Hossein Mohammadi; Hossein Moradi Shahrebabak; mohammad shamsollahi
Volume 25, Issue 3 , October 2023, , Pages 241-254
Abstract
Introduction: Identifying of genes with large effects on economically important traits, has been one of the important goal to sheep breeding. Over recent years, advances in DNA-based marker technology have made it possible to identify genomic regions or quantitative trait loci (QTLs) underlying complex ...
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Introduction: Identifying of genes with large effects on economically important traits, has been one of the important goal to sheep breeding. Over recent years, advances in DNA-based marker technology have made it possible to identify genomic regions or quantitative trait loci (QTLs) underlying complex traits, such as fleece traits, in sheep. The present study aimed to conduct a genome wide association studies (GWAS) based on gene-set enrichment analysis for identifying the loci associated with wool traits in native Zandi sheep using the 50K arrays.
Material and Methods: A total of 300 Iranian Zandi sheep used in this study came from the Zandi sheep breeding station. Wool sampling coincided with the maximum wool growth prior to the shearing of wool. In order to facilitate sampling, sheep were restrained in a lateral position and true wool from the left mid-side site was cut from a 5×5 cm2 close to the skin using regular scissors. Each sample was separately packaged and labeled with ear tag number of the sheep. We measured and recorded four wool production traits: staple length (SL), mean fiber diameter (MFD), fiber diameter coefficient of variation (CVFD), and the proportion of fiber that are equal or more than 30 µm (PR), kemp percentage (KEMP%) and outer coat fiber (OCF) were measured. Genomic DNA extraction from sheep blood was performed by the applying a modified salting out protocol and genotyping of the Sheep SNPChip 50 K SNP Bead from Illumina Inc. The gene set analysis consists basically in three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories, and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study was performed with wool traits using GEMMA software. Using the biomaRt2 R package, the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 50 kb up- and downstream of the gene and bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases. The GO database designates biological descriptors to genes based on attributes of their encoded products and it is further partitioned into 3 components: biological process, molecular function, and cellular component. The KEGG pathway database contains metabolic and regulatory pathways, representing the actual knowledge on molecular interactions and reaction networks. Finally, a Fisher’s exact test was performed to test for overrepresentation of the significant genes for each gene-set. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in GeneCards databases.
Result and Discussion: The result from genomic control showed weak population stratification with for woot traits among Zandi sheep population. We identified different sets of candidate genes related to wool traits including: CEP290, PRKCZ, TMTC3, RHPN2, TNFSF4, NLGN1, SPHKAP, PLCE1, FAT1 and PIK3R4 in Zandi sheep. Some of the found genes, are consistent with some of the previous studies related to reproductive traits. According to pathway analysis, 21 pathways from gene ontology and biological pathways were associated with the wool traits (P˂0.05). Some of the genes were found are consistent with some prior studies and to be involved biological pathways related to hair follicle development, keratinocytes differentiation, synthesizes an enzyme of threonine kinases, development of epidermal and Wnt signaling pathway.
Conclusion: In total, this study supported previous results from GWAS of wool traits, also revealed additional regions in the sheep genome associated with these economically important traits. These findings could potentially be useful for genetic selection in the breeding programs and can be used to understand the genetic mechanism controlling this trait.
Rostam AbdolahiArpanahi
Volume 19, Issue 2 , August 2017, , Pages 255-264
Abstract
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 ...
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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< 0.05). Estimates of heritability of DFS with RR model decreased from parity 1 (0.09±0.01) to parity 6 (0.03±0.01). Estimated heritability by MT model decreased from parity 1 (0.08) to parity 5 (0.04) and increased in parity 6 (0.10). The obtained heritability using repeatability model was 0.055±0.01. Genetic correlations between DFS in different parities were reduced continuously with increasing distance between parities in RR and MT models. Overall, the result of this study indicate that multiple trait model performs better than other models in estimation of genetic parameter for DFS.
Mhatab Mansori; Mohammad Mahdi sharifi Hossini; Omid Dayani; Reza Tahmasbi
Volume 21, Issue 3 , September 2019, , Pages 309-320
Abstract
This research was conducted to investigate the effects of corn and sorghum silages particle size on feed intake, digestibility, rumen parameters and feed intake behavior in Kermani sheep. Around 1000 kg of fresh corn and sorghum forages were chopped into two coarse and fine particle sizes and ensiled ...
