Rostam Pahlavan; Mohammad Moradi Shahre Babak; Ardeshir Nejati Javaremi; Rostam Abdollahi Arpanahi
Abstract
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 ...
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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.
Milad Rezaei Sinaki; Mostafa Sadeghi; Abolfazl Bahrami; Mohammad Moradi Shahrbabak
Abstract
Heat stress in poultry decreases performance, weakens immune system and increases mortality, significantly. Given the interactions between biological pathways involved in heat stress, it is necessary to use a comprehensive approach to study heat stress. In this study, the effects of heat stress on gene ...
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Heat stress in poultry decreases performance, weakens immune system and increases mortality, significantly. Given the interactions between biological pathways involved in heat stress, it is necessary to use a comprehensive approach to study heat stress. In this study, the effects of heat stress on gene expression in two groups of broilers under heat stress and without heat stress (control) were investigated. In the analysis, microarray data were extracted from 1000 genes and after removing duplicate genes and out of the level of significance in expression (P <0.01), 709 genes were identified. Using the String site and gene analysis in Cytoscape software, 115 genes were identified in four functional modules. The identified modules were involved in biological pathways of Spliceosome, Ubiquitin-mediated proteolysis, Ribosome biogenesis, Protein Processing in Endoplasmic Reticulum, Autophagy-Animal and Important Signaling pathways including Innate Immune System, MAPK pathway and Cellular Senescence. The results of this study showed that heat stress in poultry plays an important role in growth function, immune system and other biological mechanisms. Identifying the genes involved in heat stress such as PTEN and HSPs in birds, and reviewing microarray data could open new horizons for a better understanding heat stress-related biological process.
Muna Kholghi; Mohammad Moradi Shahre Babak; Mostafa Sadeghi; Seyed Reza Miraei-Ashtiani; Mohammad Mehdi Ranjbar; Mohsen Lotfi
Abstract
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. ...
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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.
Mahdi Mokhber; Mohammad Moradi Shahre Babak; Mostafa Sadeghi; Hossein Moradi Shahrbabak; Javad Rahmani-Nia
Abstract
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 ...
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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.
Hojatollah Mousapour; Ardeshir Nejati-Javaremi; Mohammad Moradi-ShahreBabak; Mahdi Saatchi
Abstract
Increased homozygosity resulted from mating of relatives is considered as one of the challenges faced in dairy farming industry which has attracted the attentions. This research has been conducted to measure homozygosity based on SNP and ROH in high- and low-producing Holstein cows. In current research, ...
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Increased homozygosity resulted from mating of relatives is considered as one of the challenges faced in dairy farming industry which has attracted the attentions. This research has been conducted to measure homozygosity based on SNP and ROH in high- and low-producing Holstein cows. In current research, both random regression and pedigree index approaches were used to obtain candidate animals for genotyping process. The samples were obtained from 150 Holstein dairy cows (75 by high- and 75 by low-EBV for milk production). We proposed a suitable method, by integrating breeding value estimation calculated by random regression and pedigree index, to select the candidate animals for genotyping. The results showed that putting too much emphasis on production traits in high-producing dairy cows had negative impact on the traits associated with fertility (DPR = -0.55) and productive life (PL = 0.1). The calculated homozygosity based on ROH showed different amount of variation in different chromosomes in the cows with high and low production which may be related to uneven distribution of genes influencing production traits in different chromosomes.
Mahdi Mokhber; Mohammad Moradi Shahre Babak; Mostafa Sadeghi; Hossein Moradi Shahrbabak; Javad Rahmani-Nia
Abstract
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, ...
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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.
Ali Jalil Sarghale; Mohammad Moradi Shahre Babak; Hossein Moradi Shahrbabak; Ardeshir Nejati Javaremi; Mahdi Saatchi
Abstract
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 ...
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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).
Mohammad Hossein Fallahi; Hossein Moradi Shahrbabak; Mohammad Moradi Shahrbabak; Rostam Abdollahi Arpanahi
Abstract
The aim of this study was to determine genomewide linkage disequilibrium (LD), Haplotype block and effective population size using the information obtained from 243 Azarbaijani breed buffalo using a high density SNP panel (Axiom® Buffalo Genotyping 90K). After quality control of SNP markers data, ...
