سید عباس رافت

Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.

Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.

Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.

The results of this research showed that lncRNAs play an important role in theoccurrence of ascites disease and that genetic management can reduce the occurrence of thiscomplication in poultry farms and control economic losses.

The genome-wide association study (GWAS) is a powerful approach to identify genomic regions associated with fertility traits that explain a significant portion of the genetic variance associated with these traits and identify the relevant causal mutations. Evaluating the correlation between each genotyped marker and trait is an essential strategy for GWAS studies that examine the effects of all markers by considering their possible interactions, environmental factors, and even mutual effects between markers. Recently, machine learning methods have been introduced to genomic topics, and the basis of these methods is different from the common methods of genomic evaluation. The machine learning method is used to estimate the genomic breeding values of the candidate animals by considering the training data (genotypic and phenotypic information of the reference population). One of the key advantages of this method is the ability to analyze large data. Machine learning is a branch of artificial intelligence whose goal is to achieve machines that can extract knowledge (learning) from the environment. A variety of machine learning methods (random forest, boosting, and deep learning) are used to model genetic variance and environmental factors, study gene networks, GWAS, study epistasis effects, and genomic evaluation. Random forest is one of the machine learning methods that has been successfully used in various fields of science. This research was conducted to identify markers and genes related to reproductive traits such as calving interval (CI), days open (DO), daughter pregnancy rate (DPR), and age at first calving (AFC) in Iranian Holstein dairy cattle. These traits have already been investigated with the ssGBLUP method and using a smaller sample size. However, in the present research, by using more genotyped animals, a random forest algorithm was used to identify markers and genes related to reproductive traits.
The records used in this research were provided by the National Animal Breeding Center and Promotion of Animal Products of Iran and included AFC, DO, CI, and DPR related to the genotyped bulls' daughters. In this research, the pedigree information of 2774183 animals was used. The genotypic information of the markers related to 2419 Holstein bulls was used. Genomic data quality control was performed using factors such as the number of genotyped SNPs per animal (ACR), the number of genotyped animals per SNP (CR), Hardy-Weinberg equilibrium (HWE), and minor allele Frequency (MAF). When filtering genomic data, the markers whose MAF was less than 5% were removed, and then the samples whose genotyped frequency was less than 90% were identified and removed. Then, the markers whose genotyping rate was less than 95% in the samples were identified and removed. Finally, the SNPs that deviated from the HWE test (P<10-6) were excluded from the analysis as a measure of genotyping error. To control the quality of genomic data, PLINK 1.9 software was used. Then Ranfog software was used in the Linux environment to perform analysis through random forest algorithm.
By using the random forest algorithm, a total of 21 important SNPs were observed, then important fertility trait candidate genes were identified by the gene ontology method, and 62 genes were within 250 Kb of these SNPs. The most significant SNP was observed for AFC. The main SNP for AFC is in ARS-BFGL-NGS-22647 BTA3, for CI is in ARS-BFGL-NGS-114194 (BTA11), for DO is in BTA-74076 -no-rs (BTA5), and for DPR is in ARS-BFGL-NGS-32553 (BTA26). The researchers, who studied fertility traits in Nellore cattle using machine learning methods, identified MPZL1 and CD247 genes on chromosome number 3 and this gene was associated with age at first calving. Many pathways of cell biology affect the performance of reproductive traits. Research has reported the relationship between the CD247 gene and pathways of biology, including cell development and function. Research has shown that the IFFO2 gene plays an important role in the molecular structure of cells, as well as in the mechanism of blastocyst formation, embryos, and the length of gestation in cattle. In a study conducted on the mouse population on the structure of the flagellum and the sperm maturation process, the role of the ALDH4A1 gene in the sperm maturation process was reported. The association of the RPS6KC1 gene with pregnancy rate and antral follicle number in Nellore heifers has been reported. The KAT2B gene is a transcriptional activator that plays an essential role in regulating the correction of histone acetylation and plays an important role in improving carcass quality, muscle and fat development, and metabolism in native Chinese cattle. In addition, they play a key role in regulating biological processes and are related to cell growth, metabolism and immune system function.
  According to the objectives of this research, new information on markers and candidate genes related to reproductive traits in Iranian Holstein dairy cattle was reported. The markers and candidate genes identified in the present research can be used in genomic selection to improve the reproductive traits of Holstein dairy cattle.

Copy number variation (CNV) consist of deletion, insertion, and duplications. It is an important source of genetic variation in organisms and thus influences on the gene expression and phenotypic variation. Copy number variation (CNV) is one of the structural variant with an intermediate size class larger than 50bp which involves unbalanced rearrangements that increase or decrease the amount of DNA (Pirooznia et al 2015, Alkan et al 2011). The size of CNVs is larger than 50bp, while smaller segments are known as insertions or deletions (indels). Thereupon these structural variations comprise more polymorphic than SNPs because of enormity, detection of them and their effect on phenotype has caught the attention of many researchers recently. It has been reported that CNVs changes in gene dosage and regulation as well as in transcript structure, and thus contribute to phenotypic variability (Pirooznia et al 2015, Alkan et al 2011). The pea-comb phenotype is caused by a CNV mapping to intron 1 of the SRY (sex determining region Y)-box 5 (SOX5) gene (Wright et al. 2009). Late feathering in chickens is due to incomplete duplication in PRLR and SPEF2 genes (Elfrink et al. 2008). In swine, dominant white colour has been related with a duplication of a 450-kb fragment of the KIT gene (Giuffra et al. 1999) and a splice mutation causing the skipping of exon 17 (Giuffra et al. 1999). In sheep, doubling in the ASIP gene results in the regulation of pigment in body coat (Norris et al. 2008). Doubling the 4.6 k base pair into the six introns of the STX17 gene results in a gray body color in the horse with age. Deletion of the intergenic region with a length of 11.7 kbp in the goat genome leads to the removal of horns (Clop et al. 2012). Chicken is the most intensively farmed animal on earth and is a major food source with billions of birds used in meat and egg production each year. A big share of chicken CNVs involves protein coding or regulatory sequences. A comprehensive study of chicken CNV can provide valuable information on genetic diversity and assist future analyses of associations between CNV and economically important traits in chickens. Unique chicken genome with macro and micro chromosomes and its biology make it an ideal organism for studies in development and evolution, as well as applications in agriculture and medicine (Burt 2005). In the last several years, There has been an increasing interest in the study of CNVs in the chicken. This study focuses on comparison of CNV between the broilers and layers chicken to find evidence of domestication on the genome using whole genome sequencing.

we used n=90 female birds of two commercial broiler (n=40) and layer (n=50) chicken. The broilers (BRs) were represented by 20 DNA samples of each of two lines (BRA and BRB) established independently and previously collected as part of the AVIANDIV project. In the layer group (LRs), data from 25 birds each from purebred white (WL) and brown (BL) egg laying populations, sequenced in the frame of the SYNBREED project (http://www.synbreed.tum.de/index.php?id=2 ,(were included. The paired-end reads with a read length of 101bp were mapped against the current reference genome assembly Galgal6 using the Burrows-Wheeler aligner (bwa, 0.6.2-r126 Version, with default parameters. Duplicate reads were masked during post-processing using the Picard tool set (version 2.9.2, http://picard.sourceforge.net). Finally, Genome Analysis Toolkit-3.3.0 was used to realign reads for correcting errors caused by InDels. Using GATK software package and Depth Of Coverage function (McKenna et al 2010), the depth of readings was calculated for each sample. Then filter out reads with mapping quality below 20. Because comparing the genomes of individuals in different groups was time consuming and computationally difficult for all parts of the genome, the genomes of each individual were divided into 1000 bp non-overlapping windows and the average reading depth per window was calculated. Then the results were normalized against the BL sample that showed highest average depth. In short, we created a correction factor per population and applied it on the depth of coverage value for each window. For all the contrasts, we performed an analysis of variance (ANOVA) as described (Carneiro et al 2014). For the Broilers-Layers contrast we scanned 935247 windows. 70372 windows showed significant by FDR with P < 0.001, with ANOVA using the Benjamini-Hochberg FDR method for multiple corrections (Benjamini and Hochberg 1995).