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This research was conducted to investigate the effects of corn and sorghum silages particle size on feed intake, digestibility, rumen parameters and feed intake behavior in Kermani sheep. Around 1000 kg of fresh corn and sorghum forages were chopped into two coarse and fine particle sizes and ensiled for 45 days. Four male Kermani sheep, 34.0±0.8 kg average BW, were used in this experiment which was conducted in a completely randomized design, with a 2 × 2 factorial experiment. There were four experimental periods and each of which lasted 21d, with 14d adaptation, 7d of sample collection. The ratio of forage to concentrate was 60: 40. Experimental diets were: 1) coarse corn silage diet, 2) fine corn silage diet, 3) coarse sorghum silage diet and 4) fine sorghum silage diet. The NDF content was higher in the sorghum silages than corn silages (p<0.05). In diets containing fine silage, ruminal pH tended to decrease after two hours of intake. Population of Holotrich and Cellulolytic protozoa increased when coarse silages were fed to animals (P<0.05). The maximum microbial protein synthesis in the rumen was achieved in diets containing fine silage(P<0.05). Duration of feed intake, rumination and chewing activity were higher in coarse silage diets (P<0.05). The types of silage did not have significant effect on animals’ performance and dietary feed intake behavior. In conclusion, corn silage can be replaced by sorghum silage, without any negative effect on feed intake, digestibility, and rumen parameters in sheep.
Saber Jelokhani-niaraki; Sholeh Ghorbani; Saeid Esmaeilkhanian
Volume 23, Issue 3 , September 2021, , Pages 313-324
Abstract
Monitoring the inbreeding rate of native chickens in breeding stations is of significant importance because of planned matings and lack of gene flow in the population. This study was undertaken to estimate the inbreeding coefficient, investigate the trend of inbreeding changes and evaluate the effects ...
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Monitoring the inbreeding rate of native chickens in breeding stations is of significant importance because of planned matings and lack of gene flow in the population. This study was undertaken to estimate the inbreeding coefficient, investigate the trend of inbreeding changes and evaluate the effects of inbreeding depression on the economic traits in Isfahan improved native chicken population. The studied traits were body weight, age at sexual maturity, weight at sexual maturity, egg number, mean egg weight and egg weight at first day. In the present study, data of 97272 birds recorded during 21 generations were included. In order to estimate the inbreeding coefficient of each bird and the effect of inbreeding on the traits, CFC and WOMBAT software were used, respectively. Pedigree analysis indicated that 79.48 percent of population were inbred. The estimated average individual and maternal inbreeding coefficients were 4.3 and 3.5 percent, respectively. According to results, for every one percent increase in inbreeding, rate of inbreeding depression for the traits including the body weight in 1 day, 8 weeks and 12 weeks, age at sexual maturity, weight at sexual maturity, egg number, average weight of eggs and egg weight at first day was -0.008, -2.52, -3.51, 0.23, -3/97, -0.13, 0/02 and 0.06, respectively. Based on the results of the present study, although in closed populations under genetic selection, the absence of inbred bird is almost impossible, but, the reduction of inbreeding can be achieved by controlling the matings, which prevents the adverse effects of inbreeding in the population.
amir hossein khaltabadi farahani; hossein mohammadi; hossein moradi
Volume 22, Issue 3 , September 2020, , Pages 325-335
Abstract
The aim of this study was to identify the molecular pathways related to litter size in sheep using gene set enrichment analysis. For this purpose, information of high prolificacy sheep breeds including Wadi, Hu, Icelandic, Finnsheep, and Romanov and low prolificacy including Texel and Rahmani ...
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The aim of this study was to identify the molecular pathways related to litter size in sheep using gene set enrichment analysis. For this purpose, information of high prolificacy sheep breeds including Wadi, Hu, Icelandic, Finnsheep, and Romanov and low prolificacy including Texel and Rahmani were used for genome wide association studies and gene set enrichment analysis. Genome-wide association study was conducted using GenABEL package of R program. Gene set enrichment analysis was performed with the goseq R package to identify the biological pathways associated with candidate genes. We identified different sets of candidate genes related to litter size: BMP5, DHCR24, BMPR1B, ESR1, ESR2 andPLCB1 in Wadi and Romanov; SMAD1, SMAD2, INSR and PTGS2 in Finnsheep and Hu; BMP7, NCOA1 and ERBB4 in Icelandic; BMP4, MSRB and SPP1 in Texel; BMP7, EGFR and KCNMA1 in Rahmani. According to pathway analysis, 30 pathways were associated with the litter size trait. Among biological pathways, the TGF-β signaling, Oxytocin signaling, Estrogen signaling, Prolactin signaling, and Insulin signaling pathways have significant association with ovulation rate and litter size trait. Overall, this study supported previous results from GWAS for litter size, also revealed additional regions in the sheep genome associated with litter size in sheep. These findings could potentially be useful for selective breeding for more litter size in sheep.
Maryam Arianfar; Mohammad Rokouei; Gholamreza Dashab; Hadi Faraji- Arough
Volume 20, Issue 3 , November 2018, , Pages 351-363
Abstract
The objective of this study was to compare some nonlinear functions (Wood, Dhanoa, Wilmink, Ali-Schaeffer, Cappio Borlino, Cobby – Le Du, Dijkstra, Rook, Gous and Nelder) to describe the milk production curve of Iranian Holstein cattle. A dataset consisted of 6079976, 4879486 and 3312416 test-day ...
