mohammad moradi shahre babak

Bovine Leukemia Virus (BLV) infection is more common in dairy cattle herds. The main cause of leukosis is the disease that leads to the creation of cancerous lymphocytes in different organisms of the body and affects different species, including cattle. This disease reduces milk production and causes reproductive diseases, and finally the removal of infected animals. Due to trade restrictions and deaths caused by lymphosarcoma, it causes direct economic losses, which is also related to the decrease in milk production and the increase in the elimination rate. No treatment or vaccine is known for this disease so far. Therfore, studying the genomic regions related to susceptibility to BLV infection can be effective in controlling and treating this disease and genetic improvement of animals. This research aimed to perform a whole genom-wide association study (GWAS) study of cattle to identify genomic regions and candidate genes associated with BLV infection.

Material and Methods:

 This study was conducted using Holstein cows that were naturally infected with BLV. For this purpose, blood samples of 150 Holstein cows in an industrial dairy cattle farm in Isfahan were collected, and DNA and serum of them were extracted. The prepared DNA samples were genotyped using k30 microarrays (SNPchip30k) (by Illumina). Quality control of sequences for rare allele frequency components (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1×10-6) and significance test was performed by PLINK software. Analysis of the ontology of genes was done by the online database https://www.Uniprot.org and finally, the ontology diagram of genes was drawn and analyzed by the online database PANTHER.

After control analyzing, 145 cows (77 cases and 68 controls) and 22868 markers were left for further analysis, finally 8 markers higher than the significant threshold were identified, and most significant markers were located on chromosomes 17 and 21. Using ensemble sites and genecards, genes associated with significant selected markers were identified. The most important of them were GRK4, TP53BP1, SCAPER, GLRB, PDGFC, TNIP2, PSTPIP1, CEP350, MR1, TOM1L2, SREBF1, COPS and TNFRS13B. Gene Ontology (GO) analysis showed that these genes are more involved in protein-coding and play a role in regulating enzyme activities, intercellular exchanges, DNA stability, calcium activity, nervous system, and lipid activity. Also, according to other research, these genes played a role in cases such as infectious poison lesions, subclinical ketosis disease, BCS of cattle, fatty acid metabolism and fat deposition, various infections such as mastitis, and in meat traits and muscle stiffness in beef cattle. It should be noted that some of these genes were related to the pathways of innate immunity, humoral immunity, and cancer tumors.

Therefore, it can be concluded that whole genome wide association study analysis as well as gene ontology analysis to identify genomic regions related to viral infections such as leukemia can be effective in designing treatment methods and prevention methods and in choosing Genomics and breeding programs in Iranian dairy cows.

The agriculture contribute to 50-60 % of global methane emission and ruminants have a key role in this contribution. Methane has an important role in global warming and it's global warming potential is 25 times greater than CO2. Furthermore, methane is the second most abundant global anthropogenic greenhouse gas after carbon dioxide. The present study aimed to perform genome wide association study to identify genome regions affecting the predicated methane production based on the concentrations of volatile fatty acids of rumen in Iranian Holstein cattle. One-hundred and fifty hair and rumen digesta samples were sampled using the two-tailed strategy based on breeding values of milk. After the measurement of the concentration of volatile fatty acids of rumen, methane emission of each animal was predicated according to these acids. DNA of animals was genotyped using GGP-LD v4 SNP panel (contains 30108 SNPs). Fourteen significant SNPs associated with methane emission trait located on 1, 2, 6, 10, 15, 17 and 18 chromosome were identified. Using annotating some quantitative trait locus (QTLs) were discovered around some of these SNPs. The results showed a genetic selection potential to mitigate methane emission per animal. Since genetic improvements are heritable, cumulative, and permanent, this improvement would be permanent and beneficial.

