gh. rahimi mianji

The number of lambs per lambing is one of the most important reproductive traits in sheep. Many studies have reported that genetic mechanisms play an important role in the variation of litter size in sheep. Selection for higher litter size in sheep has led to a variation of this trait within and across different breeds. Natural and artificial selection related to adaptation and economic traits, such as litter size, results in changes at the genomic level which leads to the appearance of selection signatures. Detection of these regions provides an opportunity for a better understanding of genetic mechanisms underlying the phenotypic variation of litter size in sheep. Several tests including the linkage disequilibrium-based approach, site frequency spectrum, and population differentiation-based approach have been developed to explore the footprints of selection in the genome. This study aimed to identify selection signatures in Baluchi sheep to investigate the genes annotated in these regions as well as the biological pathways involved. For this purpose, XP-EHH and FST analyses were conducted using the genome-wide single nucleotide polymorphisms (SNPs).

In this study, data from 96 Baluchi ewes genotyped using Illumina Ovine SNP50K BeadChip were used to identify genomic regions under selection associated with litter size in sheep. Phenotypic and pedigree data were collected at the Abbasabad Sheep Breeding Station. Based on records on different litters, ewes were divided into two groups: the case (two lambs per litter) and control (one lamb per litter).Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. To identify the signatures of selection, two statistical methods of FST and XP-EHH were used under FST and EHH software packages, respectively. We also calculated unbiased estimates of FST. Because the results were strongly correlated with the FST results, unbiased estimates have not been reported. In our study, all the SNPs ranking above 0.1 percentile of the distribution of test statistics were selected as candidates for the signature of selection. Gene ontology analysis for identified genes was performed using DAVID online database.

We used the FST and XP-EHH statistics to identify genomic regions that have been under positive selection associated with litter size in Baluchi sheep. Using FST approach, we identified 14 genomic regions on chromosomes 1 and 2 (two regions per chromosome), 3, 7, 9, 14, 18, 22, 23 (one region per chromosome), and X chromosome (three regions). Also, XP-EHH analysis identified nine genomic regions on chromosomes 2, 12, 13, and 22 (one region per chromosome), 7 (three regions), and X (two regions). Some of the genes located in identified regions under selection were associated with the number of lambs per lambing (ACVR1 and TGIF1), ovarian and follicle growth (DDX24), and fertility (FOXH1). Bone morphogenetic proteins are critical regulators of chondrogenesis during development which transduce their signals through three type I receptors namely BMPR1A, BMPR1B, and ACVR1/ALK2. TGIF1 is highly expressed in sheep ovaries suggesting that TGIF1 plays an important role in ewe reproduction. Also, TGF-β/SMAD signaling is critical in reproductive processes such as follicular activation, ovarian follicle development, and oocyte maturation. It has been evidenced that Ddx24 is highly expressed in sheep uterus affecting the development of ovaries and follicles. Foxh1 was first introduced as a transcriptional partner for Smad proteins and has been reported to play an important role in embryonic development. Results of gene ontology analysis identified two biological pathways namely defense response and cell motility which play an important role in the ovulation rate and the number of lambs per lambing. Reproductive activity and immune defenses can be mutually constraining, with increased reproductive activity limiting immune function and immune system activation leading to decreased reproductive function.

The results of this study identified candidate genes involved in the regulation of litter size in sheep suggesting that ACVR1 and TGIF1 genes can be considered as candidate genes related to the number of lambs per litter in sheep breeding programs to improve reproductive performance.