Mapping sequencing data to galGal6 assembly showed an average 98.61% mapping rate and 11.51 depth. Manhattan plot was plotted for regions of the genome that differed significantly between the two groups (FDR = 0.001). The points above the hypothetical line were identified and examined in a 25 Kbp confidence interval to identify possible genes. 39 regions were identified that half of them dose not contain any genes. Although Long noncoding RNAs are under lower selective pressure than protein-coding genes (Batista and Chang 2013), The other 11 regions contained 16 genes related to long non-coding RNAs. Long noncoding RNAs (lncRNAs) play a critical role in organizing the 3-dimensional genome architecture and regulating gene activity in cis or in trans through multiple mechanisms (Zhang et al 2019, Batista and Chang 2013). 6 othere regions also contained 12 coding genes. Most of the identified genes were somehow linked to the immune system disease or cancer. Genes such as DEDs and TNFAIP8 are involved in programmed cell death (apoptosis) and two genes NPAL3 and RCAN, which are involved in the immune system, had a copy number variation in the studied samples. In addition RCAN is involved in Down syndrome. The PFDN gene, located on chromosome 25, is also involved in Alzheimer's and Parkinson's disease.

The presence of parasites in the digestive system causes various lesions that vary in severity depending on the type and number of parasites. These disorders include diarrhea, anorexia, weakness, weight loss, decrease in animal production, decrease in absorption of food, and in acute and super acute forms cause death. Considering the importance of the infection of sheep with various gastrointestinal parasites, the purpose of this research was to investigate the effect of raw garlic on the intestinal parasites of sheep.

This experiment was conducted for 2 months from the first of November to the end of December. For this project, 40 sheep with an average weight of 58.5 kg (Averaged) were used. Animals were divided into the control group, the positive control group (drug recipient), the group receiving 10 grams of garlic (per head), and the group receiving 20 grams of garlic (per head). For this research, in addition to counting the number of parasite eggs by flotation method, the Famacha test and hematocrit test were performed and for data analysis, CRD completely random design was used.

The results showed that the Famacha test of sheep receiving garlic decreased (P<0.05) However, the results of the hematocrit test of sheep were not significantly different from the control (P>0.05). Also, the addition of garlic to the diet of adult sheep decreased the number of Strongell, Marshalalgia, Nematodirus, Trichius, and the total number of parasite eggs per gram of feces (EPG), which was significant (P<0.05). In general, it can be said that adding 20 grams of garlic to the diet reduced the number of parasite eggs.

The results of the present research show that the amount of consumption of English eggs in sheep that are used with anti-parasitic drugs is very high. For this purpose, anti-parasitic drugs or medicinal plants that have anti-parasitic effects should be used. As found in this research, the use of high levels of raw garlic in the diet reduces digestive parasites and also increases blood mass.

The longevity of cows is crucial to the profitability of a dairy farm, and the culling of cows as a result of major health disorders is a significant risk that threatens production systems today. The possibility of taking diseases into account in the selection of dairy cows depends on the economic importance of the diseases. Mastitis and metritis are common diseases among dairy cows that are considered as risk factors for culling cows. The onset of these disorders can be attributed to factors such as environmental and managerial factors, but there is also evidence of a genetic component to each. Many genes are associated with resistance or susceptibility to mastitis and metritis in cattle, and their alleles have been reported. Subclinical mastitis seems to be one of the most important and damaging diseases threatening dairy cattle herds along with reproductive diseases, lameness and possibly some other common diseases such as Para-tuberculosis. Obviously, reducing production costs supports the profitability of dairy farms. By studying the relationship between the incidence rate and health disorders, in order to minimize the deaths due to health disorders, more emphasis has been placed on the health management of cows. The direct and adverse effects of mammary gland disorders (mastitis and nipple injury) on culling are well documented, while there are differences of results on the correlation between reproductive disorders and culling. Contradictory results may be due to differences in the purpose of the study, population, or the methods used. Many factors such as age, breed, production level, and calving season can play a role in the incidence of diseases.

The purpose of this study is to report the prevalence of clinical mastitis and metritis, moreover to investigate environmental and genetic factors affecting these diseases, to estimate the heritability of disease traits and to measure the correlation between disease and production traits in a Holstein cattle herd. Due to the fact that health records are not recorded in the country's farms in a regular and uniform manner, conducting this research is an experiment to collect this type of information so that in the future models can be provided for all Holstein cows in Iran to consider disease relating traits.

Data of 5052 milk yield from 1796 Holstein-Frisian cows has been gathered that had parturition from 2005 to 2009. In this study, using the 305-day milk production variables, parity, year of calving, the frequency of occurrence of clinical mastitis and metritis in cattle diseases using SAS software, using logistic procedure is estimated. The cows have been studied for all the diseases that occurred in all milking period. In logistic regression analysis, the effect of 305 days of milk and other factors in the occurrence of the disorder was investigated as a binary model. The effect of the lactation period in which the disorder was created was included in all analyzes and the fixed effects included milk for 305 days, calving period, calving year and calving season.Log [p. (1-p)] = b0 + b1 * milk305 + b2 * parity + b3 * calveyear + b4 * calve seasonA coefficient of b1 is assigned for the risk factor of milk production, a coefficient of b2 is assigned for the parturition, a coefficient of b3 is assigned for the factor of calving year and a coefficient of b4 is assigned for the factor of calving season. b0 is the logistic regression estimate if there is no predictor other than the response variable in the model. For each estimate of regression coefficients, the probability level, standard error and 95% confidence interval are also calculated. For a particular disease b1, b2, b3 and b4 are regression coefficients. Estimated genetic parameter in this research was heritability of diseases traits that has been done with ASReml software.

Metritis incidence rate is lower than mastitis. The percentage of animals with mastitis and metritis in the herd was 3.11% and 1.67%, respectively. The average calving interval for metritis incidence was 167.3 days and 129.5 days for mastitis. Data analysis of correspondence of metritis and 305 milk yield, parity, the year and the season of calving showed none of the risk factors had relation with the occurrence of clinical mastitis. The heritability of clinical mastitis and metritis were estimated to be 0.27 and 0.23, respectively. We could not find a relationship between milk production and metritis. Can we consider the increase in milk production as a risk factor for disease occurrence? It is very difficult to prove and explain this relationship and there are many contradictions between the results of other studies. From the lack of a proven correlation between milk production and the occurrence of diseases, it can be concluded that if proper management and nutrition provided based on the biological needs of high-yielding cows, then cows with high milk production will not necessarily suffer from diseases in comparison with low-yielding cows.Genetic studies have shown a positive correlation between mastitis and milk production. Erb (1987) and Dehu and Martin (1984) concluded that high milk production could not be a risk factor for mastitis. A study of Ayrshire cows in Finland found that cows with higher milk production during the previous lactation period were at increased risk for mastitis (Grun et al. 1989 and Grun et al. 1990). There are few documented findings on the association between milk production and the incidence of disease. Of course, it should be borne in mind that "milk production" is not the only risk factor for the disease. Concerning diseases in Holstein dairy cattle it seems the occurrence of the disease can also be the result of breeding and nutrition conditions and management. However, identifying all relevant factors and determining their quality and relative importance is difficulty accessible. It is also not easy to estimate all possible interactions between production and disease traits, even with the efficiency of today's computer technology.

In dairy cattle genetic improvement programs, we suggest to record and estimate the breeding values for disease traits and consider them in multi-trait selections among elite sires. The estimated heritability of metritis was lower than clinical mastitis. Keywords: Holstein-Friesian cows, clinical mastitis, metritis, milk 305 days, heritability.

Subclinical ketosis is one of the most important metabolic diseases which irreversible economic effects on the dairy industry. Subclinical ketosis has been associated with increases reactive oxygen species and oxidative stress in cells. Since the nuclear factor kappa-B is known as a fast cellular response factor to endogenous stress; this study was conducted to evaluate relative gene expression and some blood metabolites in dairy cattle during the transition period were performed. Blood samples (5 mL) were obtained from the tail vein of 100 cows with fourth and fifth lactation one week pre-parturition and one week post-parturition. In the present study, It was found positive correlations between plasma NEFA concentrations in the pre-parturition period and BHBA, GGT, MDA, and NF-κB and negative correlations between plasma NEFA concentration and HDL. As well as, the positive correlations between BHBA plasma concentration and NEFA , ALP, GGT, MDA and NF-κB and negative correlations between plasma BHBA concentration and HDL in the post-parturition period. Also while the cut-off point BHBA≤1.2(Health) and BHBA≥ 1.2(mmol/l)(subclinical ketosis or disease) in the post-parturition period was designated, it was observed that NEFA(p<.0001), BHBA(p<.0001), MDA(p<.0001), GGT(p<.0001) and ALP(p=0.03) were gradually increased, and HDL(p= <.0001) gradually decreased in disease group. The results showed that the activity of NF-κB (p<.0001) was gradually increased in the disease group. Also results showed that increased NEFAs and BHBA increased inflammation response through activating the NF-κB pathway and oxidative stress.