The main objective of dairy farmers is to maximize their profit. Increased incidence of mastitis in farms is one of the health problems, causing in serious economic losses as a consequence of treatment costs and reduction of production and longevity. The objective of this study was to evaluate the genetic architecture and associated genomic regions with milk production and somatic cell score (SCS) as an indirect measure of mastitis and the quality of raw milk. Thus, an SNP data set from 1938 Holstein bulls were used in a single-step genome-wide association study. The proportion of additive genetic variance (agv) for each of 1.5-Mb genomic window (adjacent SNPs) was used to identify informative genomic regions, accounting for more than 1% of the agv. A total of 11 significant windows over 9 bovine autosomes were found for the SCS. A peak on BTA14 explained the largest proportion of variance (3.85%). These regions together, explained 20% of agv and harbored 94 candidate genes. For milk yield, we identified 6 informative windows across 6 chromosomes, and a peak on BTA10 explained 2.08% of agv. These regions, explained 8.8% of the agv and sheltered 89 candidate genes. For the fat yield, 9 significant windows were identified on 7 chromosomes and explained 15.6% of agv, and 9 windows contained 87 candidate genes on 8 bovine autosomes were associated with milk protein yield (10.6% of agv). Four genomic regions had a pleiotropic effect. These findings can be an important source of information in genomic evaluation of dairy cattle.

In order to evaluate the effect of genotype by environment interaction on production traits of Holstein cattle of Iran, first lactation test day records of 344170, 135000 and 156840 of milk, fat and protein yield on 34417, 13500 and 15684 cows and SNP markers of 1935 genotyped bulls were used. The production data were retrieved from the Animal Breeding Center and Productions Improvement of Iran’s database which were collected from 2013 to 2018. To consider the interaction of genotype and environment, mean of temperature-humidity index (THI) in three days before each test day records as continuous environmental effect were retrieved from the 35 closest meteorological stations in the vicinity of 139 Holstein herds from 13 provinces. Variance and covariance components were estimated through a single-trait random regression model with orthogonal Legendre polynomials of second order for days in milk and THI using AIREMLF90 software. The results showed that changes in THI across lactation led tofluctuations in additive genetic variance over time. The change in heritability of milk production traits over lactation followed the same trend as additive genetic variance. The results from cross-validation analysis showed that including genomic information into the predictive model, increased prediction accuracy and including THI information increased unbiasedness. Due to the changes in milk production of daughters of bulls across days and THI , genotype by environment interaction should be considered when selecting bulls under different conditions.

This study was conducted to evaluate prevalence of BVD and the strategies which were applied for prevention of BVD over the past 50 years in some provinces of Iran. Blood samples of 500 Iranian Holstein race were randomly collected from three dairy farms located in Tehran, Isfahan and Qazvin provinces. BVD control protocols of these farms were recorded. ELISA technique was used to measure the antibody and antigen titers for BVD. RT-PCR technique was performed to investigate the presence and the type of virus in all samples. The prevalence of Ab-/ Ag-, Ab+/ Ag-, Ab-/ Ag+ and Ab-/ Ag+ were 10.2%, 78.8%, 7.2% and 3.8%, respectively. Furthermore, approximately 4.2% of the animals were PI and the prevalence of antibody and antigen titers had not significant difference in three provinces. All positive samples were BVDV type 1. Type 2 was not observed in this study. The results of the study indicated that the efficiency of the used protocols to control BVD diseases is not successful. So, to control the BVD, applying large management policies at the national level is fundamental beside the biosecurity strategies.

In order to estimate the effective population size (Ne) in Iranian water buffalo blood and hair samples of 407 individual from Azari (N=260), Khuzestani (N=120) and Mazandrani (N=27) buffalo populations were gathered. After DNA extaraction, the samples were genotyped using Axiom® Buffalo Genotyping 90K Array. The Ne was estimated from 700 to 4 generations ago and also for the present generation by linkage disequiblirum data and based on heterozygote-excess method using NeEstimator (V2), respectively. Estimated Ne for Azari, Khuzestani and Mazandarani were calculated 1530, 1375 and 1141, respectively, for 700 generations ago. Ne for the present generation in Azeri, Khuzestani and Mazandarani were estimated 447, 226 and 35, respectively. The Ne for Azeri and Khuzestani were relatively high and these two populations were not endanger to extinction, but their Ne has been declined in the resent generations massively and it is necessary to care about the maintenance of Ne and relatively high diversity for these populations. However, the Mazandarani population is endangered because of low Ne and so it is necessary to carefully monitor their effective population size, improve the profitability of production and planning a suitable mating scheme to control inbreeding and genetically conserve this population.