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The objective of this study was to compare some nonlinear functions (Wood, Dhanoa, Wilmink, Ali-Schaeffer, Cappio Borlino, Cobby – Le Du, Dijkstra, Rook, Gous and Nelder) to describe the milk production curve of Iranian Holstein cattle. A dataset consisted of 6079976, 4879486 and 3312416 test-day milk yield records related to first, second and third three lactation periods, respectively, from 3550 herds collecting by the Animal Breeding Center of Iran from 1983 to 2017, were used. The average of test day milk records for three lactation was 31.17, 34.08 and 33.83 kg, respectively. The nlme package of R software (version 3.4.3) was used for fitting nonlinear functions. The nonlinear functions were compared using four goodness of fit criteria, including Akaike’s information criterion (AIC), Bayesian information criterion (BIC), Root mean square error (RMSE) and Durbin-Watson index (DW). The Rook function showed the best fit for the milk production curve shape for three lactations in Iranian Holstein cattle when compared to other functions. The Gous and Rook functions showed the highest accuracy in predicting peak time, peak yield and persistency of milk production parameters in different lactations, but in general, the Rook function has a high predictive value in estimating the milk curve parameter descriptors.Therefore, Rook function is recommended for describing the milk production curve of Iranian Holstein cattle.
Mostafa Akbari Alaei; Javad Rezaei; Yousef Rouzbehan
Volume 25, Issue 4 , December 2023, , Pages 357-373
Abstract
This research was conducted to compare the effect of different zinc sources on in vitro microbial populations, hydrolytic enzymes and ruminal fermentation products in sheep. Five diets without zinc supplement (control) or containing ZnSO4, ZnO, nano-ZnO and Zn-methionine were assessed. The 24 and 72-h ...
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This research was conducted to compare the effect of different zinc sources on in vitro microbial populations, hydrolytic enzymes and ruminal fermentation products in sheep. Five diets without zinc supplement (control) or containing ZnSO4, ZnO, nano-ZnO and Zn-methionine were assessed. The 24 and 72-h gas tests were conducted in a completely randomized design where the microbial populations, hydrolytic enzymes, methane, antioxidant activity, organic matter digestibility (OMD), metabolizable energy (ME), truly degraded substrate (TDS), microbial biomass, partitioning factor (PF) and volatile fatty acids (VFA) were determined. Total proteolytic bacteria count and protease activity decreased due to the usage of organic, inorganic and nano-particle sources of zinc (P<0.05). The use of methionine, oxide and sulfate sources of zinc increased alpha-amylase activity (P<0.05). Total protozoa number in the 24-h incubation tended to decrease owing to dietary zinc supplements. Total cellulolytic bacteria, carboxymethyl-cellulase, microcrystalline-cellulase, filter paper-degrading activity, antioxidant capacity, microbial biomass and PF were the same among treatments. Zinc methionine, oxide and sulfate supplements increased OMD, ME, TDS and total VFA, whereas decreased ammonia and acetate:propionate ratio (P<0.05). Also, 24-h methane production decreased with the use of zinc supplements (P<0.05). Overall, the dietary addition of sulfate, oxide and methionine- sources of zinc is recommended with the aim of improving alpha-amylase activity and digestibility and reducing proteolytic activity, ammonia accumulation and methane, but feeding nano-ZnO is not recommended. More research is needed on the effect of zinc sources on rumen microorganisms and enzymes in different dietary conditions.
Hengameh Vafaee; Mojtaba Hosseinpour Mashhadi2
Volume 18, Issue 3 , October 2016, , Pages 377-386
Abstract
This study was conducted to investigate the Single nucleotide polymorphism of STAT1 gene by PCR-RFLP technique and association of genotypes with milk production traits in Brown Swiss dairy cattle. The blood samples of ninety eight cows were collected randomly from tail vein. The DNA was extracted ...
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This study was conducted to investigate the Single nucleotide polymorphism of STAT1 gene by PCR-RFLP technique and association of genotypes with milk production traits in Brown Swiss dairy cattle. The blood samples of ninety eight cows were collected randomly from tail vein. The DNA was extracted with Cinagene kit (PR881612C). Fragment of 314 bp of STAT1 gene was amplified by PCR and digested by Pag1 restriction enzyme. Genotype frequencies were calculated by PopGene software (version 1.31). The SAS 9.1 software was used for statistical analysis and the mean of traits was compared by Duncan test. The genotype frequencies of TT, TC and CC were 0.23, 0.25 and 0.52 respectively. The T and C allele frequency were 0.355 and 0.645 respectively. The expected heterozygosity was estimated 0.458. Result of Chi-square showed that the population was not in the Hardy Weinberg equilibrium (P<0.05). The means of traits for milk, percent and yield of fat and yield of protein were not significant but means of percent of protein was significant(P<0.05). The mean of milk, fat and protein yield traits for CC genotype were more than two other genotypes. The results of present study show that the T allele is minor frequency allele and C allele has positive effect on milk, fat and protein yield traits.