Among the essential metabolic functions of the liver, the role of this tissue as a mediator in the immune system has also been considered. Although the role of cytokines and chemokines in mammalian immune systems has been well evaluated, few studies have been performed in fish. Genes involved in the immune system, such as interleukin 10 and TNF-α, play an important role in the immune system of various cells. In the present study, the expression of interleukin 10 and TNF-α genes in rainbow trout was assessed following VHS virus treatment. Six samples from each of two control group and infected group with VHS virus were selected and then total RNA was extracted from liver tissue. The differential expression of interleukin 10 and TNF-α genes between the two studied groups (infected with the virus vs control) was assessed using Real-Time PCR. Comparison of relative changes in gene expression were assessed by statistical methods in three replications of each sample. Analysis of data showed that the expression of interleukin 10 and TNF-α genes increased in response to VHS virus. In this study, although the expression of both interleukin 10 and TNF-α genes were significantly increased, but the rate of interleukin 10 expression in the treatment group was 25 times higher than the control group. Increased expression of these two cytokines, in particular over induction of interleukin 10 expression by the virus may lead to impaired of immune function. As a final conclusion, studying the relative changes of cytokine genes expression can increase our knowledge on molecular mechanism of immune function against pathogens. In this case, it is possible to develop molecular markers in order to increase resistance to viral disease in breeding programs of industrial fish farming.

Ascites syndrome is one of the most important causes of death in the poultry industry, in which various tissues of the body, including the kidneys, are involved. This syndrome occurs with different frequencies in males and females, and different mechanisms of ascites in the two sexes have not been studied to date. In this study, the gene expression profile of kidney tissue of male and female chickens with ascites syndrome from the paternal line (B) of the Arian commercial line was compared using RNA-Seq data. Due to severe cold stress applied, the mortality rate was high and about 59%, which was higher in males (63.4%) than females (54.1%). The results of transcriptome analysis showed that 240 genes were significantly different in comparison between ascites male and female birds. The annotation analysis of these genes showed that the metabolic pathways of antibiotic biosynthesis and amino acids, carbon metabolism, cell adhesion, receptor-extracellular matrix interaction (ECM) were involved in this process. The body's response to ascites-induced damage to kidney tissue is the development of renal fibrosis (to repair the damage) and reduced activity of the glycolysis pathways and increased gluconeogenesis to reduce energy and oxygen consumption in these pathways. Furthermore, an increase of the STAT-JAK2 signaling pathway activity (due to the high expression of JAK2 and STAT3 genes) was observed. This signal stimulates cell growth, angiogenesis, differentiation, migration, and apoptosis. It is expected that the results of the present study to provide new insights into understanding the molecular mechanism of ascites incidence and also differences in its occurrence in males compared to female broiler chickens.

To evaluate the influence of VHS disease on rainbow trout biometric traits, this research was conducted. Two hundred eighty-one rainbow trout (88±3.38 g initial weight ) were collected, and after 18 days of adaptation period were randomly divided into five groups. All experimental groups were fed by commercial ration. The first group was selected as a control group (no injection), but the second to fifth groups were injected with 0.03 ml physiological serum, 0.06 ml physiological serum , 0.03 ml VHSV, and 0.06 ml VHSV with the concentration of 4.5x104 pfu.ml - respectively. To diagnose the disease, RT-PCR test was used. The research period was 35 days, and records of body weight, and fish length (standard length, fork length and, total length) were collected on days 28, and 35 of rearing. Mean comparisons of these traits between different groups were conducted using the Tukey test (HSD) and R software. In the results of body weight in the first week after challenge (day 28) significant differences were observed between the control group with VHSV injected groups (p < 0.001) and also between physiological serum with VHSV injected groups (p < 0.05). In the second week after challenge (day 35), there were significant differences (p < 0.001) for body weight between VHSV injected groups with control and physiological injected groups (p < 0.001). In the second week after the challenge for traits related to fish length (standard length, fork length, and total length), there were significant differences between all experimental groups (p < 0.05). Based on the observed results, VHS disease will reduce fish growth, and it will cause economic losses.