The objective of this study was the detection of polymorphism in ATP1A1 gene and its association with conception rates in Holstein and Sarabi cows by PCR-SSCP method. For this purpose, blood samples were taken from 124 cows. DNA was extracted from whole blood using modified salting-out method and polymerase chain reactions were performed for amplification of 330bp fragment of the bovine ATP1A1gene. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to scan for the mutations within the amplified regions. Subsequently, a numbers of samples per each band pattern were sequenced for identification of Single Nucleotide Polymorphism (SNP). The results of the sequencing and alignment using available sequences in NCBI two SNPs in the ATP1A1 gene that one of those was located in exon14 and another one in intron14 area and the mutation located in exon area was along with no changes in amino acid and obtained protein of this gene. For evaluating of association between this locations and conception rate trait, the band pattern (haplotype) were considered in the model. The results showed that the observed haplotypes in the ATP1A1 gene is not significantly correlated with conception rate.

In order to detect signature of selection on buffalo genome, a set of 287 water buffalo samples from 260 Azari and 27 Mazandarani buffalo breeds were genotyped using the Axiom® Buffalo Genotyping 90K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 14 regions with outlier FST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected and 105 genes and 28 QTLs with selection signatures were detected. A high proportion of identified genes (N=27) in regions under selection were involved in olfactory receptor, also some of the detected genes were associated with growth and body development, metabolicand apoptosis possesses, immune system development, and mammary gland development. Some of the identified QTLs in regions under selection were associated with growth traits such as body weight at birth, weaning and mature, subcutaneous fat, meat yield and carcass weight. The detected QTL for milk traits were only associated with milk contents and somatic cell count. However, it is recommended to carry out association studies to show the actual function of these genes.

The methane production from ruminant production system was estimated to reach 250-500 L per animal per day which has been reported to contribute up to 8-10 % of global warming during the next 50-100 years. The aim of this study was to investigate the correlation among methane emission (predicted by volatile fatty acids) with milk production traits, its components and breeding values (BV) of these traits in Iranian Holstein cattle. The rumen digesta was obtained from 150 cattle through stomach tubing and this population divided into 2 groups with 75 cattle in each (the groups have different milk production BV). Data were analyzed by R.3.3.0. The results showed that methane emission per unit of milk and fat were different in the two groups (P<0.0001). Also, the BVs of milk production, fat and protein traits and daily production of milk, fat and protein had weak to moderate negative correlation with methane emission per unit(P<0.05). The highest correlation was observed between daily production of fat with methane emission per unit of fat (-0.79) as well as daily milk production with methane emission per unit of milk (-0.62). These results showed that methane emission may be reduced by indirect selection per generation for the traits had a high correlation with the gas (daily production of milk and fat).

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.

In this research the causal structure among calving traits of 29950 first-parity Holstein cattles of Iran including calving difficulty (CD), birth weight of calves (BW) and gestation length (GL) was revealed applying data collected by Iranian Animal Breeding in 131 herds from 1995 to 2004 by Inductive Causation (IC) searching algorithm. Significant structural coefficients were found for causal effects of BW on CD (0.060±0.002) and of GL on CD (0.007±0.002). Furthermore, the causal effect of GL on BW was significant (0.219±0.005). Considering the revealed causal structure, standard and recursive multivariate models were compared applying deviance Information criterion (DIC) and predictive ability of models in terms of two measures including mean square of error and correlation between observed and predicted values. The obtained results revealed the causal effect of BW and GL on CD and the plausibility of recursive multivariate model over standard multivariate one. Therefore, considering the causal structure among calving traits is of crucial importance.

This study was conducted to estimate the linkage disequilibrium (LD) and determine haplotype blocks structure in 93 Sarabi cow using SNP-chip 40k of Illumina company. After genotyping and quality control, 27386 SNP markers on autosomal chromosomes remained for analyzing. The LD was measured by r2 and D' statistics. In this study the average of r2 and D' for range less than of 2.5 kb were maximum with 0.505 and 0.927, respectively. The average of r2 and D' were minimum with 0.064 and 0.486, respectively in range of 2-5 Mb. 582 haplotype blocks were observed in the genome of Sarabi cow. 6.73% SNP from all of the SNPs were covered and 0.83% (21.43 Mb) of the autosomal genome were covered by the blocks haplotype. Population effective size was estimated about 40 that refer to four generations ago. The low number of haplotype block and also low LD level in Sarabi cow population showed high variation. In refer to the result and the number of haplotype blocks in this breed, applying the haplotype blocks could be improve results and high precision on genomic selection study so it was recommended that in study of genomic selection applying the haplotype blocks really useful than single SNP study