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The aim of this study was to determine genomewide linkage disequilibrium (LD), Haplotype block and effective population size using the information obtained from 243 Azarbaijani breed buffalo using a high density SNP panel (Axiom® Buffalo Genotyping 90K). After quality control of SNP markers data, 62,141 SNP markers remained for identification of linkage disequiliberum, haplotype blocks and effective population size. LD was measured by the square of the correlation coefficient (r2) between alleles. The maximum LD measured by r2 varied from 0.25 to 0.29 at a distance of < 2.5 kb, and the minimum average values of r2 varied from 0.012 to 0.014 at distances ranging from 900 to 1000 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. Overall, 1693 blocks were observed through the genome. Eleven percent of all SNPs were clustered into haplotype blocks, covering 202 ±3.4 Mb of the total autosomal genome size. Effective population size (Ne) was estimated based on expected linkage disequilibrium. Ne was estimated to be 422 in our population.
Morteza Sattaei Mokhtari; Mohammad Moradi Shahrebabak; Ardeshir Nejati Javaremi; Guilherme J. M. Rosa
Abstract
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 ...
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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.
Zahra Azizi; Hossein Moradi Shahrbabak; Mohammad Moradi Shahrbabak
Abstract
Understanding of population genetic structure is valuable for better implementation of breeding programs and most importantly, preservation of genetic resources. Genomic data provide an opportunity to consider complex evolutionary history of populations and reconstruct rare historical events. In this ...
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Understanding of population genetic structure is valuable for better implementation of breeding programs and most importantly, preservation of genetic resources. Genomic data provide an opportunity to consider complex evolutionary history of populations and reconstruct rare historical events. In this research, the structure of Iranian buffalo populations was studied by using principal component analysis and discriminant analysis principal component methods. For this purpose, the number of 404 buffalos from three breeds including North, Azari and Khozestani were sampled and genotyped by SNPChip 90k from Padano Company in Italy. The results of principal component analysis and discriminant analysis principal component showed a clear picture of the genetic structure of the studied populations. Assessing the optimal number of clusters with criteria BIC, K = 3 by the DAPC method showed the best results. The result of cross-validation for retaining principal components was optimized to 50 first components that showed the lowest MSE. In this study, DAPC predicted assignment of individuals to clusters and membership probabilities with 100% accuracy. PCA method was not able to provide a group assessment and DAPC method outperformed than PCA in achieving a clear variance difference between populations. DAPC method can be applied in quality control and stratification population correction of GWAS as an alternative to the PCA because of summarizing the genetic differentiation between groups and overlooking within-group variation and providing better population structure.
Somayeh Barani; Mohammad Moradi-Shahrbabak; Ardeshir Nejati-Javaremi; Mohammad Hosein Moradi; Mohsen Gholizadeh; Majid Khansefid
Abstract
Understanding the pattern of linkage disequilibrium (LD) in different populations provides useful information for genomic selection (GS), genome wide association studies (GWAS) and identification of genetic architecture of traits by estimating the persistence of LD phase between markers and quantitative ...
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Understanding the pattern of linkage disequilibrium (LD) in different populations provides useful information for genomic selection (GS), genome wide association studies (GWAS) and identification of genetic architecture of traits by estimating the persistence of LD phase between markers and quantitative trait loci (QTL). The aim of this research was to estimate of the extent of LD in three Iranian native sheep breeds. Therefore, 186 blood samples were taken from three sheep breeds (96 Baluchi, 45 lori-Bakhtiari and 45 Zel) and genotyped by Illumina ovine 50K SNPChip, then linkage disequilibrium in any breed were measured using r2. The results showed that the highest average values of r2 at inter marker distance of less than 10Kb were 0.392± 0.323, 0.360±0.308 and 0.340±0.306 in Baluchi, Lori-Bakhtiari and Zel, respectively. The highest average values of r2 in autosome chromosomes of each breed were obtained for chromosome 24 and 25 in Baluchi, 9 and 21 in Lori-Bakhtiari and 23 and 24 in Zel. The amount of LD reduced with increasing the distance between markers, the extent of LD was less than 0.1 at inter marker distances greater than 100Kb. The comparison of correlation coefficients LD between different breeds showed a strong persistence of LD phase between Zel and Lori-Bakhtiari breeds which is probably due to recent common ancestors between these two breeds. Generally, with increase amount of LD means that lower marker density in association studies will be required. The results of this study showed to achieve genomic prediction accuracy of 85% (assuming there is no other accuracy limiting factor) and robust GWAS results, the density of markers must be higher than 50K SNPChip.