Copy number variation (CNV), one of the most important structural changes in the genome, has been known as an important source of genetic and phenotypic variations. The purpose of this study was to compare the two different algorithms in CNV detection consisting PennCNV and QuantiSNP in Baluchi sheep.Data analysis was performed using the Illumina OvineSNP50k BeadChip on 96 Baluchi sheep.After CNV calling, the copy number variation regions (CNVRs) were determined using the CNVRuler program.91 CNVRs with a length range of 18.75 up to 511.7 kbp were identified by the PennCNV algorithm, covering 0.46% of whole sheep genome.Also, 316 CNVRs with the length range of 7.5 up to 1280 kbp were obtained using QuantiSNP algorithm, covering 1.33% of whole sheep genome. The number of loss events was about five and three times more than the number of gain events for QuantiSNP and PennCNV algorithms, respectively.Also, the number of CNVs detected by QuantiSNP was about four times higherthan PennCNV.Also, 86.6% of total CNVs (174 CNVs with average length of 12.62 kb) identified by PennCNV were common with CNVs detected by QuantiSNP. In general, the results showed that the use of several algorithms could improve the accuracy for detecting the structural variation in the genome and led to a better understanding of the sheep genome.

The goal of this study was to detect polymorphisms in Insulin like growth factor-I gene of Persian sturgeon fish (Acipencer persicus) using PCR-SSCP technique and also to investigate their association with fish growth traits (condition factor, body length & weight). In this research, 95 Persian sturgeons were randomly selected and fin clip for DNA extraction were taken from caudal fin. DNA was extracted using modified salting out method and two fragments of 171 and 362 bp in 5/-UTR and 3/-UTR regions of IGF-I gene were amplified, respectively. Genotyping of individuals showed three different banding patterns of M, K and G for the fragment of 171 and 362 bp with the frequency of 13, 39, 48 and 31, 49, 20 percent in Persian sturgeon samples, respectively. The genotype K at 3/-UTR and genotype M at 5/-UTR marker site were the most frequent genotypes. Marker-trait analysis using SAS statistical software indicated no significant association between observed banding patterns of marker loci and growth traits in Persian sturgeon. Considering the important role of IGF-I as a probable candidate gene effective on growth related traits, survey of this marker sites are recommended for larger-size populations

In the present study the allelic polymorphisms of GH, GHR and TGFβ3 genes and its association with egg production traits were investigated. Blood samples randomly were collected from breeder hens of Mazandaran native fowls breeding station and transported to the laboratory in cold chain condition. DNA was extracted using modified salting out method and the desired loci were amplified by specific primers. All samples genotyping were carried out by RFLP-PCR method. The frequency of each (+) and (-) alleles was estimated at 0.7981 and 0.2019 for GH, 0.9937 and 0.0063 for GHR and 0.8037 and 0.1961 for TGFβ3 loci, respectively. The heterozygote genotype was detected in both GH and TGFβ3 loci but all individuals showed homozygote genotype in GHR marker site. The chi-squared test showed that all individuals in both GH and TGFβ3 loci were in HW equilibrium. Statistical analysis of showed that GH marker site had a significant effect on both phenotypic and breeding values of egg weight at puberty (EWM) and age at first laying egg (AFE), respectively. The mean comparison showed that individuals with -/- genotype in GH marker site had higher phenotypic values for EWM but lower breeding values for AFE trait. The GHR and TGFβ3 loci and also the interaction between GH×TGFβ3 loci were not statistically significant on phenotypic and breeding values of mentioned traits..

In this research, association of the BoLA-DRB3.2 alleles with somatic cell score as an indicator of udder health, and clinical mastitis in Holstein dairy cows were investigated. Clinical mastitis occurrence was defined as the presence or absent of at least one case of mastitis diagnosed by farmer throughout the first lactation. Milk somatic cell count of the first lactation was converted to milk somatic cell score to achieve normality of data distribution. PCR-RFLP method, followed by digestion of the amplified fragments with three restriction enzymes, RsaI, BstYI and HaeIII, was used to determine BoLA-DRB3.2 alleles of the animal included in this study. Gene-substitution, general linear and logistic regression models were used to evaluate the effect of BoLA-DRB3.2 alleles on the LSCS and binary measures of clinical mastitis, respectively. The association results showed that BoLA-DRB3.2*11 was significantly associated with lower lactation somatic cell score, but no allele was found to be significantly associated with clinical mastitis. Although more studies are needed to confirm the present results, but it can be concluded that BoLA-DRB3 alleles may have potential usefulness as a genetic marker to improve bovine mastitis and udder health in dairy cows.