In this research، in order to describe milk production traits lactation Mahabadi goat breed، seven statistical functions were fitted using 1665 milk production traits records and 833 body weight records. The milk production traits were milk yield، fat percent، fat yield، protein percent، protein yield، lactose percent and SNF percent. These records have been recorded on 123 goats during years of 2012-2013. Based on results، there was not considerable difference in curve fitting of milk production and its composition yield among used functions. However، Ali and Schaeffer and Narushin-Takma functions in fat and SNF percentage، and inverse polynomial and Gompertz functions in protein and lactose percentage had higher goodness of fit in comparison with other function. Average daily milk production، days to peak production، milk production in peak، lactation period، and milk persistency were estimated 1 kg، 22 days، 1. 22 kg، 120 days، and 5. 59، respectively.

Potential relationships between amino acid motifs in the antigen binding groove of various alleles of the bovine major histocompatibility complex DR (BoLA-DR) molecule and Peripheral Blood Mononuclear Cell (PBMC) proliferation، in response to S. aureus and phytohemaglutinin، were investigated. The animals included in the study were approximately of the same age and comprised of pure Holstein-Friesian (n = 86)، F2 Holstein-Friesian Charolais (n = 155)، Holstein-Friesian backcross (F0 Holstein-Friesian dams crossed with unrelated F1 sires، n = 60)، Charolais backcross (F1 dams crossed with F0Charolais sire، n = 46). To determine BoLA-DRB3 alleles of the animals، a sequence-based typing method was employed. The amino acid sequence data encode various BoLA-DRB3 alleles، presented at the latest BoLA workshop، were utilized to determine the residues involved in the formation of the pockets in the antigen binding groove of various alleles of the BoLA-DR molecules. A linear mixed model was utilized to evaluate the potential relationships between amino acid motifs in the antigen-binding groove of various alleles of BoLA-DR molecule and PBMC proliferation.

PROP1 (Prophet of POU1F1) is specifically expressed in the pituitary gland. The PROP1 gene organizes three exons encoding for the 226 amino acids in humans and domestic animals; this gene is localized on chromosome 1 and regulates growth hormone، prolactin، and thyroid. The aim of this research was to study the polymorphisms of the PROP1 gene in Zel، Lori-Bakhtiari and Zel-Atabay crossbred sheep breeds، using PCR–RFLP. Blood samples from 90 Lori-Bakhtiari (research station)، 60 Lori-Bakhtiari (slaughterhouse)، 90 Zel (research station) and 40 Zel-Atabay crossbred (slaughterhouse) sheep were collected. DNA was extracted using the salting out method and the desired fragment was amplified using PCR. The genotypic frequency of GG and GA in Lori-Bakhtiari (research station)، Lori-Bakhtiari (slaughterhouse)، Zel (research station) and Zel-Atabay crossbred sheep were 0. 98%، 0. 02%، 0. 86%، 0. 14%، 0. 96%، 0. 04%، 0. 89%، and 0. 11%، respectively. The genotypic frequency of AA and AB in Lori-Bakhtiari (research station)، Lori-Bakhtiari (slaughterhouse)، Zel (research station) and Zel-Atabay crossbred sheep were 0. 70%، 0. 30%، 0. 78%، 0. 22%، 0. 68%، 0. 32%، 0. 84%، and 0. 16%، respectively. It can be concluded that polymorphism of this gene can be used as a candidate gene for some biometric traits.

The objective followed in this study was to compare six software packages (DFREML, WOMBAT, ASReml, MATVEC, DMU and Thrgibbsf90) as based on some such features as being user friendly, easing computational facilities as well as accuracy and precision of the estimated genetic vs. environmental parameters. For conduction of the study, simulated and field data (Birth weights and weaning weight of Baluchi lambs) were utilized. In all the softwares, except for Thrgibbsf 90, estimates were obtained with restricted Maximum likelihood method via AI algorithm, but in Thrgibbsf 90, the estimates were obtained using Bayesian Gibbs Sampling. The results showed that the choice of software depends on user interest and the goal followed in the research. Since the estimated parameters come out to be similar, even in confidence intervals, there seems no concern to exist in estimation of genetic and environmental parameters (for continous variables) using linear models,and through an application of different softwares.

