Ali Reza Bijan nia; Ali Reza Seidavi; Mani Ghani pour
Volume 12, Issue 2 , October 2010, , Pages 1-10
Abstract
Mulberry powdery mildew is the most important fungal disease in silkworm rearing zones. Resistance of mulberry varieties is different against this disease. The mulberry varieties have different resistance against powdery mildew disease. Percentage of moisture, nitrogen, protein, phosphor, fiber, calcium ...
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Mulberry powdery mildew is the most important fungal disease in silkworm rearing zones. Resistance of mulberry varieties is different against this disease. The mulberry varieties have different resistance against powdery mildew disease. Percentage of moisture, nitrogen, protein, phosphor, fiber, calcium and ash of powdery mildew infected leaves and healthy control in five mulberry varieties including Kenmochi, Local, Kaironozomi, Ichinose and Shinichinose were determined. Meanwhile, larvae mortality percentage, pupae mortality percentage, total produced cocoon weight, cocoon weight, single cocoon shell weight and percentage, and produced cocoon number recorded after larvae feeding with control and infected leaves. The obtained results showed that powdery mildew disease resulted to nutrients decline in mulberry leaves and economical parameters in those larvae which fed with infected leaves (P< 0.01). Moisture percentage, protein, percentage, nitrogen, phosphor, calcium decreased after powdery mildew infectious for each five races. Meanwhile, pupae mortality percentage, single cocoon weight, single cocoon shell weight and percentage, and produced cocoon number decreased after feeding with infected leaves for total five varieties significantly (P< 0.05). Therefore, quality decline of mulberry leaf under powdery mildew disease resulted to decreasing of silkworm performance in rearing process.
Hamid Reza Ansari Ranani; Hamir Reza Baghershah
Volume 13, Issue 1 , September 2011, , Pages 1-6
Abstract
This study was conducted to determine the effect of chemical methods for dewooling from skin on Moghani sheep skin and wool quality. Two treatments of sodium hydroxide (three and five percent) and two treatments of sodium sulfide (10 and 15 percent) rub to 100 skin and time spent to collect wool from ...
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This study was conducted to determine the effect of chemical methods for dewooling from skin on Moghani sheep skin and wool quality. Two treatments of sodium hydroxide (three and five percent) and two treatments of sodium sulfide (10 and 15 percent) rub to 100 skin and time spent to collect wool from skin surface, fibers staple length and diameter recorded. Dewooled skins at thin-cross stage were evaluated by three leather experts for hair follicle, shape, elasticity, flesh, softness, water absorbability, fineness, wrinkleless, thickness and footage loss. Results indicated that the time spent to collect wool from sodium sulfide treated skins was significantly (P< 0.05) lower than sodium hydroxide treated skins. Lowest and highest time for dewooling was (80.3 ± 4.1 minutes) and (180.3 ± 5.3 minutes) for skins treated with 15% sodium sulfide and three percent sodium hydroxide respectively. Quality score for skin treated with 10 and 15% sodium sulfide and three and five percent sodium hydroxide were 30.2 (± 0.1), 31.2 (± 0.5), 37 (± 0.5) and 35.8 (± 1.0), respectively. In general, skins treated with sodium hydroxide have better quality than skins treated with sodium sulfide.
Golestan Golestani Milanloo; seyed davood sharifi; Akbar Yaghoub far; Ali akbar Khadem
Volume 13, Issue 2 , March 2012, , Pages 1-10
Abstract
This study was carried out to investigate the effects of Natuzyme Plus (a multi enzyme) in diets containing wheat and canola meal on broiler performance. A total of 336 day-old Arbor Acres broiler chicks were used in a completely randomized design with six treatments and four replicates. Experimental ...
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This study was carried out to investigate the effects of Natuzyme Plus (a multi enzyme) in diets containing wheat and canola meal on broiler performance. A total of 336 day-old Arbor Acres broiler chicks were used in a completely randomized design with six treatments and four replicates. Experimental diets were: 1 . Diet based on corn-soybean meal (control), 2 . Diet containing 30 precent wheat and 3 . Diet containing 30 percent wheat + 10 percent canola meal, which Natozyme was added (350 g/ton) to these diets to make diets containing enzyme (totally six treatments). Adding enzyme to diet containing wheat and canola meal increased significantly feed intake, weight gain and feed conversion ratio (FCR) at starter and overall rearing period (P< 0.01). Use of Natuzyme Plus in diet containing wheat and canola meal reduced significantly the relative weight of digestive organs in compared of same diets without enzyme. The results of this study indicate that the performance of broiler chickens fed the diets containing wheat and canola meal could be improve by supplementing with Natuzyme plus preparations.
Omid Vosough SHarifi; Akbar Yaghoubfar; seyed davood sharifi; Ghodratollah Mirzadeh; Firouz Askari
Volume 14, Issue 1 , September 2012, , Pages 1-10
Abstract
This study was conducted to determine the nutritional value of seaweed Gracilariopsis persica and to evaluate its utilization in layer nutrition. Metabolizable Energy and chemical composition of seaweed were measured. 100 Hy-line W-36 hens were allocated to five dietary groups with five treatment group ...