Hadi Atashi; Mohammad Moradi Shar e Babak; Hassan Mehrabani-Yegane; Seyed Reza Miraei-Ashtiani; Ghodratollah Rahimi-Mianji
Abstract
The aim of this study was to investigate the association of bovine leukocyte antigen-DRB3 alleles with peripheral blood mononuclear cell (PBMC) proliferation in response to Staphylococcus aureus. The animals included in this study (n=347) were approximately of same age and comprised of F2 Holstein-Friesian ...
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The aim of this study was to investigate the association of bovine leukocyte antigen-DRB3 alleles with peripheral blood mononuclear cell (PBMC) proliferation in response to Staphylococcus aureus. The animals included in this study (n=347) were approximately of same age and comprised of 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 F0 Charolais sire, n=46) and pure Holstein-Friesian (n = 86). A sequence-based typing method was used in order to determine the genotype of the animals at BoLA-DRB3 locus and a linear mixed model was used to evaluate the association of bovine leukocyte antigen-DRB3 alleles with peripheral blood mononuclear cell (PBMC) proliferation. Beside the BoLA-DRB3 alleles, fixed effects of genetic group and gender and random effect of sires were included into the statistical model. In this research, 27 alleles were found for BoLA-DRB3 gene. The results showed that alleles BoLA-DRB3*0101 and BoLA-DRB3*0902 significantly affected on the stimulation index of S. aureus–induced peripheral blood mononuclear cell proliferation (P<0.05). The results may be useful for investigating the biological mechanism of immune response against S. aureus.
Zahra Azizi; Hossein Moradi Shahrbabak; Mohammad Moradi Shahrbabak; Abbas Rafat; Jalil Shodja
Abstract
The purpose of this research was to classify buffaloes from different areas of the two Azari (West and East Azarbayjan and Ardabil provinces) and North (Guilan province) ecotypes using support vector machine method. A total of 258 buffalo were sampled and genotyped using the Axiom Buffalo 90K Genotyping ...
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The purpose of this research was to classify buffaloes from different areas of the two Azari (West and East Azarbayjan and Ardabil provinces) and North (Guilan province) ecotypes using support vector machine method. A total of 258 buffalo were sampled and genotyped using the Axiom Buffalo 90K Genotyping Array at the Parco Technologic Padano lab in Italy. Two metric methods of cross validation and the area under the receiver operating characteristic (AUC) were used to determine the predictive performance of support vector machine (SVM) to classify individuals. The results of cross validation and methods for classifying different regions of the two ecotypes (4 provinces) were 92% and 96%, respectively that showed despite the difficulty of identifying individuals from provinces close to each other, support vector machine (SVM) method shows higher accuracy in assigning animals to their herds. Result of two ecotypes showed accuracy about 96% and 98% which represents the better ability to separate the two ecotypes. Machine learning method provides predictions for classification of each individual which can be efficient in quality control and genetic studies.
Homa Aarabi; Mohammad Moradi Shahrbabak; Abbas Pakdel; Hossein Moradi Shahrbabak; Ali Esmailizadeh koshkoiyeh
Abstract
Insulin-like growth factor-1 gene (IGF1) is a biological candidate gene for investigation traits such as growth, body weight and muscles growth in different species. In this research eight pairs of white and wild quails were crossed reciprocally as a base population. A total of 34 quails were produced ...