Bacterial infections of the uterus are known to be an important cause of infertility in the mare. The objective of this study was to determine the species of bacteria isolated from the uterus of infertile Arabic mares, and investigate how identified bacteria are related to parity. A total of 18 Arabic mares with a history of long-term infertility were evaluated. The age range of mares was 4-23 years. For statistical analysis, logistic regression and Chi-square test were used by Proc Logistic of SAS. In this study, low-volume uterine flush and culture techniques were used. P. aeruginosa was the most prevalent bacterium isolated from 26.32% of mares as pure or in conjunction with E. coli, K. pneumoniae, or Citrobacter spp. Furthermore, 23.68% of bacterial infertility cases were related to E. coli. Pure growth of E. coli was observed only in one case. However, mixed growth with P. aeruginosa, S.zooepidemicus, and S. aureus was very prevalent. The present study revealed that the most prevalent bacteria isolated from chronic endometritis in Arabic mares were gram-negative bacteria (p < 0.05), while in some cases may be accompanied by gram-positive bacteria. C. albicans was isolated in only 8% of mares with chronic endometritis. Moreover, older age and higher parity number of the mares were not related to the presence of intrauterine fluid or the species of bacteria (p > 0.05). It can be concluded that the most prevalent bacteria isolated from infertile Arabic mares with chronic endometritis are gram-negative bacteria.

Cellulose is the most abundant linear homopolysaccharide in nature, which has always raised great attention from investigators and industrial investors for use in wood and paper pulp industries, biofuel, and nanocellulose products due to its semi-crystalline nature and unique physicochemical properties. However, the cell wall recalcitrance and high cellulose crystallinity of wood biomass are the most challenging issues during cellulose extraction and its saccharification in bioethanol and nanocellulose production industries. Here, we have investigated the effect of CRISPR/Cas9-mediated mutagenesis on the Pro435 and Try436 residues at the binding site of PalCESA4-specific P-CR domain from white poplar. As the result, we generated a PalCESA4P435del_W436del homozygous T0 mutant plant with normal growth that showed a significant decrease in cell wall area (21.89%), cell wall thickness (7.5%), cellulose content (~ 44%), and cellulose crystallinity (19.5%) compared to the WT plant. Our findings reveal a promising approach to achieving genetically edited woods with suitable physicochemical properties of cellulose microfibrils in different plant species for industrial applications.IntroductionCellulose is the most abundant linear homopolymer in wood biomass of woody plants. Due to its semi-crystalline nature, it uses in various industrial applications, including wood and paper, textile, pharmaceutical and medicinal, agriculture, biofuel, and bio-nanomaterials (Littlewood et al., 2014; Trache et al., 2020). Despite its wide applications, high cellulose crystalization is the most important challenge in the production processes of bioethanol and nanocellulose from wood biomass (Vermerris and Abril, 2015). As the previous reports associated with the cellulose biosynthesis pathway in Arabidopsis and poplar, the CrI and DP of cellulose, the number of microfibrils in the cell wall architecture is highly influenced by the arrangement of cellulose synthase A (CESA) subunits during the formation of the cellulose synthase complex (CSC) (Luan et al., 2011; Scanlon and Timmermans, 2013; Speicher et al., 2018). In our previous study, we identified the strong binding site containing four amino acids Pro435, Trp436, Pro437, and Gly438 in the P-CR domain of poplar CESA4 subunit, which is involved in the CESA4 and CESA8 heterodimerization. The CRISPR/Cas9-mediated mutagenesis in Trp436 and Pro437 residues could alter plant growth and photosynthesis rates, a cell wall thickness of xylem and phloem cells, lignocellulose content, CrI, and DP of cellulose fibers in poplar (Nayeri et al., 2022). Materials and Methods The CESA4-specific sgRNA (5′-CAGGATGGTACCCCCATGGCCTGG-3′) was designed using CRISPRdirect, CHOPCHOP, and CRISPOR-Tefor tools. The genome sequence data of P. trichocarpa v 4.1 was used to determine the sgRNA on-target and off-target sites. The molecular cloning of the recombinant CRISPR/Cas9 expression vector (Figure 1) was performed according to the method described by Nayeri et al., 2022. The pulvini tTCL explants from the petioles of 4th nodes close to apical buds of P. alba L. were transformed using competent bacterial cells of Agrobacterium tumefaciens strain LBA4404 as described by Nayeri et al., 2022. The T0 plants were screened and validated using PCR analysis of bar and pcoCas9 genes. The bacterial contaminations of to plants were examined using PCR analysis of the Vir G gene. The screening of T0 mutants and identification of mutation types in the PalCESA4-sgRNA target site gene were performed using heteroduplex PCR genotyping methods (Guo et al., 2018), amplification of PCR fragments using mutation site-specific primers (MSBSP-PCR) (Bhattacharya and Van Meir, 2019) and sanger sequencing analysis. The sequence data of primer sets were presented in Table 1. The wood anatomy of the T0 mutant was investigated using light microscopy (LM) and field emission scanning electron microscopy (FE-SEM) analysis. The contents of lignocellulosic components were determined according to the TAPPI international standard guidelines. The cellulose crystallinity index (CrI) and its degree of polymerization (DPN, DPW, PDI) were determined using XRD analysis patterns and gel permeation chromatography (GPC), respectively. The statistical analysis was performed using one-way ANOVA analysis of variance and mean comparison based on LSD posthoc's minimum significant difference using SPSS IBM v. 22.0 (SPSS Inc, Chicago, USA). The maximum significance level was set at 5% (p-value ≤0.05). Results and discussionAs shown in the PCR analysis results, 14 out of 15 regenerated T0 plantlets had DNA bands of PCR products belonging to bar and pcoCas9 genes. Furthermore, 11 out of 14 T0 plants showed a lack of DNA bands from the PCR2 products (196 bp), which indicates homozygous or biallelic mutations in T0 mutants. In the rest of the T0 plants, no mutation or heterozygous mutations were observed due to the sharp DNA bands from the PCR2 products. The heteroduplex genotyping results showed the double DNA band of CESA-PCR3 fragments (160 bp) in 5% agarose gel, indicating heterozygous mutation in the T0 mutant poplar. However, the DNA hybridization in potent biallelic/homozygous T0 mutants indicates homozygous mutation in all 11 T0 mutants. Among the T0 mutants, we identified a homozygous T0 mutant plant (L7) with double deletion mutations in P435 and W436 residues (Figure 3E). As the wood anatomy analysis results, the Vd value of the homozygous palCESA4P435del_W436del (L7) T0 plant showed a significant decrease of 74.85% compared with the WT. The cell wall area (21.89%), cell wall thickness (7.5%), cellulose content (approximately 44%), and CrI of cellulose (19.5%) significantly decreased. According to the previous reports, the knockdown or knockout of PtriCESA4, PtriCESA7a/b, and PtriCESA8a/b genes cause a remarkable decrease in the thickness of the cell wall and cellulose content (~90%), resulting in the production of unhealthy and abnormal mutants (Abbas et al., 2020; Xu et al., 2021). Our previous findings reveal that substitution and deletion of Trp436 and Pro437 residues in the binding site of CESA4-specific P-CR domain led to a 13-25% decrease in the cellulose CrI from wood biomass of T0 poplar mutant (Nayeri et al., 2022).   ConclusionThese findings can be used in the production of gene-edited plants using the CRISPR/Cas9 system with desirable traits such as low cellulose crystalization, leading to saving in costs and time in the pure cellulose extraction process and preparation of cellulose-based biomaterials. Therefore, this isa promising technology for the mass production of cellulose-based products, which increases export volume and develop new and environmental-friendly technologies in the country. AcknowledgementThis article was extracted from the final report of the research project under contract number 346/27/D, which was applied to the research grant of the University of Tabriz, Tabriz, Iran. Our special thanks to Iranian Research Institute for Information Science and Technology (IranDoc) for technical and financial suports of our genetic engineering lab, the center of graduate education, faculty of agriculture, university of Tabriz, Tabriz-51666, Iran IR.