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This study was conducted to determine the nutritional value of seaweed Gracilariopsis persica and to evaluate its utilization in layer nutrition. Metabolizable Energy and chemical composition of seaweed were measured. 100 Hy-line W-36 hens were allocated to five dietary groups with five treatment group (experimental diets containing zero, five, 10, 15 and 20 percent seaweed) and it lasted for 12 weeks. Egg production, feed intake, feed conversion ratio, egg weight and egg mass were measured weekly. The results showed that the CP, CF, EE, Ca and P of the seaweed were 23.05, 7.2, 0.1, 0.9 and 0.34 percent, respectively. Apparent Metabolizable Energy and Apparent Metabolizable energy corrected for nitrogen were 2185.04 and 2195.72 Kcal/Kg, respectively. The treatments contain more than five percent seaweed, decreased egg production and increased feed conversion ratio (P< 0.05). There was significant decrease in egg mass for more than 10 percent seaweed treatments (P< 0.05). These results showed that usage of five percent seaweed Gracilariopsis persica in the layer hens' diet doesn't have negative effect on production performances.
M. A. Alamian; A. A. Khadem; S. D. Sharifi
Volume 14, Issue 2 , January 2012, , Pages 1-10
Abstract
The effects of phytase and glycosidase supplementation to diets containing rice bran on broiler performance were investigated by using 200 day old (308 Ross) broiler chicks in a completely randomized design with five treatments and four replicates. The five dietary treatments were as: corn-soybean meal ...
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The effects of phytase and glycosidase supplementation to diets containing rice bran on broiler performance were investigated by using 200 day old (308 Ross) broiler chicks in a completely randomized design with five treatments and four replicates. The five dietary treatments were as: corn-soybean meal based diet; diet containing rice bran; diet containing rice bran supplemented with Natafous; diet containing rice bran supplemented with Safizyme, and diet containing rice bran supplemented with Natafous and Safizyme. The dietary levels of rice bran were 15, 20 and 25 percent for the starting, growing and finishing diets, respectively. Birds fed on rice bran + enzyme added diets consumed less feed (P< 0.05) than those fed on unsupplemented rice bran contained diets. The enzyme addition to rice bran containing diets improved the villi length and weight gain of birds at different rearing periods (P< 0.05). In conclusion, results showed that the Natafous or Safizyme supplementation in diets could improve the performance of broiler chicks when rice bran was used at a level of 15, 20 and 25 percent in starter, grower and finisher diets, respectively.
Mohammad Yazarloo; Seyed Davood Sharifi; Farid Shariatmadari; Abdolreza Salehi
Volume 15, Issue 1 , July 2014, , Pages 1-10
Abstract
In order to determine the optimal levels of energy and protein in grower diet of Japanese quail, 360 dayold Japanese quails were used in a 3×3 factorial arrangement of dietary treatments that comprised threelevels of metabolisable energy (2750, 2850, and 2950 Kcal/kg) and three levels of crude ...
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In order to determine the optimal levels of energy and protein in grower diet of Japanese quail, 360 dayold Japanese quails were used in a 3×3 factorial arrangement of dietary treatments that comprised threelevels of metabolisable energy (2750, 2850, and 2950 Kcal/kg) and three levels of crude protein (24, 26and 28 percent) with four replicates per treatment in a completely randomized design. Feed intake andbody weight were measured weekly and feed conversion ratio was calculated. At 35 d of age, four birds(from both sexes) from each replicate were randomly selected and killed following blood sampling toevaluate carcass traits. The blood samples were assayed for the sera concentrations of growth hormone.Results indicated that birds fed on diets containing 2850 kcal/kg metabolisable energy and 26 percentprotein had higher daily weight gain and better feed conversion ratio and carcass yield (P<0.05). The seraconcentration of growth hormone was higher in birds fed on diet containing 2750 kcal/kg metabolisableenergy (P<0.05). This study indicated that Japanese quails can grow faster and more efficiently on dietcontaining 2850 kcal/kg metabolisable energy and 26 percent protein. Therefore, the diet containing 2850kcal/kg metabolisable energy and 26 percent protein could be recommended as dietary metabolisableenergy and protein requirements for growing Japanese quails.
Ghasem Motaghinia; Homayoun Farhangfar; Mohsen Ahmadi Shahrakht; Abdolahad Shadparvar; Majid Jafari
Volume 16, Issue 1 , May 2014, , Pages 1-9
Abstract
Effects of lamb and parents coefficient of inbreeding (CI) on wool weight were studied using 10,868 wool records belonging to 3,244 Iran Black lambs (1,633 males and 1,611 females) representing 96 rams and 995 ewes collected during 1983-2006 from Animal Breeding Station of Abbas Abad. Year and month ...