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Insulin-like growth factor-1 gene (IGF1) is a biological candidate gene for investigation traits such as growth, body weight and muscles growth in different species. In this research eight pairs of white and wild quails were crossed reciprocally as a base population. A total of 34 quails were produced in first generation (F1) and 422 quails were generated by intercrossing the F1 population. Body weights at the time of hatching and different weeks were recorded in the second generation. The association between IGF1 promoter region polymorphism and body weight in different ages was investigated in F2 generation. Using PCR-SSCP assay and sequencing, a novel single nucleotide polymorphism (SNP) was identified in IGF1 promoter region in 472 birds from three Generations. Genotypic frequencies of AA, AG and GG genotypes were 0.05, 0.62 and 0.33, respectively for all generations. The frequency of A and G alleles were 0.36 and 0.64, respectively. The AA genotype was lower than AG and GG genotypes for body weights in ages of one to five weeks and slaughter time and the average of daily gain was also lower from week first to four but these differences weren’t significant. The average of daily gain was higher in females compared to males for AG genotype (P<0.001). Comparison between detected allele in the present study with reported allele by other research groups in chickens revealed a novel SNP in promoter of IGF1 gene in Japanese quail, but association between this polymorphism with body weight and growth rate were not significant.
Reza Faraji; Mostafa Sadeghi; Mohammad Moradi Shahrbabak
Abstract
This research was conducted to study polymorphism of intron 44 of ACACA gene and its association with milk traits in Mahabadi goats. Blood samples were taken from 81 Mahabadi goats. DNA was extracted from blood using salting out method. 897 base pair fragment of intron 44 ACACA gene was amplified using ...
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This research was conducted to study polymorphism of intron 44 of ACACA gene and its association with milk traits in Mahabadi goats. Blood samples were taken from 81 Mahabadi goats. DNA was extracted from blood using salting out method. 897 base pair fragment of intron 44 ACACA gene was amplified using polymerase chain reaction. SSCP method was used to investigate the amplified DNA fragment polymorphism. Amplified products were sequenced in both directions. Finally, seven different patterns were obtained and sequences compared with each other also with Capra hircus ACACA gene sequence on NCBI (NC_022311). Seven novel SNPs were identified which were NC_022311: nucleotide 154503(T/G), 154518(A/G), 154577(A/G), 154640(C/T), 154712(A/C), 154928(C/T), 154956(C/T). Then a mixed animal model was used by SAS9.1 analysis system to evaluate the association of these SNPs with milk traits. In this model, variables of age of dam, genotypes and mount of recording were considered as fixed effects. There were significant association of SNP2 (P=0.05), SNP3 (P=0.05) and SNP5 (P<0.01) with milk yield. SNPs 1 (P=0.017), 6 (P=0.017) and 7 (P<0.01) had also significant effect on milk fat-percentage.
Nemat Hedayat-Evrigh; Seyed Reza Miraei-Ashtiani; Mohammad Moradi Shahrbabak; Saber Mohammad Maghsoodi
Abstract
Camel is a resistant species to drought and cold weather and produces milk and meat in harshest environmental condition. Camel population in Iran has been decreasing during last decades, and genetic studies are quite necessary for considering the conservation and productivity of this species. In this ...
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Camel is a resistant species to drought and cold weather and produces milk and meat in harshest environmental condition. Camel population in Iran has been decreasing during last decades, and genetic studies are quite necessary for considering the conservation and productivity of this species. In this study growth hormone gene influencing growth, milk production and reproduction was considered. The blood samples were collected from 25 Bactrian (Ardebil province) and 50 dromedary camels (Yazd province (n=15), Toroud Camel Research Station (n=20) and Semnan province (n=15)), and DNA was extracted. Using sequencing and alignment method, seven mutations were detected in GH gene. Two of them were substitution mutation and changed amino acid sequence of growth hormone protein. The results of genetic distance analysis showed that the genetic distance between Bactrian and one-humped camel was the highest. Within dromedary camels, the camels of Yazd and Semnan provinces showed biggest genetic distance and camels of the Toroud camel research station were Intermediate of two populations.
Abbas Rezaei; Gholamali Nehzati-Paghgale; Mohammad Moradi Shahr Babak; Mehdi Ghanjkhanlo
Abstract
This research was conducted to evaluate the effects of feeding fermented diets as a protein supplement, using different diets in a completely randomized design with 6 treatments and 7 replications per treatment for 50 days in apiary in Karaj area. Honey bee colonies were assimilated in terms of honey, ...