In this study, body weight records of 19171 American Simmental beef cattle including 8758 bull and 10413 cows from 2000 to 2016 were used to estimate genetic parameters and trend. We conducted genetic evaluation of data from 5199, 10926, 7362 and 5636 genotyped beef cattle of gene-based single nucleotide polymorphisms (SNPs) for birth weight (BW), weaning weight direct (WWD), yearling weight (YW) and post-weaning weight gain (PWG), respectively. Genetic parameters estimated using univariate and bivariate animal models and BLUPf90 software. Heritabilities were estimated for BW, WW, YW and PWG 0.38 ± 0.02, 0.24 ± 0.01, 0.35 ± 0.01 and 0.22 ± 0.02 using univariate analysis, respectively. Genetic correlation between BW and PWG was 0.31. The highest and the lowest genomic accuracy were estimated for WWD (0.68) and PWG (0.27), respectively. Genetic trends were estimated for BW, WW, YW and PWG 0.13, 0.28, 3.43 and 0.05, respectively. In addition, slight changes were observed in the genetic trend of all traits, especially weaning weight direct and yearling weight across years of study which indicates the existence of specific selection goals and criteria in each of these traits. In general, three large-effect closely linked QTLs identified on BTA6 at 37 Mb, on BTA7 at 90 Mb and on BTA14 at 22 Mb. Because correlations were favorable between body weight traits, breeding program should be based on the simultaneous selection of these traits through the selection index.

The object of this study was to identify the novel nucleotide polymorphisms in the second exon of MHC-DRB1 gene that has association with genetic resistance to gastrointestinal nematodes in Iranian indigenous Ghezel sheep breed. In this investigation 100 indigenous Ghezel sheep breed male lambs in 4 to 6 months age were used that were randomly chosen from five different flocks in all over the East Azerbaijan province, In these lambs, the preliminarily nucleotide polymorphisms were identified using the PCR-RFLP technique and the relationship between these polymorphisms and fecal egg counts were investigated and also in present study four samples of PCR product randomly selected from each five flock's lambs (one sample from each flock) and were sequenced subsequently. The nucleotide sequencing results of the PCR products were aligned with other registered nucleotide sequence in NCBI (National Center for Biotechnology Information) gene bank for second exon of Ovar-DRB1 gene in various sheep breeds of world. In the results of alignments, nine novel polymorphisms (two deletions, five substitutions and two insertions) were identified in the second exon of MHC-DRB1 gene sequences of Ghezel sheep breeds. Existence of these nucleotide polymorphisms were caused to substitution of all the amino acid sequence and consequently lead to changes in the structure of foreign peptide binding cleft in the DR heterodimeric proteins in the membrane of antigen presenting cells. Existence of novel polymorphisms in the second exon of Ovar MHC-DRB1 gene has led to changes in protein structure and increased the validity of observed association between identified polymorphism and studied trait.

The aim of the present study was to estimate the molecular characteristics, structure, genetic diversity and genetic bottlenecks in the three sheep populations native to Iraq (Awassi, Naaimi, and Arabi). For this purpose, 12 microsatellite loci with chromosomal distribution distributions (1, 2, 5, 9 and 14) were used according to the recommendations of FAO and the International Society for Animal Genetics (ISAG). Sixty samples of whole animal blood (both sex) were randomly collected from the relevant populations in Karbala, Najaf and Babel provinces. The genomic DNA extraction, quality and quantity, preparation of PCR, electrophoresis photography was done accordingly based on standard available methods. After observation of raw genotype per investigated loci, allele binning was done for minimizing genotyping errors. More than 9 types of molecular statistical indices (allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Wright coefficient, Shannon index, F-statistical indices, genetic distance and the bottleneck) Checked out. The results were presented in two parts: evaluation of microsatellite loci utility and evaluation of genetic diversity within and between the population. The results of the first part showed that the highest polymorphism was observed in OarFCB226 and TGLA13 markers and the rest had the lowest polymorphism. The results of the second part showed that the Awaasi and Arabi breed have the highest and lowest diversity, respectively. The highest genetic distance was between Arabi and Naaimi breeds and the smallest was between Naaimi and Awassi breeds. Furthermore, bottleneck L-Shape curve showed that the studied populations are in a genetic predicament.

One of the disadvantages of estimating genetic parameters based on the absolute weight of sheep at a given age is that some genes affect growth only in a specific period of animal life. There are also pleiotropic effects between weight cross-sectional traits of different ages. Therefore, that selection for one trait causes a correlated response in other traits. So focusing on all the stages of the growth curve and the components that characterize the curve can produce more genetic progress. Research results show that growth curve variables are heritable in different species. Therefore, it is possible to modify the growth curve through selection. Understanding the genetic and environmental relationships between different weights, maturity and growth rates at all stages of development is essential for designing a breeding program to improve production efficiency over the lifetime of the animal. Therefore, identifying and locating QTLs controlling growth curve parameters as heritable traits could be a useful research scenario for investigation. Ultimately, it will increase meat production.

Growth curve parameters were estimated using the Brody model and data of 27537 Ghezel sheep. These population pedigree checked by software pedigree viewer and the two families were selected for this project To do present research two half-sib family, 51 offspring of two genera of sheep breeding in the Ghezel Miandoab Breeding station of were taken. The chromosomal positions were located on 2 and 5 of the microsatellite were used to determine the genotype. The marker spacing on the chromosomal map was under 30CM. The DNA extraction was performed using Sammady Shams and colleagues from the whole blood and 4% metaphor agarose gel was used for multiplication of microsatellite sites using Touchdown PCR and. UVDOC software was used to score bands. Descriptive statistics were calculated for molecular indices of each markers locus using POPGENE software. Upon completion of genotyping three files map, genotype and records phenotype were prepared and then evaluated normality raw data and correction for fixed effects (gender, type of birth,) by the procedure GLM in SAS 9.2 software made in 2015 was carried out. The analysis results microsatellites showed that polymorphism fit there, but alleles heterozygous rams similarity high, suggesting consanguinity with alleles of the sheep show. The method used to The QTL analysis was identified the relationship between genetic markers and QTLs by two markers.

The results of microsatellite analysis showed that there is a good polymorphism in the studied population. Finally, the results of the two families indicated no significant QTL identification on chromosomes 2 and 5 for traits of brody growth curves parameters (A, B, C).

No significant differences were found in the QTL analysis. Of course, the plan was criticized because of the low number of markers, the number of families and each family member. These factors may, in turn, be the reason for the lack of QTL identification in this design.

Fertility is considered an important economic trait in cattle, yet despite its importance, reproductive efficiency of dairy cattle has decreased dramatically in the past decades and is of increasing concern to farmers and the dairy industry (Ghiasi et al. 2011; Pryce et al. 2010). The decline in the reproductive efficiency of dairy cattle has become a challenging problem worldwide. Genetic response for fertility traits is expected to be small due to low heritabilities as shown in many studies. In the past decades, more attention has been placed on milk production in selection programs worldwide, which has caused a decline in female fertility due to the antagonistic genetic relationship between milk production and fertility (Pryce et al. 2010; Toghiani 2012). Therefore, it is necessary to include fertility traits in the breeding programs for improving fertility or stopping its downward genetic trend (Penagaricano et al. 2012). It is well documented that bull fertility is influenced by genetic factors. Semen production traits, such as volume and sperm concentration, were found to have moderate heritabilities (from 0.15 to 0.30), whereas some of the semen quality traits, such as motility and percentage of abnormal sperm, had moderate to high heritabilities (close to 0.60) (Rezende et al. 2018). The objective of this study was to assess genetic parameters for fertility traits in Holstein dairy cows and sire conception rate (SCR) a new phenotypic evaluation of bull fertility.

In this study information's related to heifers and cows 1 to 3 parity, 1992 to 2018, by the National Animal Breeding center and promotion of Animal Products of Iran and sire conception rate (SCR) 2008 to 2018, a phenotypic evaluation of bull fertility, has been provided to dairy producers the Council of Dairy Cattle Breeding (CDCB) were used. Traits included: sire conception rate (SCR), age at first service (AFS), age at first calving (AFC), days open (DO), calving interval (CI), gestation length (GL), Pregnancy rate (PR), Interval between first and last insemination (IFL), Days from calving to first service (DFS) and number of services per conception (NS). Edited data included the following: SCR between 7.6 % to -16 %, AFS between 320 and 900 days, AFC between 630 to 1350 days, CI between 300 and 700 days, IFL less than 290, GL between 260 and 290 days, DFS between 20 and 300 days, DO between 40 and 350 days, PR between -28 and 55 and NS between 1 and 10. Select the model equations and fixed effects were optimized using GLM procedure in SAS package. Subsequently, the multi-variate animal model analyses was carried out in order to estimate of direct additive genetic and phenotypic correlations between fertility traits. Estimation of genetic parameters using animal model in REML methodology was done by REMLF90 program.