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Effects of lamb and parents coefficient of inbreeding (CI) on wool weight were studied using 10,868 wool records belonging to 3,244 Iran Black lambs (1,633 males and 1,611 females) representing 96 rams and 995 ewes collected during 1983-2006 from Animal Breeding Station of Abbas Abad. Year and month of shearing, CI of lamb and dam, sex and birth type had significant affect on wool weight Among 3,244 pedigree animals, 3,005 heads (92.6 percent) were found to be inbred. Mean and standard deviation of CI of lamb, sire and dam in whole population were 8.1±6.1, 6.5±6.1 and 5.3±5.8 percent, respectively. The corresponding figures in inbred population were 9.0±5.7, 7.0±6.1 and 5.7±5.8 percent, respectively. Minimum and maximum CI of lamb was 0 and 36.4 percent, respectively. Increase of CI by one percent was accompanied with a decrease of 26.9 g (quadruplet male), 4.8 g (twin female), 4.3 g (triple female) and 13.1 g (quadruplet female) in wool weight. A decrease of 1.4 g in wool weight of lamb was observed as the CI of dam was increased by one percent. Statistically significant annual change trend were estimated to be 0.2±0.02 percent and 0.1±0.02 percent for whole and inbred populations, respectively. A controlled mating is needed to reduce deleterious effects of inbreeding.
Mokhtar Ali Abbasi; Sima Savar Sofla
Volume 17, Issue 1 , April 2015, , Pages 1-8
Abstract
This study was evaluated some strategies and determined the suitable selection index for Afshari sheep using simulated data. The relative importance of traits was determined based on the estimated economic values and consequently, the most benefit traits were applied to selection indexes construction. ...
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This study was evaluated some strategies and determined the suitable selection index for Afshari sheep using simulated data. The relative importance of traits was determined based on the estimated economic values and consequently, the most benefit traits were applied to selection indexes construction. The interest indexes were different combination of traits including ewe body weight (EBW), annual wools weight (AWW) and total weaning weight for each exposed ewe (TWWEE). The index 1 was included all three mentioned traits. The indexes two, three and four were included (AWW, TWWEE), (EBW, TWWEE) and (TWWEE), respectively. The results indicated that the aggregate genotype, selection index and economic progress increased by increasing in the population size and decreasing in ram ratio, but made reduction in inbreeding average, in all indexes. In more cases, the aggregate genotype decreased by removing a trait in the index. The comparisons among indexes indicated that the most suitable selection index for this breed is index 1 which included EBW, AWW and TWWEE. This index had a maximum selection index average, aggregate genotype and economic progress.
Yahya Mohammadi; Mohammad Mahdi Shariati; Saeed Zerehdaran; Mohammad Razmkabir; Mohammad Bagher Sayyadnejad; Mohammad Bagher Zandi
Volume 18, Issue 1 , April 2016, , Pages 1-11
Abstract
Genomic Selection (GS) is a tool for prediction of breeding values for quantitative traits. For a successful application of GS, accuracy of predicted genomic breeding value (GEBV) is a key issue to consider. Here we investigated the accuracy of GEBV in 345 genotyped Iranian Holstein cattle. The study ...
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Genomic Selection (GS) is a tool for prediction of breeding values for quantitative traits. For a successful application of GS, accuracy of predicted genomic breeding value (GEBV) is a key issue to consider. Here we investigated the accuracy of GEBV in 345 genotyped Iranian Holstein cattle. The study was performed on milk, fat, protein yield and somatic cell count. Four methods G-BLUP, Bayes B, Reproducing kernel Hilbert Spaces (RKHS) and Neural Networks (NN) were used to predict genomic breeding values and their accuracies. The GEBV accuracies varied between 0.39 for somatic cell count to 0.73 for fat yield. Bayes B gave the highest accuracies among methods. Bayes B and non- parametric methods tended to produce inflated predictions (slope of the regression of GBV on EBV greater than 1). However, in all traits, lower estimates of MSE were obtained using G- BLUP. Bayes B regression model are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions.
Rostam AbdolahiArpanahi
Volume 19, Issue 1 , May 2017, , Pages 1-12
Abstract
The objective of this study was to compare three parametric (GBLUP, BayesB and RKHS) and two resampling (Bagging GBLUP and Random Forest) statistical methods in genomic prediction of traits with different genetic architecture. A genome consisting of three chromosomes, 1 Morgan each, was simulated on ...
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The objective of this study was to compare three parametric (GBLUP, BayesB and RKHS) and two resampling (Bagging GBLUP and Random Forest) statistical methods in genomic prediction of traits with different genetic architecture. A genome consisting of three chromosomes, 1 Morgan each, was simulated on which 5000 SNPs and 50, 100 and 200 QTLs were distributed. The substitutions effects of QTLs were modeled with normal, gamma and uniform distributions with a level of heritability equal to 0.30. The predictive performance of statistical models was evaluated using the correlation between predicted and true breeding values as well as the regression of predicted values on true breeding values. In the target population, Random Forest resulted in overestimation of estimated regression coefficients while GBLUP, BayesB and RKHS led to an underestimation of regression coefficients of true breeding values on predicted breeding values. In exception of Bagging GBLUP, the performance of all statistical methods was the same in three gene effect distributions. However, the performance of GBLUP and BayesB was better than other statistical methods. A reason for this superiority could be the additive architecture of simulated traits. In conclusion, GBLUP and BayesB were superior over resampling methods in genomic predictions.
