariate animal and Threshold models. Also, estimation of genetic and phenotypic correlations between Lameness and production traits was performed by bivariate animal model by using the ASREML Software. Results showed that heritability of Lameness with Animal and Threshold models were 0.02 and 0.057, respectively. Estimated heritabilities with two methods were low, but with Threshold model were more than linear model, also genetic correlations between Lameness and persistency of milk, fat and protein yield were 0.31, 0.23 and 0.27, respectively and phenotypic correlations between Lameness and persistency of milk, fat and protein yield were 0.048, 0.037 and 0.029, respectively. Positive correlations between Lameness and production traits show that long term selection for production traits could be the most important factor for culling by Lameness disorders.

In order to estimate the genetic parameters for days from calving to first service (DFS) in Iranian Holstein cattle by using repeatability, multiple-trait (MT) and random regression (RR) models, 159,482 records of parities 1 to 6 collected during 1981 to 2013 and distributed over 33 large Holstein herds were used. Bayesian information criterion of MT model was lower than other models and Bayesian factor of MT model was significant compared to other models (P

Estimation of variance components is necessary for precise planning of animal breeding programs. The present study was conducted to estimate genetic parameters of milk yield traits in the first parity of Holstein cattle in Hamedan province.
First parity records of 4027 lactating cows from 148 herds, collected by Agricultural Jahad Institute of Hamedan province, were used for this study. (Co)variance components of milk yield traits were estimated by bivariate analyses of mixed animal models based on Average Information algorithm of Restricted Maximum Likelihood (AI-REML). In these models the fixed effects were herd-year-season of calving and Holstein percentage (for all traits) and calving age (for 305 d milk yield, fat corrected milk and fat yield traits). The animal additive genetic effect was considered as the random effect in the model.
Heritabilities of 305 d milk yield (MY), fat corrected milk yield (FCM), fat percentage (F), protein percentage (P), fat yield (FY) and protein yield (PY) at the first parity were estimated 0.16, 0.17, 0.25, 0.18, 0.20 and 0.14, and their genetic trends were 2.510 and 2.010 kg/yr, -0.001 and -0.000 %/yr and 0.068 and 0.022 kg/yr, respectively. The estimated genetic correlations between MY and FCM, F, P, FY and PY traits were 0.86, -0.27, -0.25, 0.60 and 0.90, respectively. Genetic correlations of FCM with F, P, FY and PY were estimated 0.25, 0.25, 0.94 and 0.94, respectively.
Regarding the higher heritability of FCM than MY and also its high and positive genetic correlations with milk contents, it seems that selection based on FCM is better than the MY.

The aim of this study was to investigate genetic diversity in Mazandaranian native cattle in compared to Holstein breed, using Inter microsatellite (ISSR) markers. A total of 175 animals, including 71 Mazandaranian and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out using modified salting out method. (AG)9C was used as ISSR primer in PCR reaction. Analyzing of banding patterns showed 30 (93.75%) and 24 (75%) polymorphic bands in native and Holstein herds, respectively. Genetic variation indices, including observed number of alleles, effective number of alleles, Shannon index and Nei’s gene diversity in indigenous cattle were higher than in Holstein. Lower level of diversity in Holstein cattle may be of the consequence of applying intensive selection programs and artificial insemination; however native cattle have been less affected by artificial selection. Knowledge of genetic diversity in indigenous breeds provides important information for management of native resources in order to avoid inbreeding depression and maintain genetic variability.

The Toll-like Receptor 4 (TLR4) is an innate immune protein on cell surfaces that identifies Lipopolysaccharide (LPS) of gram-negative bacteria. Genetic markers associated with innate responses during mastitis could help in selection of cattle to improve disease resistance. The objective of this study was to determine the association between TLR4 gene and clinical mastitis، using selective genotyping method. A total of 270 cows of two extreme groups namely: top clinical mastitis resistant vs. top susceptible ones were selected. For genotyping، the 2 methods of: PCR-RFLP and PCR-SSCP were made use of. Identified polymorphisms induced A-G in exon 2، and C-T in exon 3. Following sequencing، polymorphism effects on clinical mastitis were analyzed using logistic regression. The results indicated that TLR4 gene was significantly associated with clinical mastitis resistance.

In order to evaluate paternity test using microsatellite markers، a small sample of Iranian Holstein cattle population including 8 unknown individuals without any given prior knowledge on their genetic relationships were tested using 12 microsatellite loci recommended by International Society of Animal Genetics (ISAG). They were genotyped by a multiplex PCR set consisted all 12 fluorescently labeled primer pairs. Allele and genotype frequencies were estimated and simulated by CERVUS 2. 0 software for paternity analysis. Using this software parentage test and relationship between samples have been determined and confirmed by sample’s provider. Paternity relationship including one or two parents for an offspring and also repeated samples were observed. The average expected heterozygosity of 11 analyzed loci and the mean value for PIC was 0. 72 and 0. 631 respectively. Except TGLA53 locus that was excluded from further analyses due to low quality of alleles and genotype detection، total exclusion probability of 11 loci showed that the paternity test using microsatellite loci mentioned here can be successfully implicated in large scale in Holstein dairy cattle population in Iran.