Heritability estimates for all fertility traits were low, minimum heritability were estimated for IFL trait by heifers (0.002) and maximum amount for SCR trait (0.303). Heritability were estimated for other fertility traits 0.033, 0.005, 0.052, 0.048, 0.085, 0.108, 0.095, 0.059, 0.031, 0.025, 0.023, 0.017, 0.018, 0.013, 0.009, 0.013, 0.032, 0.028 and 0.018 for AFS, AFC, CI, OD, PR, GL_H, GL, DFS_1, DFS_2, DFS_3, IFL_1, IFL_2, IFL_3, IFL_123, NS_H, NS_1, NS_2 and NS_3, respectively. These estimates are in agreement with the results obtained by Ghiasi et al. (2011) and Rahbar et al. (2016) in Holstein cows. Heritability estimates obtained in this study were larger than the ones obtained by Toghiani Pozveh et al. (2009) for CI, DFS and DO in the previous study of Iranian Holsteins. The heritability estimates obtained for interval traits (DO, CI, and GL) were higher than those obtained for categorical (NS) or binary traits. However interval traits may be affected by management decisions such as the length of the voluntary waiting period or estrus synchronization applied in some farms (Ghiasi et al. 2011). In general, negative and moderate additive genetic and phenotypic correlations estimates were obtained between fertility traits. Estimated additive genetic correlations in the range of -0.56 (between GL and AFC) and 0.83 (between IFL and NS). However, estimated phenotypic correlations in the range of -0.80 (between PR and OD) and 0.85 (between GL and OD). The first one is formed by the traits that measure overall fertility of the cow (i.e. CI, OD and PR) which can be obtained directly from calving dates. In particular, OD and PR showed additive genetic (-0.39) and phenotypic (-0.80) correlation estimates which indicates that these two traits are genetically the same as expected because PR is a linear function of OD. The same results were found by VanRaden et al. (2004) and Ghiasi et al. (2011) in Holstein cattle. The mean breeding values were estimated -0.31 to 0.38, -4.14 to -3.34, -6.70 to -5.64, -0.0435 to -0.0064, -2.20 to -1.93, 9.16 to 10.73, 8.72 to 10.15, 3.29 to 4.21 and 4.34 to 5.84 for SCR, AFC, AFS, GL, PR, CI, OD, IFL DFS, respectively. However, the mean phenotypic values was positive, except SCR (range -0.62 to 0.66). These results were in agreement with reported Aghajari et al. (2015); Ansari-Lari et al. (2009) and Shirmoradi et al. (2010). Were estimated negative genetic trend for SCR (-2.22), AFS (-4.02 %), AFC (-2.66 %), GL (-0.07) and PR (-0.83) traits. Subsequently, for CI, DO, IFL and DFS traits, positive phenotypic trends were obtained. These estimated genetic and phenotypic trend agreed with other reports (Faraji-Arough et al. 2011; Rahbar et al. 2016).

Genetic parameters (heritabilities and genetic correlations) have been estimated for fertility traits in heifers and cows and fertility bulls. The results of this study indicated that breeding programs have paid little attention to reproductive traits in Iranian Holstein cows, and therefore it is recommended to pay more attention to these traits in order to improve the performance of Holstein cows. According to the results suggest that the genetic prediction of dairy bull fertility is feasible. This could have a positive effect on the dairy industry, for example, the early culling of bull calves with very low SCR predictions.

The main goal of proper scientific management is to achieve maximum profitability and productivity. It is necessary to identify the role of management factors on the performance of livestock units. Therefore, the present study aimed to identify the role of social, environmental, genetic factors in goat breeding through analysis of questionnaire data and phenotypic traits. At first, the number of breeders and participants in the "World Goat Day Conference" of the Institute of Animal Science Research of Iran was obtained and the questionnaire was filled up through interview on virtual channels and through face-to-face interviews with 82 active growers from different provinces. In the second step, all row data collected from farmers from including technical and breeding information management statue, pest contamination medicinal usage, Nutrition and formulation of data (forage and concentration), marketing place, number of kids and input and equipment and the main problems of breeding has been instigated, then a statistical index of all collected records was analyzed in all groups. Result of present study show number of kidding and mortality is two important factor in this specific raising, kidding number also effect result of survivability in goat raising due to Nutritional condition of does in third step analysis of data collected from two Research station of South Khorasan and Sagez analyzed using cfc, SAS and Result of study shows sex of kid, year of birth and interaction between year and type of birth show significant effect of different live weight in different stage of life(p < 0.05) in both station. The use of livestock experts in livestock farms can provide university educators with livestock breeders, which brings about a bridge between science and the introduction of theory into a practical step to maximize livestock production potential.

Ghezel is an Iranian medium-sized and fat-tailed sheep breed and is native in the East and West Azarbaijan provinces. Ghezel sheep plays an important role in supplying meat and milk in the region of Azerbaijan (Ghasemi-Panahi et al. 2016). Also, an important source of farmer's income is lambs production (Nabavi et al. 2015). Therefore, one of the prospects for improving the region's production is improving reproductive performance of sheep flocks. In order to suggest a proper approach to improve reproductive performance, there should be a comprehensive information from the livestock farms of these two provinces. Therefore, the present study was conducted with the aim of evaluating reproductive performance of Ghezel ewes in a couple of sheep farms in the East and West Azarbaijan provinces.

After designing questionnaire in this study, 30 Ghezel sheep flocks were randomly selected from different regions of East and West Azarbaijan provinces (15 flocks in each province). Then, livestock farmers of the region were interviewed using questionnaire and information on reproductive performance of flocks were collected including: pregnancy rate, multiparty, lambs' birth weight, age at the first parturition, weaning age, lambs weaning weight, number of unfertile and fertile ewes, flock surface area, farmers' education, and etc. The flocks were divided into four flock sizes. The breeding systems were also studied based on the three groups of nomadic, rural, and industrial breeding systems. The results of the questionnaires were reported as percentages (for classified data) and mean ± SD (for other data). Also, correlation coefficients between important traits were calculated using Spearman’s rank-order correlation of SAS 9.2 (2008) software.

Based on the results of this experiment, 87% of the breeding systems of two provinces were rural. Other reproductive indexes of two provinces included 65% lambing rate, 79% pregnancy rate, 24% ewes' fecundity rate, 20% estrus synchronization usage, 5% flock mortality rate, 9% ewe's infertility rate, 0.1 ram to ewe ratio, and 17 months of age for ewes at the first mating. Seifi et al. (2014), with evaluating Ghezel and Afshari sheep breeds, reported low reproductive performance in these two breeds. Khodayi-Motlagh et al. (2014) reported low knowledge of farmers about the methods of estrus synchronization. However, a number of studies reported an extraordinary improvement in the reproductive performance of Ghezel ewes using different methods of estrus synchronization or using flushing rations (Najafi et al. 2014; Ghasemi-Panahi et al. 2016; Hasani Dash Tapeh et al. 2017; Ahmadzadeh et al. 2018). Therefore, it seems that improving knowledge and skill of farmers about estrus synchronization methods and/or proper rationing can improve reproductive performance of Ghezel sheep in the region. According to the correlation results, there was a negative correlation between the breeding system and the flock size (correlation coefficient: -0.6) and between the flock size and estrus synchronization usage (correlation coefficient: -0.51), (P<0.05). These results indicated that the breeding system has been changed into the nomadic system in the larger breeding flocks and there is a less interest in the use of new methods of estrus synchronization in this kind of breeding system. Also, results indicated a significantly negative correlation (correlation coefficient: -0.42) between ram to ewe ratio and lambing rate (P <0.05). So, regardless of the role of rams on flock fertility, asymmetrical increase in ram to ewe ratio causes a negative impact on lambing rate by reducing the ewe population (which are the animals whom produce lambs). The results showed a significant positive correlation (P <0.05) between lambing rate and the age of ewes at the first mating (correlation coefficient: 0.54) and also the age of ewes at the first delivery (correlation coefficient: 0.66). These positive correlations indicate poor rearing condition of young ewes and are consistent with the general believe of farmers, which they breed ewes at the second year (age 16-18 months) to obtain optimum fertility rate. Results showed a negative correlation between the age of ewes at the first mating and birth weight of lamb (correlation coefficient: -0.60), while indicating a positive correlation between the age of ewes at the first mating and age of weaned lambs (correlation coefficient was 0.49), (P <0.05). These results can be explained by higher fecundity rate in older ewes, which reduces lamb birth weight, while it increases weaning age of lambs. The negative correlation (correlation coefficient: -0.41) between weaning age of lambs and estrus synchronization use (P <0.05) can be due to the fact that lambs from the synchronized ewes born and weaned at the same time and then, reared under better nutritional and management conditions.