Sara Nadri; Ali Sadeghi-Sefidmazgi; Gholam Reza Ghorbani; Pouya Zamani
Volume 24, Issue 4 , December 2022, , Pages 383-393
Abstract
The aim of this study was to estimate the economic values for residual feed intake and some production and performance traits in Iranian Holstein dairy cow. For this purpose, trait by trait or multiple traits of bio-economic modeling along with production and economic data ...
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The aim of this study was to estimate the economic values for residual feed intake and some production and performance traits in Iranian Holstein dairy cow. For this purpose, trait by trait or multiple traits of bio-economic modeling along with production and economic data were used. These data were collected from seven large herds of dairy cows in 2020. The economic values of the residual feed intake was calculated in four different age groups. The diets of different groups were formulated using CNCPS software. Index economic weights (multiplication of the economic values by discounted genetic expressions, in Rial and one cow per year) on average at the level of the studied farms were estimated to be IRR 14280 per kg of milk yield; IRR 291060 per kg of fat yield; IRR 232260 per kg of protein yield; IRR - 790860 per kg of residual feed intake; IRR 702588 per month of longevity and IRR- 113820 per day of days open. The sensitivity analysis showed that the price of concentrate ingredients has a greater effect on the economic value of the residual feed intake than of forage ingredients. In the genetic- economic analysis, the milk production with a relative emphasis of 50 percent was the most important trait in the breeding of Iranian dairy cows, while the relative emphasis on feed efficiency was only about 5 percent. The results of this research provide valuable information for economic values of traits that can be used to complete the national selection index and cost-benefit analysis.
Behzad Rajabi Marand; Hossein Moradi Shahrbabak; Mostafa Sadeghi; Rostam AbdolahiArpanahi
Volume 21, Issue 4 , January 2020, , Pages 419-430
Abstract
The aim of current study was to evaluate the accuracy of genomic breeding values (GEBV) for two important economical traits of milk yield and somatic cell score using SNP markers and LD-based haplotype blocks (haploblocks) by two statistical methods of GBULP and Bayes B. The data set consisted ...
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The aim of current study was to evaluate the accuracy of genomic breeding values (GEBV) for two important economical traits of milk yield and somatic cell score using SNP markers and LD-based haplotype blocks (haploblocks) by two statistical methods of GBULP and Bayes B. The data set consisted of 1654 bulls genotyped with different marker densities. When SNPs were used, the accuracy of breeding values obtained by Bayes B was better than GBLUP. In other words, for milk yield and somatic cell score traits, the prediction accuracy of GBLUP was 0.54 and 0.44 and by Bayes B was 0.58 and 0.44,respectively. For milk yield, the prediction accuracy of using haploblocks in both statistical methods was higher than the prediction accuracy using SNPs, while for the somatic cell score, this increase was more pronounced when GBLUP was used. However, when Bayes B was used this superiority was only obtained when the r2 statistic used to build the haploblocks was higher than 0.2. The results showed that the optimum level of r2 for building haploblocks depends on the trait type and its heritability. As a result, using r2 statistic more than 0.2 for building haploblocks can increase the accuracy of breeding valuesfoe both traits compared to SNP markers.
Hossein Mohammadi; Amir Hossein khaltabadi farahani; Mhammad hossein Moradi; Abouzar Najafi
Volume 23, Issue 4 , January 2022, , Pages 481-490
Abstract
Understanding the genetic control of temperament as a complex trait and correlated with economic traits is one of the breeding goals in beef cattle industry. The aim of the current study was genome wide association studies (GWAS) based on Gene set enrichment analysis for detecting the loci associated ...
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Understanding the genetic control of temperament as a complex trait and correlated with economic traits is one of the breeding goals in beef cattle industry. The aim of the current study was genome wide association studies (GWAS) based on Gene set enrichment analysis for detecting the loci associated with temperament traits in Brahman cattle breed. Therefore, 1370 Brahman cattle and phenotype records associated with temperament traits including Exit velocity, Pen Score, and Temperament Score were used. The evaluation of genome-wide association was carried out using PLINK package 1.90. The gene enrichment analysis was performed by the goseq R package for identifying biological pathways of nearby genes in selected candidate regions and finally, GO, Metacyc, KEEG, Reactome and panther databases were applied for bioinformatics analysis. By Gene set enrichment analysis, the biological pathways and candidate genes of neurotransmitter secretion (NRXN3 and CACNG3), Dopamine Neurotransmitter Release Cycle (PPFIA2), regulation of neuron projection development (GRID2), neuron projection (SLC8A1 and KCNQ2), Axonal growth inhibition (RTN4R), Neurotrophin signaling pathway (MAP2K2, MAP3K5 and PSEN1) and Focal adhesion (TLN2) were identified. The detected candidate genes played an important role in differentiation of synapse, neurotransmitters, neurological diseases and disorders, oxidative and environmental stresses, hormone receptors and glucose homeostasis. Considering the confirmation of the previous region of genome wide association and the identification of new genomic regions, the findings of this study can be useful in the genetic selection of higher production cattle through calm animals.