Zahra Alimoradi Tamrin; Hassan Darmani Kohi; navid gavi hosseinzadeh
Volume 20, Issue 1 , May 2018, , Pages 1-14
Abstract
In order to investigate the effects of Galbanum essential oil (GEO) and xylanase on performance and intestinal microflora of broiler chicks, a total of 160 one-day old chicks (Ross 308 strain) were used to four dietary treatments based on a completely randomized design in a factorial arrangement. The ...
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In order to investigate the effects of Galbanum essential oil (GEO) and xylanase on performance and intestinal microflora of broiler chicks, a total of 160 one-day old chicks (Ross 308 strain) were used to four dietary treatments based on a completely randomized design in a factorial arrangement. The factors included were xylanase (0 and 0.2 gr/kg of diet) and GEO (0 and 0.1 gr/kg of diet). During the experimental periods (0-10 d, 11-24 d and 25-42 d), body weight gain (BWG), feed intake and feed conversion ratio (FCR) were measured. At days 21 and 42 of age two chicks from each replicate were slaughtered to determine carcass characteristic and ileal microbial populations of E. coli and Lactobacillus. Adding enzymes to the diet increased BWG in growing period and improved FCR in the growing and in the entire period of the experiment. At 21 day of age, GEO supplementation alone or GEO and xylanase as mixed significantly (P
Farzo Allah Mostafaei; Mohammad Ebrahim Nooriyan Soroor; mohammad moeini
Volume 21, Issue 1 , April 2019, , Pages 1-10
Abstract
This study was conducted to determine the effect of adding of dried Molasses Distillers Condensed Soluble with bran (MDCS+B) to diets on growth performance, fermentation parameters, protozoa population and some blood biochemical parameters of fattening lambs. Twenty-one Mehraban male lambs (Weight average ...
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This study was conducted to determine the effect of adding of dried Molasses Distillers Condensed Soluble with bran (MDCS+B) to diets on growth performance, fermentation parameters, protozoa population and some blood biochemical parameters of fattening lambs. Twenty-one Mehraban male lambs (Weight average 35 ± 0.5) and 4 month age old were used in 3 treatments for 74 (14 days adaptation and 60 days experiment) days in randomized completely design. Lambs were offered either MDCS+B (control, CON) or the concentrate supplemented with 25 % MDCS+B; or 50% MDCS+B. Lambs were weighed at weekly intervals and blood samples were collected on days 30 and 60 .The rumen fluid samples were collected on days 60 during the fattening period. The results showed that dry matter intake were not different between dietary treatments at second month and total period of experiment as compared to the control group. The addition of MDCS + B at level of 25% increased ruminal ammonia concentration by 10.35% (P=0.054) and total rumen volatile fatty acids concentration increased by 46 % as compared to the control group (P= 0.016). The total protozoa population were not influence by MDCS+B. The price of each kilogram of ration for 25 and 50% MDCS + B were 74 and 155 Tomans respectively, when compared with the control group. The overall results of this study showed that the use of MDCS + B reducing feed costs and can be used up to 50% of concentrate.
masoud alipanah
Volume 22, Issue 1 , March 2020, , Pages 1-8
Abstract
In order to determine the interference of dominant effects on the estimation of genetic parameters, two models including additive and additive-dominance were used for estimation of genetic parameters of carcass traits in 631 hybrid beef bulls. Data analysis was conducted using Plink (V. 1.9) ...
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In order to determine the interference of dominant effects on the estimation of genetic parameters, two models including additive and additive-dominance were used for estimation of genetic parameters of carcass traits in 631 hybrid beef bulls. Data analysis was conducted using Plink (V. 1.9) and GVCBLUP (V. 3.9) softwares. Results of this study showed that most carcass quality traits have high heritability,but two traits namely hot carcass weight and ultrasound ribeye area had low heritability (0.15 and 0.11). Dominance variances have high contribution to the total variation of hot carcass weight, ultrasound ribeye area, ultrasound backfat thickness and ribeye area (0.13, 0.44, 0.89 and 0.33 respectively). However, dominant effect for other traits (lean meat yield, marbling score, backfat thickness, ultrasound ribeye area and grade of carcass) was not observed or was in very low amount. When dominance variance is low, its effect on GBLUP estimates is negligible. The estimates of heritability did not change significantly by the adding dominance effect into the model. The most important genomic regions that affect the carcass quality traits were belong to LAP3, THBS4 and PCDH9 genes. It is suggested that for the better understanding of the genetic structure of traits and better breeding plan, the dominance effects should be added into the model for geneticparameter estimation.
Siavash Manzoori; Amir Hossein Khaltabadi Farahani; Mohammad Hossein Moradi
Volume 25, Issue 1 , April 2023, , Pages 1-11
Abstract
The present study was conducted in order to select effective markers in breed discrimination and compare the performance of SNP marker selection methods with the data of 304 animals from 14 different breeds that were genotyped using the Illumina SNP50K marker panel. Knowledge of genetic structure are ...
