Introduction: 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.Material and methods: 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).Results and discussion: 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.

Antineutrophil CYTOPLASMIC autoantibodies were detected in patients with some autoimmune and vascular disease such as Wegner’s granulomatosis polyarthritis nodosa and systemic lupus erythematosus. Indirect immunofluorescence technique was employed to detect these autoantibodies. By this method, two general patterns of antineutrophil CYTOPLASMIC autoantibodies were seen: a CYTOPLASMIC (C-ANCA) and a perinuclear form (P-ANCA). These antibodies also were observed in uveitis. In this study the presence of antineutrophil CYTOPLASMIC autoantibodies in 25 patients with uveitis and its relationship with uveitis and its relationship with anatomical location of the disease is evaluated. According to the results antineutrophil CYTOPLASMIC autoantibodies was detected in 16% (4 out of 25) of the patients all of them being C-ANCA type. The results also showed that there was not any significant correlation between the presence of antineutrophil CYTOPLASMIC autoantibodies and anatomical location of the disease (P=0.65).

Antineutrophil CYTOPLASMIC autoanibodies (ANCA) were detecte in patients with certain autoimmune vascular disease such as Wegner’s granulomatosis, polyarthrits nodosa and systemic luuc erythematous. Indirect immunofluorescence (IIF) technique was employed to detec these autoantibodies.ANCA have been recently detected in some forms of inflammatory bowel disease (IBD), ulcerative colitis (U.C). Crohn’s disease (C.D) and primary sclerosing cholangitis (PSC). By IIF method, two general patterns of ANCA were seen: a CYTOPLASMIC (C-ANCA) and perinuclear form (P-ANCA). In this study we evaluated the presece of ANCA in 52 U.C. patients and 69 matched normal control group by IIF technique, and it’s relationship with disease activity. Site of colon involvement and, lesion extent. The results showed that all control group were ANCA negative, but 58% of patients had ANCA, and most cases (70%) had C- ANCA. The obtained results also revealed that there was no relationship between ANCA and disease activity

Antineutrophil CYTOPLASMIC autoantibodies (ANCA)were detected in patients with autoimmune and vascular diseases such as Wegener"s granulomatosis, polyarteritis nodosa and systemic lupus erythematosus. Indirect immunofluorescence (IIF)technique was employed to detect these autoantibodies. By this method, two general patterns of ANCA were seen: a CYTOPLASMIC (c- ANCA) and perinuclear form (p-ANCA). These antibodies were also observed in rheumatoid arthritis (RA)but their prevalence and clinical significance have not been determined. In this study the presence of ANCA in 52RA patients (10 males and 42 females) and its relationship with disease activity was evaluated. 26.9% or patients were ANCA-positive, 36% of whom had c-ANCA and 64% a p-ANCA pattern. The results also showed that there is no significant correlation between ANCA titer and disease activity (p<0.05). Thus according to the results obtained, the detection of these autoantibodies are not useful for the diagnosis or prognosis of these disorders.

Estimation of CYTOPLASMIC effects of Baluchi sheep breed for production traits were studied. The data used in the present study were collected from flocks at the Abbasabad sheep breeding research station in north east of Iran included 13625 animals descended from 275 sire and 3863 dam.Traits were birth weight, waning weight, 6-month weight, 12-month weight and greasy fleece weight at 18 month. CYTOPLASMIC origin was found by tracing the individual progeny to the earliest ancestor in the pedigree. Genetic Parameters were estimated by Derivative Free Restricted Maximum Likelihood (DFREML) using univariate animal models. For all traits CYTOPLASMIC effects were not important. The evidence is broadly consist with 4% for BW and 2% for GFW of VARIATION in performance due to CYTOPLASMIC effects. However effects in genetic evaluations are likely to be small. Maternal genetic effect contribution on greasy fleece weight was very low.

In this research, CYTOPLASMIC inheritance of yearling mohair weight (YMW) in Markhoz kids were studied by using Bayesian statistical method. Using records which gathered through 1992-2011 in Markhoz goat breeding research station in Sanandaj. GLM procedure of SAS statistical software was used to verify statistical significant of environmental factors on YMW and Gibbs1f90 software, based on animal model and Gibbs sampling, were used to estimate genetic parameters. Environmental factors such as year of birth, maternal age and sex as fixed effects, and animal age and body weight at recording time as covariates were considered in the model. Based on the results of this research, the minimum DIC was detected in Model 12. Which includes direct additive genetic effects, maternal additive genetic, maternal permanent environment and CYTOPLASMIC genetic effects, taking into account the covariance between direct and maternal genetic effects. The ratios of direct additive genetic variance, maternal additive genetic, maternal permanent environment, CYTOPLASMIC genetic on phenotypic variance were respectively 19. 27, 6. 6, 3. 03 and 1. 82 percent based on the selected model (model 12). In general, the results showed that selection based on direct genetic potential and partly on maternal genetic can improve the YMW. Due to the significant of CYTOPLASMIC effects to enter the model on one hand and the low value of its variance on the other hand, it can be concluded that the role of CYTOPLASMIC inheritance as a correction factor is important, but it cannot be considered as selection criteria.