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This research was conducted to evaluate the effects of feeding fermented diets as a protein supplement, using different diets in a completely randomized design with 6 treatments and 7 replications per treatment for 50 days in apiary in Karaj area. Honey bee colonies were assimilated in terms of honey, population and same age sister queen. Experimental treatments included: 1. Fermented gluten meal, 2. Gluten meal, 3. Fermented soy bean meal, 4. Soy bean meal, 5. Pollen, 6. Sugar syrup. Actually, sugar syrup and pollen were used as control treatments. The results of statistical analysis of data showed significant difference in food consumption (P<0.05), where the highest to lowest food consumption of belonged to: fermented Gluten meal, Pollen, fermented Soy bean meal, Gluten meal, Soy bean meal and sugar respectively. Significant effect was seen on brood rearing (P<0.05), Fermentation gluten and soybean meal had the highest and lowest brood rearing between treatments respectively. No significant differences were seen in body protein and population size (P>0.05). The results of this experiment showed that fermenting protein sources has positive effects on health and increasing brood rearing in honeybee colonies.
Mahdi Mokhber; Mohammad Moradi Shahrbabak; Mostafa Sadeghi; Hossein Moradi Shahrbabak; John Williams
Abstract
Identification of selection targeted genomic regions is one of the most challenging areas of research in animal genetics, particularly in livestock. We carried out a genome-wide scan for signatures of positive selection to identify genomic regions that had been under selection in Iranian Khuzestani and ...
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Identification of selection targeted genomic regions is one of the most challenging areas of research in animal genetics, particularly in livestock. We carried out a genome-wide scan for signatures of positive selection to identify genomic regions that had been under selection in Iranian Khuzestani and Mazandrani buffalo breeds. A total of 148 water buffalo from Khuzestani (N=121) and Mazandrani (N=27) buffalo breeds were genotyped using Axiom® Buffalo Genotyping 90K Array. Unbiased method of population differentiation index (FST) was applied to detect signatures of selection. In total, 23 regions exceeding the 0.1 percent threshold of the empirical posterior distribution were identified as extremely differentiated. These selected genomic regions were surveyed to find encoding putative candidate genes and 64 genes and 27 QTL were extracted from the corresponding areas in UMD3.1 Bos Taurus Genome Assembly. Some of these genes have previously reported as signature of positive selection in the last studies. Some of these genes were also found to be involved in milk production traits and domestication-related changes include sensory perceptions, brain and neural system development, pigmentation, and geographic adaptation. Also, survey on extracted QTLs was shown that these QTLs involved in some economicl important traits in buffalo such as feed conversion ratio, subcutaneous fat, body weight, average daily gain, type, Meat tenderness, milk production conentent, udder attachment, calf size and calving ease traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.
Azadeh BOOSTAN; Ardeshir NEJATI-JAVAREMI; Mahammad MORADI SHAHRBABAK; Mehdi SAATCHI
Abstract
Throughout the present study the effect of using markers close to genes affecting a trait, ascompared with the use of all the markers of a genome, and also the effect of on increase in thenumber of reference groups, on the accuracy of a genetic evaluation, was investigated. Genomicevaluation was done ...
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Throughout the present study the effect of using markers close to genes affecting a trait, ascompared with the use of all the markers of a genome, and also the effect of on increase in thenumber of reference groups, on the accuracy of a genetic evaluation, was investigated. Genomicevaluation was done using BLUP method. The results indicated that use of markers close to genesaffecting a trait and on increase in the number of reference groups would enhance the accuracy inan evaluation of the Estimated Breeding Values (EBVs). Use of phenotypic records (incomparison with breeding values of reference group) would result in an increase in the accuracy ofestimating the breeding values by use of markers close to the effective genes on the trait ascompared with the use of all the markers of a genome. Increase in number of generations betweenreference and validation groups would result in a decrease of the accuracy of EBVs.
Mohammad Moradi Shahre Babak; hasan mehrabani
Abstract
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 ...
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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.
Abdollah Rezagholivand Lahroud; Mohammad Moradi Shahrebabak; Abbas Pakdel
Abstract
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, ...
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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.
Mohammad Sahebhonar; Mohammad Moradi Shahrbabak; Seyed Reza Miraei Ashtiani; Abbas Pakdel; Dorian J. Garrick
Abstract
In this study, effect of two genotype imputation strategies, relatedness between reference panel and test populations and minor allele frequency on imputation error rate were examined with using a stochastic simulated population. Reference panel and test populations were composed of 1,000 and 500 individuals, ...