Abdollah Rezagholivand Lahrud; Mohammad Moradi Shahre Babak; Hossein Moradi Shahrbabak; Morteza Sattaei Mokhtari
Volume 20, Issue 4 , February 2019, , Pages 499-511
Abstract
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 ...
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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.
Roqiah Mahmodi; Mohammad Hossein Moradi; Amir Hossein KhaltAbadi Farahani; Mohammad Osman Karimi
Volume 22, Issue 4 , December 2020, , Pages 501-513
Abstract
The aim of this study was to identify the genome-wide copy number variations (CNV) in one of the sheep breeds in Afghanistan named Arabic breed, and to study the associations between these regions containing this kind of diversity with different biological pathways. For this purpose, 15 animal samples ...
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The aim of this study was to identify the genome-wide copy number variations (CNV) in one of the sheep breeds in Afghanistan named Arabic breed, and to study the associations between these regions containing this kind of diversity with different biological pathways. For this purpose, 15 animal samples from different ages were collected from their natural rearing environment in Herat province of Afghanistan and then were genotyped using Illumina Ovine 50kSNP array. After various steps of the data quality control, the genome-wide detection of CNVs was carried out using Hidden Markov Model in PennCNV (version 1.0.3) software. The results showed that all animals used in this study have CNVs in their genome. In total, 306 CNVs were observed for autosomal chromosomes. The total genomic length of CNVs was 128 Mbp and the average CNV numbers per animal was 20.4. After merging overlapped regions, a total of 286 CNVR regions were identified. These genomic regions were then further evaluated using bioinformatics tools for identifying the metabolic pathways associated with them. The results of gene ontology study indicated that many of these regions are associated with different metabolic pathways such as fertility and reproductive performance, body weight and carcass characteristics, immune system development, and skeletal-muscular system.
Parisa Mahvari; Abbas Doosti
Volume 19, Issue 3 , November 2017, , Pages 521-532
Abstract
The aim of this research was to recognize genetic polymorphism in intron place of BMP15 gene and its relationship with growth and reproduction traits in Lori-Bakhtiari sheep breed using sequencing method. Blood samples of 80 ewes and 20 rams of Lori-Bakhtiari sheep from breeding station of Shahrekord ...
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The aim of this research was to recognize genetic polymorphism in intron place of BMP15 gene and its relationship with growth and reproduction traits in Lori-Bakhtiari sheep breed using sequencing method. Blood samples of 80 ewes and 20 rams of Lori-Bakhtiari sheep from breeding station of Shahrekord were collected. DNA was extracted from whole blood and their quality was evaluated using 1% agarose gel electrophoresis. A fragment with the size of 356 bp from extracted DNA was amplified using polymerase chain reaction (PCR) with a pair of specific primers. The PCR products were sequenced. Sequenced result was compared with sequenced gene in world gene bank by Blast program in NCBI. Results founds only a deletion mutation (D75A) in this gene that in this mutation thymine with 41.2% frequency was deleted .This mutation wasn't effect on reproduction and growth traits. Of course, it's better than polymorphisms in other segments of this gene were studied and then decided about effect of this gene on reproduction and growth trait.
Volume 18, Issue 4 , December 2016, , Pages 647-659
Abstract
Bovine mastitis is an inflammation disease of the mammary gland that impose considerable costs to the dairy industry. Regulatory mechanisms of this disease is complex and controlled by various gene regulatory elements and more studies are needed to better understand this disease. In the present study ...
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Bovine mastitis is an inflammation disease of the mammary gland that impose considerable costs to the dairy industry. Regulatory mechanisms of this disease is complex and controlled by various gene regulatory elements and more studies are needed to better understand this disease. In the present study aimed to better understand of regulatory elements involved in mastitis, milk samples of two groups of healthy and infected cows during time series of 0, 12, 24, 36 and 48 hours after contamination were collected. The miRNA-seq data obtained from the milk samples and using the advanced bioinformatics, novel miRNAs, their targets and probability functions, isomirs and novel miRNAs* were identified. The results led to the identification of 92 novel miRNA including 26 miRNAs with homologous and 66 miRNAs without homologous genes in other species. Investigation of the functional groups of predicted targets genes, confirmed the roles of new miRNAs in response to internal and external stimulations, apoptosis and production of immunoglobulin. Furthermore, 135 novel miRNAs were identified. Also, 493 novel isomeric sibling miRNAs (isomers) were discovered that immune related functions of these isomirs were demonstrated in some species like human and mouse. Identification of miRNAs target genes with associated functions in mastitis, including safety, apoptosis and inflammation, can indicated the possible regulatory roles of the identified miRNAs in mastitis.
gholamhosein tahmasbi; mohammad babaei; naser tajabadi; einollah seyfi; nader mashayekhi; hosein rezazadeh
Volume 19, Issue 4 , March 2018, , Pages 739-750
Abstract
The current study was aimed to evaluate the performance of the 13th generation of breeding improved queens in Iran Honey Bee Breeding Program, and to compare them with control queens kept in private apiaries. The mother queens were reproduced by beekeepers in south of Iran to evaluate and compare these ...