The overall results of the present study showed low reproductive performance in the Ghezel sheep flocks of East and West Azarbaijan provinces due to the low use of estrus synchronization methods and poor management. Therefore, it seems that by informing the farmers about the new methods of estrus synchronization, raising their level of knowledge in this field, ration training, and management of synchronized animals can improve reproductive performance and increase profitability in the region.

Infections with gastrointestinal (GI) nematodes severely affect small ruminant health and compromise their productivity and reproductive performances and can be a major cause of economic losses in small ruminant production. High burden of infections with nematodes may lead to death; and under field conditions, most infections are usually mixed consisting of different species of nematodes. Sheep and goats are infected with gastrointestinal nematodes while grazing and the biology of the infective larvae on the pastures is important in planning effective control programs. In general, the development of the free-living stages of gastrointestinal nematodes is largely dependent on temperature, with development rate increasing at warmer temperatures, while moisture is also required for the development cycle to proceed. Temperature also influences grass growth and hence exposure independently of larval development and survival. East Azerbaijan province in terms of livestock animal population in particular sheep breeding is one of the most important provinces of Iran and due to the amount of rainfall is susceptible to worm’s contamination in livestock animal. In this survey, fecal samples of 5934 sheep in 19 cities in East Azerbaijan, from 2002-2009 were examined by the Clayton-Lane method. Briefly, a sample of feces, 1-5 g, was well mixed with water (about 30-50 ml) and strained through a sieve (1 mm mesh) to remove coarse fecal material. The mixture was sedimented for 10-15 minutes on the bench, or by light centrifugation for two or three occasions, until the supernatant was clear. The sediment was then mixed with a saturated solution of sugar in a centrifuge tube (15 ml volume) and centrifuged for one or two minutes at 500 g. The egg floated and coverslips were placed on the tubes in centrifuge and after 5 min the samples were examined for the presence of eggs at 100x and 400x magnifications under the light microscope and the number eggs of Nematodirus, Marshallagia, Trichuris, unknown nematodes parasite eggs and the whole of the nematode eggs were determined in these cities by their shape and size. These data were analyzed by the SAS software. The results showed that the Kaleibar was the most infested city and the Malekan had the lowest contamination to gastrointestinal nematode parasites. Marshallagia and Trichuris had the maximum and minimum quantities of means with 11.12±32.02 and 2.23±13.78, respectively. A study on the correlation between humidity in the second month and humidity average and fecal egg count showed that there is a positive and significant (p<0.01) correlation between them. Base on the results of this survey high humidity in regions and seasons are risk factors for propagating worm infestations and distinct handlings are necessary for preventing the mentioned phenomenon. This study survey on geographical situation in 19 cities of East-Azerbaijan indicated that the infestation rate to gastrointestinal nematodes in south of province (Malkan city) is at the minimum rate and in north province (Kaleibar city) is in maximum rate. Because the north region of East-Azerbaijan province is warmer and moister from the other regions, the high rate of infestation to GI nematodes was expected. Furthermore, differences in the population of livestock animals in the two regions are important in the rate of infestation to nematodes. In conclusion, the results of the study denoted that even approve the anthelminthic drugs in the livestock animals, the rate of infestation to GI nematodes is high. Also, the results of this survey are showed that a positive correlation is between EPG and the mean of humidity and this is important that treatment and prophylaxis are needed to decrease the risk of the disease. This research serves as a baseline for future studies on prognosis and prophylaxis of GI nematodes. These regional differences appeared to be systematic and can be ascribed to differences in applied pasture management and climatic conditions, and cause a need for regionally adapted monitoring and control systems. Keywords: Sheep, Nematode, EPG, Correlation, Humidity. Infections with gastrointestinal (GI) nematodes severely affect small ruminant health and compromise their productivity and reproductive performances and can be a major cause of economic losses in small ruminant production. High burden of infections with nematodes may lead to death; and under field conditions, most infections are usually mixed consisting of different species of nematodes. Sheep and goats are infected with gastrointestinal nematodes while grazing and the biology of the infective larvae on the pastures is important in planning effective control programs. In general, the development of the free-living stages of gastrointestinal nematodes is largely dependent on temperature, with development rate increasing at warmer temperatures, while moisture is also required for the development cycle to proceed. Temperature also influences grass growth and hence exposure independently of larval development and survival. East Azerbaijan province in terms of livestock animal population in particular sheep breeding is one of the most important provinces of Iran and due to the amount of rainfall is susceptible to worm’s contamination in livestock animal. In this survey, fecal samples of 5934 sheep in 19 cities in East Azerbaijan, from 2002-2009 were examined by the Clayton-Lane method. Briefly, a sample of feces, 1-5 g, was well mixed with water (about 30-50 ml) and strained through a sieve (1 mm mesh) to remove coarse fecal material. The mixture was sedimented for 10-15 minutes on the bench, or by light centrifugation for two or three occasions, until the supernatant was clear. The sediment was then mixed with a saturated solution of sugar in a centrifuge tube (15 ml volume) and centrifuged for one or two minutes at 500 g. The egg floated and coverslips were placed on the tubes in centrifuge and after 5 min the samples were examined for the presence of eggs at 100x and 400x magnifications under the light microscope and the number eggs of Nematodirus, Marshallagia, Trichuris, unknown nematodes parasite eggs and the whole of the nematode eggs were determined in these cities by their shape and size. These data were analyzed by the SAS software. The results showed that the Kaleibar was the most infested city and the Malekan had the

The study of milk production and composition curves in buffalo provides key pieces of information about genetic potentials and management-related strategy to both breeders and farmers. The objective of this study was to identify of the non-genetic factors of parameters for fitted Wood function on milk fat content (MFC) and milk fat percentage (MFP) curve of Azari and Khuzestan buffalo. The data were collected from 15065 and 15225 from Khozatani buffalo and 9571 and 9721 lactation period of Azari buffalo on MFC and MFP were used for further analyses. For the first phase, the Wood function for each individual within the investigated population was fitted. Then, environmental factors affected MFC and MFP in both populations were assessed. In the last step, after the estimation of curve parameters, the phenotypic correlation for both populations was estimated. Results of the present study showed the MFP of Khuzestan breed was almost % 0.5 lower than Azari breed and faster reached to the lowest point within MFP curve shape. Furthermore, because of the higher milk production rate of Khuzestan breed, the MFC of this breed showed almost % 25 higher at the peak,  compared to the Azari buffalo. Also, due to higher observation of daily milk production in Khuzestan buffalo, this breed has good potential to produce more daily MFC and less MFP than Azari. Finally, the outputs of the report this research may be effective in help to improving nutritional the feeding formulation and genetics programs of Iranian buffaloes.

The purpose of this study was to compare the accuracy of genomic evaluation for Bayes A, Bayes B, Bayes C and Bayes L multi-step methods and SSBR-C and SSBR-A single-step methods in the different values of π for predicting genomic breeding values of the genotyped and non-genotyped animals. A genome with 40000 SNPs on the 20 chromosom was simulated with the same distance (100cM). The π values that maximized the prediction accuracies in BayesC were 0.980 and 0.995 for the normal and gamma distributions of QTL, respectively, and were also used in SSBR-C method. Genomic prediction accuracy in the SSBR-C (π = 0.99) method was higher than multi step methods from 0.02 to 0.09 for gamma distribution. Results showed that considering mixture distribution and use of phenotype, genotype and pedigree information simultaneously, the SSBR-C (π = 0.99) method had higher accuracy than other methods and is considered a better choice in this scenario. Moreover, both single and multi-step methods showed similar prediction accuracy when the genetic architecture appeared to approach the normal distribution. Furthermore, SSBR-C (π = 0) method appeared to be more reliable choice that was due to regressions of true breeding value on estimated breeding value close to one in normal distribution. Generally, GEBV accuracy decreased as the distance increased between validations and training set, which was more sensitive for non-genotyped individuals compared to genotyped individuals.