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The present study was conducted in order to select effective markers in breed discrimination and compare the performance of SNP marker selection methods with the data of 304 animals from 14 different breeds that were genotyped using the Illumina SNP50K marker panel. Knowledge of genetic structure are very important for better understanding of genetic changes in genomic studies. The information content of each marker is used as an index for selecting markers in reducing the size of marker panels. To estimate the information content of each marker, the following selection methods were used: Fst (pairwise & global), Theta, Delta, D, Gst, G'st, G"st and Principal Component Analysis. In this study, the logarithm of the likelihood ratio was used to select markers. According to the results, all selection methods for identifying markers had similar performance. The number of common markers between the methods was at least 42 markers and at most 499 SNP markers. In general, the F_ST statistical method required a smaller number of markers to achieve a successful assignment. G'st and G"st statistics showed poor performance with more than 350 markers to achieve 95% correct assignment. It should be noted that with only the top 60 selected markers, it is possible to achieve a success rate of more than 70%. According to the results, Wright's paired Fst had better performance than other SNP selection methods. The obtained results lead to the creation of exclusive panels to identify various breeds, which have great economic importance.
seyyed ziaodin mirhosseini; Shahla Nematollahian; Seyed Hossein Hosseini Moghaddam; Navid Ghavi-Hossein-Zadeh; Ramin Abdoli; Yosof Kheikhah
Volume 24, Issue 1 , April 2022, , Pages 1-11
Abstract
The aim of the present study was to investigate the performance of the hybrids obtained by crosses of the six Japanese silkworm lines named IRA1, IRA3, IRA5, IRA7, IRA9, and IRA11 and six Chinese silkworm lines named IRA2, IRA4, IRA6, IRA8, IRA10, and IRA12. The new hybrids derived from these lines along ...
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The aim of the present study was to investigate the performance of the hybrids obtained by crosses of the six Japanese silkworm lines named IRA1, IRA3, IRA5, IRA7, IRA9, and IRA11 and six Chinese silkworm lines named IRA2, IRA4, IRA6, IRA8, IRA10, and IRA12. The new hybrids derived from these lines along with available commercial hybrids (as control groups) for six traits including cocoon weight, cocoon shell weight, cocoon shell percentage, best cocoon weight, pupation rate and best cocoon pupation rate were measured and recorded in spring 2020. The IRA7×IRA6 and IRA7×IRA12 hybrids had more performance in comparison with commercial hybrids in terms of productive traits including cocoon weight and cocoon shell weight (p<0.01), but, when productive and viability traits (pupation rate and best cocoon pupation rate) were considered together in an evaluation index, they were not among the selected hybrids. Commercial 31×32 hybrid in terms of cocoon shell weight and cocoon shell percentage had more performance in comparison with the other hybrids (new and commercial) (p<0.01). Hybrids had a significant difference for pupation rate and best cocoon pupation rate (p<0.01), and the IRA5×RA12, IRA1×IRA10 and IRA11×IRA6 hybrids showed the lowest mean for both traits in comparison with other hybrids (p<0.01). The obtained results showed that seven hybrids including IRA9×IRA2, IRA11×IRA2, IRA3×IRA6, IRA3×IRA2, IRA7×IRA4, IRA7×IRA10 and IRA7×IRA8 were greater than the minimum set for every six traits. Among these hybrids, some will be chosen in the commercial production line based on their performance in the field and regional experiments to supply the country's required silkworm eggs.
Abbas Mirzapour-Abibagloo; Nemat Hedayat; Reza Khalkhali-Evrigh; Reza Seyedsharifi
Volume 26, Issue 1 , March 2024, , Pages 1-13
Abstract
Introduction Iranian sheep breeds, due to the climate diversity of country, show high diversity and have acquired high adaptability. Compromise with poor quality feed, tolerance of adverse weather and manageable body size are among the factors that probably caused sheep to adapt to different climates. ...