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The current study was aimed to evaluate the performance of the 13th generation of breeding improved queens in Iran Honey Bee Breeding Program, and to compare them with control queens kept in private apiaries. The mother queens were reproduced by beekeepers in south of Iran to evaluate and compare these queens with queens reproduced in private apiaries across the country. To evaluate the queens, specific questionnaires were designed based on Likert scale and completed by beekeepers. The results showed that the improved queens had better performance than control queens in terms of swarming, defensive behavior and overwintering in comparison of queens kept in private apiaries. In other words, the genetically imprived colonies significantly are different from control colonies (P<0.05). Furthermore, swarming evaluation revealed that the superiority of bred colonies (P<0.05). For example, despite of limited space and compacted frames the colonies did not start to make queen cells. The results demonstrated that Iranian honey bee breeding is effective in improving of target traits and the use of these queens is essential for increasing beekeeping performance in Iran. According to the results, in spite of comparative advantage, there was no significant difference between the bred queens and control queens in terms of honey production and population. From the results, although all the efforts in desirable honey production were paid off, more time and novel methods are required to improve above mentioned traits. From the other side, resistant races against biotic and abiotic stresses should be conserved to produce high quality honey in serious time and conditions.
Seyd Davoud Sharifi; Amin Dibamehr; Houshang Lotfollahian
Volume 13, Issue 1 , September 2011, , Pages 7-16
Abstract
The effects of probiotics and antibiotics and fat type in diet on broiler performance were studied by using 900 one-day old Ross 308 chicks in a three × three factorial arrangement with three types of fat (nonfat, three percent fatty acid and three percent soy oil) and three growth promoters (without ...
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The effects of probiotics and antibiotics and fat type in diet on broiler performance were studied by using 900 one-day old Ross 308 chicks in a three × three factorial arrangement with three types of fat (nonfat, three percent fatty acid and three percent soy oil) and three growth promoters (without GP, flavomycin and protexin) in completely randomized design with four replicates per each treatment. Fat and its type had significant effects on weight gain and the body weight gain of birds fed diets containing soy oil were better (P< 0.05). Dietary flavomycin supplementation improved weight gain and FCR (P< 0.05). The fat type × growth promoter’s interaction influenced broiler performance, significantly (P< 0.05). Birds fed on diets containing soy oil and flavomycin showed the highest feed intake and weight gain, whereas, the lowest feed intake and weight gain was belonged to birds fed diets containing fat and protexin (P< 0.05). From the results obtained, it can be indicated that addition of protexin to diets containing fat has negative effect on broiler growth performance.
Sana Farhadi; Ali Akbar Masoudi; Rasoul Vaez Torshizi
Volume 17, Issue 1 , April 2015, , Pages 9-18
Abstract
The TLR4 gene structure as the main receptor for lipopolysaccharide recognition of Gram-negative bacteria was investigated in two strains of Iranian commercial Arian line and west Azerbaijan native chicks and its expression was studied in some major organs. Blood samples of the 120 birds were taken and ...
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The TLR4 gene structure as the main receptor for lipopolysaccharide recognition of Gram-negative bacteria was investigated in two strains of Iranian commercial Arian line and west Azerbaijan native chicks and its expression was studied in some major organs. Blood samples of the 120 birds were taken and total DNAs extracted. Then, the target gene was sequenced using four pairs of primers on four samples of each strain. The effects of amino acid changes on protein function were assessed by PANTHER software. To investigate the gene expression, total RNAs were extracted from liver, spleen, and lung tissues after slaughter of the birds. Gene expression was assessed by semi-quantitative RT-PCR. The amplified RNAs from tissues of liver, spleen and lungs. Then electrophoresis images were processed with the Image software and quantitative data analyzed by MINITAB. The results showed three new single polymorphisms (T1147C, C2246A and A1832G) in the sequence of TLR4 gene in the studied populations. The effects of variations on TLR4 protein structure indicated a deleterious effect of mutations on protein structure. The TLR4 gene expression in case of native and commercial strains did not show significant differences. Due to importance of the TLR4 in innate immunity and identification of some novel mutations affecting on protein structure, this gene could be a valuable candidate related to genetic resistance in poultry.
Mojdeh Mahmoudi Zarandi; Mohammad Rokouei; Mehdi Vafaei Valleh; Ali Maghsoudi
Volume 22, Issue 1 , March 2020, , Pages 9-22
Abstract
This study was done in order to estimate genetic parameters of growth and feed efficiency traits in Japanese quail. The data set consisted of 7762 records for feed efficiency traits and 12113 records for body weight gain traits were collected at Research Center of Special Domestic Animals, University ...