To study the effects of environmental factors on milk and fat yields (240day) traits of Iranian buffaloes, 22596 and 22165 records were utilized for milk and fat yield traits, respectively. Uni and bivariate analysis for estimation of (co)variation components of the traits were done in five lactations. Milk yield in the 1st lactation had the highest number of records (4482), collected through Center of Animal Breeding during 1986 2009. Estimation of genetic trends for both traits in the 1st lactation was also done. All factors except age at calving and season of calving exerted significant effects (p<0.01) on mile yield. Also all factors except age at calving significantly affected fat yield (p<0.01). High additive genetic variation was observed in this population and resulted in high heritability for either of the traits. Average heritability obtained from single and double trait genetic analyses for milk yield at five lactations were 0.49, 0.41, 0.54, 0.47 and 0.35 while for fat yield they amounted to 0.45, 0.36, 0.55, 0.40 and 0.50, respectively. Genetic correlations of milk yield in different lactations were higher than those for fat yield in different lactations. Genetic correlations among milk and fat yields in different lactations were high and positive.

The aim followed in the present study was to investigate the economic aspects of, and to derive Economic Weights (EWs) for Mature Body Weight (MBW) as well as for age at First Calving (AFC) in Holstein dairy cattle of Iran. Economic values (EVs) for traits were estimated using trait-by-trait bio-economic models. Absolute EVs were RLs -16400 and -17900 per cow per year for MBW and AFC, respectively. Because of the negative effects of these traits on profitability, EWs of -7540 for MBW and -3760 for AFC are suggested for a national selection index. A one day increase in AFC increased production costs by Rls 39600 per cow per year. Sensitivity analysis revealed that the EV for MBW was more sensitive to changes in live weight price than to feed costs. Results obtained in this study can be used in the development of breeding objectives and in the cost- benefit analysis of management programs which aim at changing the attitudes of farmers and of their consultants towards decreasing costs and therefore increasing profitability.

The relationship between live body weight, body length, girth circumference, animal hight, upper, middle as well as lower width of fat-tail, fat-tail length, fat-tail gap length, fat-tail depth and fat-tail circumference along with fat-tail weight were determined using records of 731 Loribakhtiari sheep. Principal Component and Least Square Analyses were applied to solve the collinearity instability. Collinearity problems as portrayed by variance inflation factors above 5 or 10 were evident in some of independent variables. Results showed that the problem of collinearity in relation with fat-tail weight of 11 independent variables could be solved by using Principal Component Analysis method. Fat-tail gap length, fat-tail depth, and fat-tail circumference vs. girth circumference, and fat-tail length respectively represented the highest and the lowest coefficients regarding the estimation of fat-tail weight.

To compare the effect of strains and levels of yeast on fattening calves. Design: 2"3 factoial affangement Animalls: Thirty five male Holstain calves(average live weight 296.8 kg). Procedure: Animal were divded into five experimental goups each reciving a diet supplementd with one of the two strains yeast saccharomyces cerevisiae including Sc.47 (Biosaf) and (han mayeh) at tow different leves (expressed as x and 2x) or control diet (no yeast).The arnount ofx were 2.5 and 5 g /100 kg LWd for Biosaf and Iran mayeh, respectively. The diet containd forages and concentrate (70:30 ratio). Average daily gain and feed intake of each calf were measured during 1 35 days of the experimental period. At the end of the fattening period rumen liqure were obtained at 0,3 and 6 hours post -feeding. Blood samples were also taken at 0 and 3 hours post -feeding and subjected for the blood metabolites analaysis. Statistical analysis: The completely randomized desigin and the randomly complete blockdesign with analysis of covariance.

Growth rate was improved(p>0.05) in the animals using Biosaf at the level of x compared with those of contoral group (1457 vs1351lg/day). Despite that feed intake did not differed between the animals. the addition of Biosaf made cause a better feed conversion rate and higher rumen pH than the of other treatment. The total number of rumen bacteria was also increased numerically. No changes on blood serum metabolites were observed.

The use of yeast Biosaf may result in a better stability of rumen pH and so increase rumen bacterial population which in turn can improve ruminal fermentation and growth rate in calves.