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Introduction Iranian sheep breeds, due to the climate diversity of country, show high diversity and have acquired high adaptability. Compromise with poor quality feed, tolerance of adverse weather and manageable body size are among the factors that probably caused sheep to adapt to different climates. Heretofore, several studies have been carried out in the field of identification of selection signatures in the different native breeds based on SNP-chip data. However, the use of whole genome data can provide researchers with more information about the differences between breeds and their genetic capacities. Identifying and evaluating the effects of climate on the genome of native breeds of Iranian sheep can be effective in designing breeding and conservation strategies. The aim of the present study was to identify the signs of selection related to Iranian sheep compared to the Romanov breed at the genomic level.Materials and Methods For present study, we used the whole-genome sequencing data related to 43 Iranian and non-Iranian sheep available in the NCBI database. These reads, after performing quality control, were aligned to the sheep reference genome by BWA program. Here, RealignerTargetCreator and IndelRealigner commands available in the GATK program were used to realign around insertions and deletions. Then, the HaplotypeCaller algorithm was used to identify the variants of all samples in ERC GVCF mode. Further, using GenotypeGVCFs module, the variants of all samples were simultaneously identified and finally a VCF file containing raw variants was created. Using the SelectVariants command of the GATK program, all SNPs were separated from other variants. After applying multiple quality filters, high-quality SNPs were extracted and only bi-allelic SNPs present in autosomal chromosomes were used for downstream analysis. Putative selection signatures were identified by using two methods including Fst and XP-EHH. Genes located in positively selected genomic regions were extracted using BEDtools program and the GTF file related to the sheep genome. Gene ontology (GO) analysis was performed on selected genes by "g:Profiler" web-based tool.Results and Discussion Here, Fst and XP-EHH methods were used to identify the signatures of selection related to Iranian sheep in comparison with Romanov sheep. After converting Fst values to ZFst, 958 genomic windows containing 907 protein-coding genes were detected that had scores above the threshold (ZFst > 3.35). GO analysis on 907 genes identified by the ZFst method led to the identification of 157 significant GO terms in the field of biological processes. In addition, 26 significant terms related to molecular functions and 5 significant terms related to cellular components were also identified. The number of genomic windows identified by the XP-EHH method was 953, which contained a total of 311 protein-coding genes. Among identified genes for each method, 29 genes were detected by both methods as signatures of selection for Iranian sheep. From the GO analysis of 29 common genes, no significant term was obtained. However, these genes were involved on traits related to improving milk fat quality (PCCB), fertility (SPATA5, RAB35 and DICER1), muscle growth and development (NF1, AKAP6 and HDAC9), body weight (FBXL3, GRID2 and ADAMTS17), adaptability to harsh desert and mountain condition (BMPR2 and NF1) and also, milk related traits (EXOC6B).Conclusion The results showed that Iranian sheep were probably selected to adapt to dry desert areas and improve the quality of meat and milk. The gradual accumulation of such information in different populations will improve the understanding and knowledge of researchers and breeders and will help them to implement efficient breeding programs.
Javad Mohammad Moradi; Ali Akbar Khadem; Seyed Ahmad Hosseini; Arash Veshkini; Ali Asadi Alamouti; Abdollah Mohammadi-Sangcheshmeh
Volume 16, Issue 2 , October 2015, , Pages 75-83
Abstract
In vitro maturation (IVM) was carried out in the presence of different concentrations (10, 50, 100 or 200 µM) of α-linolenic acid (ALA). Embryonic cleavage, blastocyst formation following parthenogenetic activation (PA) and in vitro fertilization (IVF), and numbers of total and apoptotic ...
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In vitro maturation (IVM) was carried out in the presence of different concentrations (10, 50, 100 or 200 µM) of α-linolenic acid (ALA). Embryonic cleavage, blastocyst formation following parthenogenetic activation (PA) and in vitro fertilization (IVF), and numbers of total and apoptotic cells in blastocyst were then determine for the 50 μM concentration and compared with the control group. Out data revealed that ALA increased maturation (MII) rate as compared with control group (P<0.05) and oocytes in 200 μM ALA group showed a lower MII rate as compared with the control group. When oocytes treated with 50 μM ALA were subsequently used for PA or IVF, a higher (P<0.05) rate of blastocyst formation was observed and these embryos had a higher total cell number and a lower apoptotic cell number (P<0.05) as compared with the control group. In conclusion, our results show that supplementation of maturation medium with 50 μM ALA had a positive effect on meiotic maturation by increasing the MII rate and this in turn, stimulated blastocyst formation and also improved quality of the yielded blastocysts.
Maryam Moghadam Mousaabadi; Homayoun Farhangfar; Moslem Bashtani; AliReza Eghbal
Volume 15, Issue 2 , October 2013, , Pages 79-88
Abstract
The objective of the present research was to apply logistic analysis for investigating some factorsaffecting incidence probability of milk fat depression (MFD) in early lactation of Iranian Holstein cows.The data set was comprised 80381 test day records (milk, fat and protein traits) belonging to 80254 ...
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The objective of the present research was to apply logistic analysis for investigating some factorsaffecting incidence probability of milk fat depression (MFD) in early lactation of Iranian Holstein cows.The data set was comprised 80381 test day records (milk, fat and protein traits) belonging to 80254 firstparity cows in 427 herds with calving year between 1995 and 2009. Based on fat to protein percentagesfor the first month of the lactation and also with respect to threshold point of -0.12, dependent variablewas defined as a dichotomous (zero code for lack of MFD and unit code for MFD) variable. A logisticmixed generalized linear model was fitted on the data using GLIMMIX procedure of SAS software. Inthe model, fixed effects of sperm type (local or exotic), production season, first calving age, cow type(grade or pure Holstein) and random effect of animal’s sire were included. Cow type had no significantaffect on MFD. Estimation of odds ratio for comparing different ages was found to be 1.112 indicatingthat cows calving at lower age of 25 months are expected to show MFD by 11.2 percent smore than thecows calving at the greater ages. The estimate of odds ratio for comparing of spring with summer, autumnand winter seasons were 0.73, 0.722 and 1.182, respectively. The corresponding figures for summer ascompared to autumn and winter seasons were 0.987 and 1.615, respectively, and autumn as compared towinter was found to be 1.636. Daughters of the local bulls are expected to show MFD by 10.8 percentmore than that of the daughters of the foreign bulls.