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This study was done in order to estimate genetic parameters of growth and feed efficiency traits in Japanese quail. The data set consisted of 7762 records for feed efficiency traits and 12113 records for body weight gain traits were collected at Research Center of Special Domestic Animals, University of Zabol. The following traits including body weight gain from 20 to 25, 25-30, 30-35, 35-40, 40-45 and from 0 to 45 days of age, feed intake, feed conversion ratio and residual feed intake from 20 to 45 days of age were evaluated. The genetic parameters were estimated through single and bivariate animal models via Gibbs sampling method. Heritability estimates for body weight gain varied from 0.02 to 0.23 and for feed intake, feed conversion ratio, residual feed intake was in ranges of 0.04 to 0.11. Genetic correlations estimates between body weight gain and feed conversion ratio 20-25, body weight gain and feed conversion ratio 25-30, body weight gain and feed conversion ratio 30-35, body weight gain and feed conversion ratio 35-40, body weight gain and feed conversion ratio 40-45 were -0.56, -0.49, -0.57, -0.70 and 0.25 respectively. Considering estimated genetic correlations of this study, we recommend that selection for body weight gain and decrease feed efficiency have potential to improve feed efficiency traits in Japanese quail. It is expected that by selecting for these traits the costs of breeding programs such as feeding and phenotyping would be reduced.
Seyed Davoud Sharifi; Ehsan Tavazoei; Ali Akbar Khadem; Abbas Barin
Volume 12, Issue 2 , October 2010, , Pages 11-20
Abstract
In this study, the effect of different levels of fat with antibiotics and probiotics on blood biochemical traits and performance of broiler chicks was investigated. In a factorial experiment, 288 Day-old Ross broiler chicks treated with two level of fat (3 and 6 percent) and three additives (Flavomycin, ...
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In this study, the effect of different levels of fat with antibiotics and probiotics on blood biochemical traits and performance of broiler chicks was investigated. In a factorial experiment, 288 Day-old Ross broiler chicks treated with two level of fat (3 and 6 percent) and three additives (Flavomycin, Protexin and none-additive). The birds were allocated randomly in six treatments with four replicates and 12 birds per replicat. Results showed that the chicks fed on diets containing 3 percent of fat + Flavomycin had higher feed intake and body weight gain compared to birds fed with fat + Protexin (P< 0.05). The concentration of cholesterol, HDL and LDL in serum of birds of 6% fat was more than of those fed diets with 3% fat. Birds fed diets containing protexin had lowest cholesterol, HDL and LDL (P< 0.05). It was concluded that supplementing the rations containing fat with probiotics decrease feed intake and body weight gain in broilers chicks and their performance decrease by increasing fat in diets.
Hassan Fazaeli; Esmaiel Ismaily Rad; Mohammad Babaie
Volume 13, Issue 2 , March 2012, , Pages 11-18
Abstract
This experiment was conducted to improve the nutritive value of barley stubble for two consecutive years. After harvesting crop, at first year, a completely randomized design, with a 3 × 3 factorial experiment was conducted in which 27 plots were divided into nine treatments. The treatments including ...
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This experiment was conducted to improve the nutritive value of barley stubble for two consecutive years. After harvesting crop, at first year, a completely randomized design, with a 3 × 3 factorial experiment was conducted in which 27 plots were divided into nine treatments. The treatments including zero, 2.5 and five percent urea each with zero, three and six percent molasses were mixed with water and sprayed on the stubble (three plots per treatment). During five periods, all plots were sampled before and after spraying with 10 days intervals for the chemical analyses. The crude protein (CP) was increased but crude fiber (CF) decreased in urea-molasses treatments (P< 0.05). The Ash content was increased (P< 0.05) only in the treatments contained 6 percent molasses. At the second year, after harvesting the barley crop, four hectares of stubble was divided in four parts and sprayed with four treatments of urea-molasses liquor including: 1) 2.5 percent urea, 2) 2.5 percent urea +3 percent molasses, 3) 5 percent urea, 4) 5 percent urea +3 percent molasses. Forty eight Shal ewes were divided among the treatments and grazed for 50 days. All ewes showed body weight gain, during the experiment but the body weight changes were not different between the treatments. As a result of twining, the lambing rate was increased about 25 percent for the animals received five percent urea +3 percent molasses comparing to the other treatments.
Mahnaz Salehi; Jaleh Mirabdolbaghi; Mohammad Ali Kamali Sarvestani
Volume 14, Issue 1 , September 2012, , Pages 11-17
Abstract
The study was consequently investigated effect of different tanning methods on apparent density, thickness, tensile strength and also extension percentage in three different tanning (chromic, alum and vegetable) of grown part of ostrich skins (n = 15; 12 to 14 months). Average apparent density and thickness ...