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In this study, effect of two genotype imputation strategies, relatedness between reference panel and test populations and minor allele frequency on imputation error rate were examined with using a stochastic simulated population. Reference panel and test populations were composed of 1,000 and 500 individuals, respectively. Individuals in the reference panel were genotyped with using a high and a medium density chips. The high density chip contained 75,000 SNPs plus QTLs. The medium density chip contained 7,500 SNPs. Individuals in the test populations were genotyped with using a low density chip with 500 SNPs. Two strategies were applied for genotype imputation. In 2-tiered strategy, genotypes of low density chip were directly imputed from high density chip. In 3-tiered strategy, genotypes of low density chip were imputed from high density chip with using a medium density chip. In order to impute genotypes, BEAGLE method was used. Correlation between imputation error rate and minor allele frequency showed that imputation error rate was affected by minor allele frequency in both strategies. Imputation error rates were decreased when using a medium density chip to predict genotypes of low density chip. Closer relationship between reference panel and test populations led to a higher accuracy.
Hamed Rezaei; Hosein Moradi Shahrbabak; Mohammad Moradi Shahrbabak; Mahdi Bayeriyar
Abstract
The data used in this research were according to survival rate records of 9700 lambs from 735 rams and 8082 ewes, which collected at Moghani Flock Breeding Research Station during the year 1365 to 1390. The frequency distribution causes of culling and survival distribution function of lambs to yearling ...
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The data used in this research were according to survival rate records of 9700 lambs from 735 rams and 8082 ewes, which collected at Moghani Flock Breeding Research Station during the year 1365 to 1390. The frequency distribution causes of culling and survival distribution function of lambs to yearling age were estimated by SAS (2000). Results revealed that 49.81 percent of total lambs were culled from the flock until the first year of life because of reasons including illness, lack of breed purity, etc. The mortality rate over this period was estimated 20.81 percent which occurred 8.03, 7.5, 4.43 and 0.85 percent in first three months, second three months, third three months and fourth three months of lambs life, respectively. According to percentage of mortality rate, the accumulative survival of lambs from birth to yearling age was calculated 79.19 percent. The regression coefficient of lambs survival from birth up to yearling age showed a monthly 1.77 percent decrease in lambs survival of this breed. The most mortality rate occurred in first, fifth, second, fourth, sixth and ninth months of lambs life, respectively. In comparison with third and fourth three months of lambs life, the fatality in first and second three months were higher because of heavy rainfall and frigid weather in winter quarters.
Raheleh Sadeghi; Abbas Pakdel; Mohammad Moradi Shahr Babak
Abstract
The aim followed in the present research was to investigate the effect of nine generations of divergent selection on some reproductive and egg production traits in Japanese quail. The results indicated that selection for 4-week body weight, increased the age at sexual maturity of HW and of LW lines, ...
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The aim followed in the present research was to investigate the effect of nine generations of divergent selection on some reproductive and egg production traits in Japanese quail. The results indicated that selection for 4-week body weight, increased the age at sexual maturity of HW and of LW lines, in comparison with control, for about 7 and 3 days, respectively (P<0.05). At the ages of sexual maturity, there weren’t significant differences observed within the selected lines (P<0.05), but these lines were significantly different from control. Body weight at sexual maturity was higher in HW line than in LW and in C. The differences between lines were significant (P<0.05). Body weight at sexual maturity and average egg weight at different productive stages increased in HW in comparison with control (P<0.05). This was while, percentage egg lying at the point of sexual maturity was higher in LW than in control (P<0.05). Total number of eggs laid was higher in LW than in HW and in control while the difference being significant only with HW. The highest percentage of egg-laying was recorded within 3-6 pm in any of the three lines. Peak egg production occurred during the second month. It can finally be concluded that because of the interrelated response between body weight and reproductive traits, it’s important to consider the reproductive and safety traits beside growth traits in selection programs.
rostam abdollahi; Mohammad Moradi Shahre Babak; mohammad bagher zandi; mohammad razm kabir
Abstract
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. ...
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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.