MohammadTaghi Fayazikia; Mohammad Dadpasand; Hamideh Keshavarzi
Volume 25, Issue 2 , July 2023, , Pages 123-132
Abstract
Introduction Mastitis is one of the most frequent and costly diseases of the dairy cattle industry and causes many economic losses, which negatively affects milk yield and composition, fertility, longevity and welfare of cows. The best solution for reducing the economic and biological consequences is ...
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Introduction Mastitis is one of the most frequent and costly diseases of the dairy cattle industry and causes many economic losses, which negatively affects milk yield and composition, fertility, longevity and welfare of cows. The best solution for reducing the economic and biological consequences is early and accurate prediction of mastitis based on indicator factors. So far, various statistical methods have been used to predict mastitis such as linear and multiple regression, and threshold models. Machine learning is another method that has recently widely been used to predict farm profitability, reproductive traits, longevity and abortion in dairy cow. Machine learning is defined as a set of methods for automatically finding patterns in data and then using those patterns to predict possible future data.Material and Methods In this research, the performance of four machine learning algorithms including random forest, decision tree, Naïve Bayes and logistic regression and two sampling methods, over-sampling and under-sampling, were compared to predict risk of clinical mastitis based on data collected in two Holstein dairy herds in Isfahan province. Final dataset included 393504 records on cows calved during 2007 to 2017 of which 13653 cases (3.47%) were infected and 379851 cases (96.53%) were healthy. Factors related to mastitis, including parity, daily milk production, calving
Mohammad Abdoli; Mohammad Bagher Zandi; Taher harkinezhad; Masoud Kahlili
Volume 23, Issue 2 , July 2021, , Pages 155-163
Abstract
The aim of this study was to investigate the genetic structure of Iranian native horse breeds to compare genetic diversity and understanding the relationships between the populations using 11 ISAG microsatellite markers. For this reason, 565 samples of the Iranian Equestrian database from different ages ...
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The aim of this study was to investigate the genetic structure of Iranian native horse breeds to compare genetic diversity and understanding the relationships between the populations using 11 ISAG microsatellite markers. For this reason, 565 samples of the Iranian Equestrian database from different ages including the Iranian Arab Asil, Caspian, Darehshouri, Kurdish and Turkmen and 113 samples were used for each breed. The number of observed alleles for each locus was 7 to 19 alleles with an average of 10.81 alleles, and it was 19 for ASB17 and 7 for HTG4 locus with the highest and lowest observed alleles ranking respectively. The average observed heterozygosity from the largest to the lowest rank was, Turkmen (0.68±0.11), Caspian (0.67±0.07), Kurdish (0.66±0.06) Darehshouri (0.65±0.07), and Arab Asil (0.62±0.08). Population structure analysis with UPGMA method showed that Caspian and Kurdish populations were grouped as a unit cluster while the other populations grouped as a separate cluster. These results confirmed this hypothesis that the Caspian and Kurdish populations are close to the Nisa horses. In general, the results of this study indicate that the Iranian native horses have got a high genetic diversity, despite of populations have genetic similarity and the other hand genetic clustering of the populations is consistent with their geographic distances. The result of this study shows that the ISAG microsatellite markers are polymorphic and have more efficiency for assignment genetic diversity and genetic structure analysis of Iranian native horse breeds.
Fatemeh Mir; Mohammad Rokouei; Gholamreza Dashab; Hadi Faraji- Arough
Volume 17, Issue 2 , October 2015, , Pages 161-170
Abstract
The aim of this study was to design the base breeding plan in Sistani cattle by using of stochastic simulation. For this purpose, three population size (500, 1000, 2000 heads), three levels of herd number (5, 10, 20), two levels of selection intensity (high and low) and two levels of mating method (random ...
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The aim of this study was to design the base breeding plan in Sistani cattle by using of stochastic simulation. For this purpose, three population size (500, 1000, 2000 heads), three levels of herd number (5, 10, 20), two levels of selection intensity (high and low) and two levels of mating method (random and Minimum co-ancestry) were combined together and in total 36 scenarios were compared for 30 years. Results showed that the effect of all factors on the annual genetic gain for total merit, the annual genetic gain of birth weight (except in mating method and selection intensity) and yearling weight, the annual inbreeding rate (except in herd number), generation interval (except in mating method and selection intensity) and selection accuracy of sire and dames was significant. The annual genetic gain in high selection intensity, population size of 2000 and less number of herd (5 herds) was 8.5, 93.2 and 38 percent higher than low selection intensity, population size of 500 and more number of herd (20 herds). Despite having less total genetic gain (11 percent) in Minimum co-ancestry mating, the annual inbreeding rate in this mating method was 18 percent lower than random mating. The results of this study showed that less number of herd, large population size and high selection intensity considered in breeding plans of Sistani cattle and minimum co-ancestry mating used for control of population inbreeding.
Seyed Nader Albooshoke; Mohammad Reza Bakhtiarizadeh
Volume 21, Issue 2 , July 2019, , Pages 165-180
Abstract
This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume ...