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The study was consequently investigated effect of different tanning methods on apparent density, thickness, tensile strength and also extension percentage in three different tanning (chromic, alum and vegetable) of grown part of ostrich skins (n = 15; 12 to 14 months). Average apparent density and thickness of leathers were 0.7 ± 0.0gr/cm2 and 1.7 ± 0.1 mm, respectively. The breaking load, tensile strength and extension of chromic tanning leather (33.0 ± 4.9 kgf, 197.2 ± 23.9 kgf/cm2 and 53.3 ± 7.0 percent) were more than alum tanning leather (27.4 ± 5.5 kgf, 161.7 ± 26.7 kgf/cm2, 46.4 ± 7.8 percent) and vegetable tanning leathers (13.0 ± 4.5 kgf, 70.7 ± 21.8 kgf/cm2 and 40.1 ± 6.4 percent). However, the best physical quality was found in the chromic tanned leather for ostrich skin proccesing related to alum and vegetable leathers.
A. Karampour; F. Hozhabri; F. Kafilzadeh
Volume 14, Issue 2 , January 2012, , Pages 11-20
Abstract
The effect of Aspergillus niger waste, a by product of citric acid extraction (yeast waste) on in vitro digestibility of alfalfa hay at different times of incubation (24 and 48h) and fattening performance of male lambs studies. Different levels (five, 10, 15 and 20 percent) of yeast waste were added ...
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The effect of Aspergillus niger waste, a by product of citric acid extraction (yeast waste) on in vitro digestibility of alfalfa hay at different times of incubation (24 and 48h) and fattening performance of male lambs studies. Different levels (five, 10, 15 and 20 percent) of yeast waste were added to alfalfa hay and subjected to the in vitro digestibility trial. In fattening trial, twenty Sanjabi lambs (20.8 kg initial BW, three months of age) divided into two groups in a CRD design. The use of yeast waste of different levels, increased Dry matter (DM) and organic matter (OM) digestibility of alfalfa hay at initial 24 h of incubation (P< 0.05) but the difference in digestibility at the last 48 h of incubation was not significant. Average daily gain, FCR and DM intake and carcass parts between treatments were not significant.
Mohammad Vahid Kimiaeitalab; Shahab Ghazi; Sara Mirzaie Goudarzi
Volume 15, Issue 1 , July 2014, , Pages 11-20
Abstract
This experiment was conducted to investigate the effects of various levels of cichorium intybus andcopper on performance and egg yolk cholesterol. Total of 324 layer hens (Hy-Line W-36) were used in arandomized complete blocks with nine treatments, three replications of 12 birds in each from 38 to 50weeks ...
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This experiment was conducted to investigate the effects of various levels of cichorium intybus andcopper on performance and egg yolk cholesterol. Total of 324 layer hens (Hy-Line W-36) were used in arandomized complete blocks with nine treatments, three replications of 12 birds in each from 38 to 50weeks of age. Experimental diets include control, four levels of copper (150, 200, 250 and 300 mg/kg)and four levels of cichorium intybus (15, 20, 25 and 30 percent of diet). Different levels of cichoriumintybus and copper significantly decreased serum and yolk cholesterol than control. The level of 300mg/kg copper significantly reduced serum and yolk cholesterol but significantly decreased egg weight,egg production and increased feed conversion ratio compared to control. Levels of 25 and 30 percent ofcichorium intybus significantly decreased egg production than control treatment. Yolk color improved bydifferent levels of cichorium intybus than control and copper levels. In conclusion, the best result forlower yolk cholesterol were achieved by those laying hens fed a diet with 150 mg/kg copper of diet or 15percent of cichorium intybus.
Mehdi Dehghani Sanij; Ahmad Afzalzadeh; Kamran Reza Yazdi; Mohammad Ali Norouzian
Volume 16, Issue 1 , May 2014, , Pages 11-20
Abstract
The effect of replacing alfalfa by artichoke hay on nutrient digestibility, gas production parameters, performance and carcass characteristics of Lori-Bakhtiari lambs was studied. The lambs in control group received diet containing 30 percent alfalfa, 15 percent barley straw and 55 percent concentrate ...
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The effect of replacing alfalfa by artichoke hay on nutrient digestibility, gas production parameters, performance and carcass characteristics of Lori-Bakhtiari lambs was studied. The lambs in control group received diet containing 30 percent alfalfa, 15 percent barley straw and 55 percent concentrate and in test group alfalfa hay was replaced with artichoke hay, completely. Dry matter intake was higher for test group lambs (P<0.05), but average daily gain and feed conversion ratio were not differed between experimental groups. Gas production rate was not differed between groups, but b fraction was higher for test group (P<0.05). Replacing alfalfa by artichoke caused to increasing digestibility of dry matter and organic matter (P<0.05). However, control diet had higher digestibility of crude protein and NDF (P<0.05). After slaughter, there were no significant differences between groups in carcass characteristics and percentage of internal organs. Results of this study showed that artichoke hay could be replaced with alfalfa hay in finishing lambs diet.