Cashmere is a very fine fiber that is produced by secondary hair follicles in cashmere goat. Based on American test and material association description, cashmere is fine fiber in Asian Indian goat hair follicles with diameter lower than 30 microns. Cashmere is growing as “under coat” in cold season and it shedds during the time from late winter until early spring. It is estimated that 68 goat breeds produce cashmere fibers in the world. Cashmere goats are originated from Asia. The important countries that can produce a large amount of cashmere are China, Mongolia, Iran, Turkey, and India. Total production of cashmere is estimated to be 5mt. During the last decades, due to the economic importance of cashmere, USA, Australia, and NewZealand joined to the cashmere producing countries. Many researchers reported that cold climate is suitable for production of quality cashmere. In this research, effects of nutrition and age on histological characteristics of Raeini Cashmere goat were studied in Tabriz, East Azerbaijan.

For this research, 24 female Raeini cashmere goats were selected. The goats were selected from Baft Raeini cashmere goat breeding and husbandry station. Goats were fed individually   and were treated for 8 months of study based on feeding levels (Maintenance, 0.7 M, 1.4 M, and 1.8M) and age (6 months and 18 months) on fleece growth. The trial was conducted at the khalat-Pushan Research Station, University of Tabriz. The goats allocated to four feeding levels: M (goats fed to maintain live weight, 0.7M (goats fed to lose 3Kg live weight from February to September), 1.4M, and 1.8M (goats fed to gain live weight). Patches of fleece from defined areas were repeatedly shorn at 4 weekly intervals from the right mid side of each goat. For follicle study, in the fist, 120cm2 of left side of animals was marked firstly; then, these region fibers shaved by electrical shaver. Shaving was repeated monthly (for four weeks). Skin biopsy was taken monthly from left mid side of skin of abdomen. samples were fixed in 10% formalin. Paraffinized block were prepared and then, they are sectioned as serial section in 8-micron thickness. Histological sections were stained by sak pic method (reference ????). Results were analyzed by analyses variance and paired t-test.   

This research results, showed that there was no significant effect of feeding level or age on weight of cashmere and hair per area, secondary follicle activity, cashmere length, and yield (P<0.05). Fleece and live weight for young goats were significantly less than that of old goats (P<0.05). Result were appeared that mean cashmere diameters of patch shorn in September of goats fed M, 1.4M and 1.8M were significantly greater than that of goats fed 0.7M (P<0.05). In group feeding more than maintenance requirements, results indicated no increase in cashmere production. Average fiber diameter of cashmere in June was higher than in May. Results of this research indicated that there are not any significant differences between different levels of feeding and age on fiber growth rate (P<0.05). The highest fiber production and the maximum mean of fiber growth rates (1.64 and 1.48 g/120cm2 / 28 days) were observed in June and July. Secondary to primary follicle ratio of all goats was 12.60. Study of secondary follicles ratio showed that different levels of feeding cannot reduce number of secondary follicles. Many researchers reported that increase in feeding levels to over maintenance rate cannot increase cashmere growth rate. This research results confirmed by previous studies. it was reported that feeding limitation can reduce diameter of cashmere, but there is not any increasable effect during over maintenance feeding and an increase in dietary protein. This research indicated that cashmere diameter was more in two-years old goat than one-year old goat cashmere diameter. These   results were similar with reports of Klor et al. (1993), Rafat (1997), and Salehi (1997). Increase in diameter of wool fibers with increasing in the age of animals was reported in sheep and goat. In other studies, it is shown that effect of age on diameter of Norway cashmere goats was significant (P<0.05). Results of our research show that diameter of cashmere in Raeini goats increases at June. Similar results are illustrated in Kerman (with the same age and sex). The weight of produced fibers / body surface was the same in four feeding treatment groups, but diameter of cashmere was different. Numbers of secondary follicles   increased in April. Minimum weight of fibers was observed in April in all of the treatments, which may be because of low activity of follicles in this month. Variation of cashmere diameter and cashmere growth rate can explain differences in total cashmere production. Changes of feeding level from under maintenance to high levels cause increase in cashmere diameter. This study appeared that diameter of cashmere fibers can have reaction to feeding rate. Accordingly, energy has important effect on growth of hair and cashmere. The animals with low energy diet produce low amount of cashmere, Other researchers have opposite idea. According to their statement, there are not any difference in partition for nutrient between primary and secondary follicles. This research result showed that increase feeding cannot increase cashmere production. Jia et al (1995) reported that increase of diet net protein has not any important effect on cashmere goats production in Spain. In other study using unpregnant goat it has been indicated follicular activity and fiber growth is not under influence of pregnancy and milking. However, some researches showed that reproduction condition of animal, as pregnancy and milking, has effect on cashmere fiber growth.  

Generally, results of this study showed Raeini cashmere goats in East – Azarbayjan climate did not show any fundamental changes in diameter and length of cashmere in comparison with Raeini cashmere goats which reared in Kerman province.

Arkharmerino sheep breed is a fine wool type. Crossbreeding can lead to combination of favorable characteristics from the breeds involved. The greatest part of the wool produced by the indigenous sheep breeds in Iran is used in the hand woven carpets. It is estimated that 5.1 million m2 hand woven carpets is produced in Iran annually; therefore, the country needs 28 thousand tons of washed wool. Approximately 8 thousand tons of wool is imported as merino wool from Australia and New Zealand. Iranian wool is suitable for use in coarse-carpet industry, but it has some difficulties for use in the fine carpets. Fine carpet makers usually utilize imported wool, which has more uniformity of diameter. For finding suitable sheep breed to produce more uniform wool, we interest to Arkhar-Merino breed at University of Tabriz. The Kazakh Arkhar-Merino breed was produced at Kurmektinski experiment station of the Academy of Sciences of the Kazakh.  The purpose of research was to introduce a new breed of fine wool sheep which would combine the good production characteristics of the Merino with adaptability of local Arkhar. The breed is based on crossbreeding of wild Arkhar rams with ewes of the Novocaucasian Merino, Précoce and Rambouillet breeds. Crossbreeding between Iranian wool sheep and foreign wool breeds can lead to the production of a genetic combination with the better wool fibers. In order to evaluate fleece characteristics, wool samples of 451 yearlings of Arkharmerinos×Ghezel (ArGh) were collected by Mokhber et al. (2008). At first generation of ArGh, mean (± standard error) of fiber diameter, fiber diameter variability, staple length and percentage of true wool, medulla and kemp percentage were 27.10 ± 3.36 μ, 36.60 ± 7.84 %, 11.81 ± 4.06 cm, 91.31 ± 9.32%, 7.27 ± 6.90%, and 1.40 ± 3.03 %, respectively. At second generation of ArGh, the same traits were 26.33 ± 3.41μ, 34.64 ± 9.36 %, 10.15 ± 3.99 cm, and 95.41 ± 4.70 %, 3.39 ± 5.85 % and 2.01 ± 2.65 %, respectively.  The main aim of this work was to study the morphological and structural properties of breed wools of first and second generation of Arkharmerino ×Ghezel with breed Arkharmerino as a father's base and comparing with their parent's wool characteristics. The aim was to obtain information about crossbreeding of local fat tail rams with Arkhar-Merino ewes regarding the wool traits. Arkhamerino breed has been imported from Kazakhstan. For this purpose, the wool fibers were sampled from the middle region of the sheep's body. The physical properties of the wool fibers, such as fiber diameter, staple length, Kemp fiber percentage and modulation fiber percentage were measured. For study the morphological properties of fibers, surface image of the fibers was prepared using a scanning electron microscope. In order to measure the structural properties of the fibers, which is one of the important factors in the production of textile products, the infrared spectrum of each fiber was obtained according to the relevant standards. The chemical structure (such as the components of the main and side chains, functional groups, various linking bonds, etc.) and the chain conformation in wool fiber play a crucial role in its mechanical, other physical, and service properties. The effect of wool breeding on the chemical structure and chain conformation of wool samples, which were from Ghezel sheep and Arkharmerino Sheep in first and second generations, were investigated by employing an FT-IR spectrometer (IR Affinity-1s ATR-FTIR, Shimadzu, Japan) in a spectral range from 500 to 4000 cm-2. The infrared spectra of the control sample of wool in Fig. 1 indicate that the strong peak with absorption band at 3399.5 cm-1 was assigned to the combined stretching vibrations of N-H and O-H (νN-H, νO-H), and the absorption bands at 2960.2 cm-1, 2930.0 cm-1, 2870.0 cm-1were assigned to the asymmetrical and symmetrical stretching vibrations of C-H in CH3 and -CH2- groups, respectively. Moreover, the strong peak with absorption band at 1639.8 cm-1was due to the stretching vibration of C=O from amide Ι (νC = O), which was essentially relative and indicative to the α-helix conformation of the main chains of wool (Wojciechowska et al. 2002). The medium peaks with absorption bands at 1540.1 cm-1 and 1239.9 cm-1 were attributed to the bending vibration of N-H (δN-H) from amide ΙΙ and the stretching vibration of C-N (δC-N) from amide ΙΙΙ, respectively. Moreover, the stretching vibration of C-N (δC-N) from amide ΙΙΙ was considered to be relative and indicative to the β-sheet conformation in wool fiber (Cai and Singh 1999). The peak at 1079.3 cm-1 was due to the vibration of sulfur-containing group of cystine in wool. Table 2 shows the average and standard deviation of absorption band of the functional groups in the wool fibers. The results showed that the fiber scales in crossbreed and Arkharmerino fibers have a telescopic and regular state that are different from the irregular structure of the Ghezel fiber scales. The measurement of structural properties showed that the wave number of amide, amine, hydroxyl and C-N bonds in the second generation was more similar to Arkharmerino and it can be concluded that in the second generation of Arkharmerino × Ghezel, genetic structure of fibers has the most similarity to Arkarmerino breed. In general, the results show that the second-generation fibers of the Arkharmerino × Ghezel have a good structural and superficial quality for usingin textile products.