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This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume Hiseq 2000 platform. Hisat2 software was used to align the clean reads to the chicken reference genome and the Stringtie software was used to assemble the transcripts. A total of 1097 lncRNAs were identified as 925 of which were intergenic and 172 were intronic. Also, the number of novel LncRNAs in intergenic and intronic groups were 432 and 128, respectively. Differential gene expression analysis led to the identification of 19 genes and 20 transcripts differentially expressed lncRNAs between two groups. Syntenic analysis showed that differentially expressed lncRNAs are located near by 45 protein encoding genes. Of these, the expression of five gene coding proteins (SCD gene in commercial chickens and GALNT15, KLHDC4, USP7 and ASB1 genes in native chicken) - whose expression was consistent with the expression of their lncRNA - were significantly expressed between two breeds. Functional enrichment analysis of these genes showed that all of them are involved in the skeletal muscle growth. The results of this study showed that the identified lncRNAs probably have the potential to regulate the genes involved in skeletal muscle growth. In this regard, they possibly cause the differences in growth rates between the two chicken breeds.
batol asghari esfedan; Gholam Dashab; mohammadhossein banabazi; mohammad Rokouei
Volume 22, Issue 2 , June 2020, , Pages 187-198
Abstract
The aim of the present study was to investigate the codon usage pattern and their relationship with gene expression for genes with different expression between pure and crossbreed Sistani and Montbeliared breed. In this study, the results of differential gene expression analysis using RNA-Seq technology ...
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The aim of the present study was to investigate the codon usage pattern and their relationship with gene expression for genes with different expression between pure and crossbreed Sistani and Montbeliared breed. In this study, the results of differential gene expression analysis using RNA-Seq technology between pure and crossbreed Sistani and Montbeliared breed (two pure and two its crossbreed) were used. For this purpose, after determining the ORF regions for these genes, CodonW software was used to estimate codon usage pattern indices including CAI, ENC, GC and GC3s. Results showed that there was a significant correlation between total GC and GC3s (0.74). There was also a significant correlation between ENC and GC and GC3s (0.65, 0.77), indicating the role of mutation in codon formation. Based on the results of this study, the factors such as nucleotide composition (GC content), mutation, and gene expression level played important roles in codon formation in the genes studied in this study. This study is the first comparison between pure and crossbreed Sistani and Monti-billiard samples, which helps to better understand the evolutionary mechanisms of codon usage pattern formation and its association with gene expression.
Nader Forough Ameri; Masoud Asadi Foozi; Ali Esmailizadeh Koshkoiyeh
Volume 18, Issue 2 , June 2016, , Pages 201-213
Abstract
This study aimed to identify genes that show signatures of selection for mutations in Iranian native cattle breeds. The data consisted of genotypes for ~777962 SNP markers of 90 animals from eight Iranian native cattle breeds distributing over the country. Therefore, the aim was to identifying divergently ...
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This study aimed to identify genes that show signatures of selection for mutations in Iranian native cattle breeds. The data consisted of genotypes for ~777962 SNP markers of 90 animals from eight Iranian native cattle breeds distributing over the country. Therefore, the aim was to identifying divergently selected regions of the genome. Study of population differentiation across the genome using Weir and Cockerham’s FST test revealed some regions showing evidence of selection. Across the 30 bovine chromosomes (BTA), seven putative selection signatures were detected. These regions were located on chromosomes 1, 2, 7, 8, 12, 13 and X. Finally, study of the reported QTL regions in the orthologous areas of the cattle genome showed that the genomic regions identified in this study overlapped with the reported QTL representing economically important traits such as milk yield, cold tolerance and reproductive traits. Result of this research provided important information on existence of genetic diversity and selection signatures in Iranian native cattle.
Mehdi Noorani; Shaban Rahimi; Abdolhoseein Shahverdi; Mohsen Sharafi
Volume 20, Issue 2 , August 2018, , Pages 203-212
Abstract
The aim of this study was cloning of the beta subunit of human chorionic gonadotropin in an appropriate vector for production of transgenic chicken trrough sperm mediated gene transfer. In this regard, transgenic chicken production tecnology has taken into consideration for having many advantages such ...
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The aim of this study was cloning of the beta subunit of human chorionic gonadotropin in an appropriate vector for production of transgenic chicken trrough sperm mediated gene transfer. In this regard, transgenic chicken production tecnology has taken into consideration for having many advantages such as short generation times, the large number of production of offspring and suitable pattern of protein glycosylation. To date, no study has been conducted on the cloning of the beta subunit of human chorionic gonadotropin for rooster sperm. For this purpose, the hormone beta subunit were amplified by a specific primer pairs, and cloned in T vector. The recombinant plasmid was transformed into Competent E. coli cells and colonies that containing recombinant plasmids were selected by colony PCR.The validity of extracted plasmid were analyzed by enzyme digestion and sequencing. The beta chain of T vector was isolated and was cloned again into pcDNA3.1 + expression vector. The results of enzyme analysis and sequencing indicated that recombinant plasmid pCDNA3.1 +/βhCG were cloned with the correct sequence and completely matched up with human chorionic gonadotropin beta subunit gene that can be concluded that it has sutible stracture for sperm mediated gene transfer.