In this study, lutein Pigment (0.07, 0.13 and 0.2 %w/w ) and whey protein concentrate (0.2, 0.3 and 0.4 %w/w) were added to the milk.  Qualitative characteristics of yogurt samples were analysed regarding physico-chemical, microbiological, textural and sensory properties over 21 days. Adding whey protein concentrate and lutein, lowered the level of synersis and acidity but increased the amount of dry matter, fat, viscosity and pH of yogurt samples. According to the results of microbe analysis, there was not any evidence of the growth of mold, yeast and coliform bacteria in the samples. In the case of sensory properties, adding whey protein concentrate and lutein, raised the scores of texture, mouthfeel evaluation and lowered the scores of appearance evaluation. Among all treatments, yogurt containing 0.2 %, w/w whey protein concentrate and 0.07 %, pigment lutein earned the best score with respect to overall flavor and quality acceptability.

About 6 million heads of cows in Iran are native cattle, but their characteristics and production potential remains unknown. Inbreeding is one of the important factors which must be considered in the herd and can be of considerable economic loss to producers. In this research, we tried to investigate the occurrence of inbreeding and its effects on the production traits of Serabi native cattle in a breeding center related to agricultural ministry located in Sarab. The aim of this study was to evaluate inbreeding effects on milk yield, fat percentage, protein percentage, and birth weight of Sarabi dairy cattle. In this research, the effects of inbreeding and environmental factors on production traits and birth weight of Sarabi cows have been studied. The data were collected from 1250 Sarabi cows during 1992- 2012 years by Sarabi Breed Center in East Azerbaijan province. In the present study, a pedigree file containing 1250 head (764 females and 486 males) of dairy cows was used, including data about the registration number of the livestock, date of birth, gender, father's registration number, and registration number of the mother, date of birth, parity, and production records. After the removal of animals with unknown and unregistered parents in the flock, the pedigree was arranged using pedigree software. Pedigree software was used to calculate the inbreeding coefficient for each animal. The principles of this software in the calculation of inbreeding coefficient is based on the formation of a kinship matrix among the individuals. The inbreeding coefficients of animals were considered as a discrete trait in 4 groups. In this herd, inbreeding coefficient was estimated between 0- 0.28. Average inbreeding coefficients of all cows and inbred cows are 0.0109 and 0.0574, respectively. Totally, 19% of all animals were inbred. In this study, inbreeding coefficient has been included in the model either as a continuous variable or as a classification variable. When inbreeding factor considered as continuous variable in the model, its effect on milk yield, fat and protein percentage, and birth weight was significant (P<0.01). When inbreeding considered as a continuous trait, 1% increase in inbreeding coefficient had an effect equal to -2.69 kg, 1.59%, and +18.1% on milk yield, fat, and protein percentage, respectively. Miglior et al. (1995a) reported a 1% increase in inbreeding coefficient in Holstein cows reduced calf weaning by 0.44 kg and reduced milk production by 25 kg. Mohammadkarim (2006) using a univariate model reported for 1% increase in inbreeding coefficient, changes in milk yield, fat yield, open days and length of first lactation equal to -14.02, -0.349 kg, + 0.4839 and + 0.148 days, respectively. Inbreeding has a negative effect on production traits and birth weight. Results showed that the effects of year-season of calving and parity on production traits and birth weight were significant (P<0.01). The regression coefficient of milk, fat and protein percentages and birth weight on inbreeding, when inbreeding considered as a discrete variable, were -0.129kg, +0.093%, +0.072% and -0.564 kg, respectively. In this study, when inbreeding traits considered as a continuous variable, did not show any linear or nonlinear relation with birth weight trait of Sarabi cows. It can be concluded that in order to maintain the genetic reserves of Sarabi cattle breed, it is necessary to carefully monitor the reproduction breedings in this native cattle population. In the case of endangered breeds, such as Sarabi breed, these breeds have beneficial properties, particularly in relation to resistance to diseases, and tolerance to stressful environments. These desirable traits can be transferred to future genetic composition cattle breeds. Preserving the genetic resources of the country's livestock and pay attention to similar breeds of Sarabi should be taken into consideration by decision makers at livestock breeding centers. In Holstein cows it has been found that high milk production is associated with a genetic susceptibility to disease (Khaleghi & Rafat 2018), so the desirable characteristics of the Sarabi breed should be studied in this regard of susceptibility to diseases. The existence of a complete family tree in computer registrations is the first step in controlling inbreeding. The existence of this pedigree will help breeders to avoid breeding between close-up animals, like a brother-sister and a father -daughter, which will increase the incidence of inbreeding in the population. For this purpose, it is recommended to use optimal mixing softwares that controls inbreeding. There are programs for managing the breeding to identify animals as soon as possible and calculate their relativeness in the herd. By this method, it is possible to prevent the occurrence of high inbreeding in the herd and produce calves with high profitability. The prospect of this research is to carry out further research on the issue of inbreeding and effective population size on local breeds of dairy cattle to prevent the replacement of these breeds with Holstein. It is imperative to prevent the replacement of the foreigner breeds (Holstein generally) instead of Sarabi breed and its extinction as much as possible.

Reproductive traits in sheep are the most important traits affecting profitability. These traits have categorical nature, but in practice the continuous distribution of traits is analyzed. In addition, to have true and accurate pedigree records, applying the appropriate model for analyzing the characteristics of high precision in the estimation of genetic parameters will be evaluated.Accurate prediction of animals breeding values is one of the best tools available to maximize the response to a selection program. Development of effective genetic evaluation and improvement programs requires knowledge of the genetic parameters for these economically important production traits. many studies, LS is analyzed by linear models, and the variance components are obtained by REML methods. Compared to linear models, non-linear models have disadvantages in goodness of fit or predictivty and they are time consuming in computation, which might be prohibitive for routine calculations The main objective of this study was to obtain effects of genetic estimates of reproductive traits in Makooei sheep using repeatability linear and threshold models that are necessary to develop an efficient selection strategy for improvement of reproduction. For this purpose, were estimated using linear and threshold univariate animal model on the data of 4319 records of 1629 ewes, collected during 1996 to 2014 in rearing and improvement of Makooei sheep for conception rate, number of lambs born, number of lambs alive at weaning, number of lambs born per ewe exposed and number of lambs born per ewe exposed traits. The model was included fixed effects (year and age of ewe) and random effects additive genetic of ewe, permanent environmental of ewe and residual. The overall mean of traits were as 0.93 for conception rate, 1.16 for number of lambs born, 0.98, for number of lambs alive at weaning, 1.07 for number of lambs born per ewe exposed and 0.91 for number of lambs born per ewe exposed. The heritability coefficient of traits were estimated as 0.05, 0.11, 0.06, 0.08, and 0.04 respectively, resulted from linear analysis and 0.12, 0.20, 0.15, 0.18 and 0.10 respectively, resulted from threshold analysis. The estimation of repeatability coefficient of traits were as 0.09, 0.16, 0.18, 0.15 and 0.12 respectively, for linear analysis and 0.48, 0.51, 0.34, 0.50 and 0.41 respectively for threshold analysis. The results of this study showed that, using threshold models for analyzing reproductive traits in genetic evaluations, comparison with linear models, caused relatively increasing genetic parameters and accuracy of evaluations.