فهرست مطالب محمد شمس الهی

 Suboptimal levels of kid survival are the largest contributor to reproductive wastage in goat flocks. This results in substantial loss of production, producer, and industry income, and is increasingly being perceived as poor animal welfare. Improving kid survival is therefore a priority for the industry. Nutrient provision during gestation not only affects maternal status and reproductive performance but also affects prenatal and postnatal offspring growth and health. Although trace minerals (TM) are needed by the body in small amounts, they are essential nutrients for several metabolic functions such as growth, development, reproduction, and immunity. Furthermore, newborn animals are dependent upon their dams for the transfer of these nutrients via the placenta and the mammary gland. The antibodies obtained from colostrum are the only defense mechanism against environmental factors in neonatal ruminants. Inadequate nutrition of the dam, immune system suppression, and stress factors may lead to the production of low-quality colostrum. Management and feeding of high-quality colostrum can reduce kid mortality, strengthen immunity, and increase animal life span. Nutrition affects the development of the mammary gland, the onset of lactogenesis, and colostrum production, either by affecting some of the hormones that control these processes or by contributing nutrients that are in demand at this stage of pregnancy. Selenium plays an important role in preventing impaired function of the immune response. Copper deficiency has been shown to result in lowered bactericidal activities of blood leukocytes in ruminant animals. Zinc sufficiency has also been linked to proper immune functions. Therefore, this study aimed to investigate the effect of TM injection in late pregnancy on colostrum quality and plasma metabolites of Lori does and their kids.
Thirty Lori mature does with an average body weight of 40 kg and an age of 2-3 years were used. One month before the expected kidding, animals were divided into two groups (n=15 does/group) and randomly assigned to experimental treatments. Experimental treatments were no injection of trace minerals (Control; C) and injection of 1 mL of TM at four and two weeks before expected kidding. Blood samples were taken through the jugular vein. Each mL of TM solution contained 2.5 mg of Cu, 1.25 mg of Se, 5 mg of Mn, and 5 mg of Zn. All does were kept in similar nutritional and managerial conditions from mating to one month before kidding.
Results showed that plasma concentrations of glucose and total cholesterol (TC) tended to be higher and lower in the TM group at day 7 before kidding, respectively (P=0.06). Experimental treatments did not affect plasma triglyceride (TG), Ca, and Mg concentrations, and glutathione peroxidase (GPX) activity of does at day 7 before kidding (P>0.05). Whereas, TM injection before mating decreased plasma malondialdehyde (MDA) and increased total protein (TP), BRIX index (BI), superoxide dismutase (SOD), and total antioxidant activity at day 7 before kidding (P<0.05). Colostrum of does received TM had a higher fat, protein, and BI content and a lower lactose content than the colostrum of the C group (P<0.05). Plasma concentrations of glucose and MDA were lower in kids born from does received TM than those born from the C group (P<0.05). Experimental treatments did not affect plasma concentrations of TC, Ca, and Mg concentrations in kids (P>0.05). Kids born from does received TM had higher plasma concentrations of TG, TP, BI and SOD, GPX, and total antioxidant activity than those of the C group (P<0.05).
According to the results of the present experiment, injection of a TM solution containing Cu, Zn, Se, and Mn four and two weeks before birth increased the concentrations of TP and BI as well as the activity of antioxidant enzymes (SOD, GPX) and antioxidant capacity and reduced MDA concentration in Lori goat plasma. This improved the quality of colostrum produced by these does. Kids born from does receiving trace minerals had higher plasma concentrations of TP, BI, and activity of antioxidant enzymes (SOD, GPX), higher total antioxidant capacity, and lower concentrations of MDA compared to the C group. Therefore, this strategy may have beneficial effects on the health, viability, and performance of kids before weaning.

Sheep producers would benefit from the opportunity to change offspring sex ratio towards their preferred gender. For example, male lambs have higher average daily gain and better carcass quality than female lambs. Thereby reaching a higher market weight over a set time period. However, sheep interprises require breeding females, which may lead to a higher sale price of first-cross ewes at weaning. Maternal nutrition has potential to affect many aspects of reproduction outcomes including ovulation rate, pregnancy rate, embryo survival and sex ratio of offspring. It has been indicated that some dietary nutrients including glucose and polyunsaturated fatty acids as well as total energy could affect offspring sex ratio in different mammalian species. The influence of dietary mineral balance affect offspring sex ratio in sow and ewe. Experiments on pre- and postconception mechanisms demonstrated that these mechanisms influence the sex ratio in mouse embryos. Some studies based on theories that sperm carrying the X or Y chromosome favored different vaginal pH. Therefore, it has been suggested that the pH of the vagina at the time of fertilization may have a differential effect on X- or Y- sperm, thus affecting the sex of the offspring. Feeding a negative dietary cation- anion difference (DCAD) in prepartum dairy cows improves Ca metabolism in the peripartum cow through instigating a mild metabolic acidosis via feeding excess dietary anions. We hypothesized that feeding diet with negative DCAD around mating would decrase the pH of veginal fluid and subsequently might affect lamb sex ratio in Kurdish ewes. Therfore, the aim of this experiment was to investigate the effect of dietary DCAD of flushing diet around mating on plasma metabolites and hormones concentrations and reproductive performance of Kurdish ewes as well as lamb sex ratio.

 Eighty four Kurdish ewes with average BW of 40±5 kg, BCS of 2.75±0.25 and 2-4 years were used. Ewes were divided into two similar groups and randomly assigned to experimental diets. Experimental diets consisted of 1- cationic diet (diet with DCAD of +193 mEq/kg of DM) and 2- anionic diet (diet with DCAD of -21 mEq/kg of DM). Ewes fed experimental diets from 2 weeks before estrous synchronization till 3 weeks after mating. Estrous of ewes were synchronized by 9-d intravaginal sponge and intramuscular injection of 5 mL vetaroline at the day of sponge removal. Blood samples were collected from jugular vein using 10-mL evacuated tube containing sodium heparin at the day before the beginning of experiment, at the day of sponge removal and at the day of estrous and mating. Plasma concentrations of total cholesterol, total protein, urea nitrogen, glucose, triglyceride, insulin, progesterone, estradiol, testosterone, calcium, magnesium, potassium and sodium were determined.

 Experimental diets had no effect on estrous response, fertility rate, lambing rate, twining rate and birth BW and sex of lambs. Ewes fed anionic diet had higher plasma progesterone and lower estradiol levels at the days of sponge removal and estrous than those fed cationic diet (P<0.05). Plasma concentrations of total protein, glucose, sodium, potassium, calcium and magnesium did not influence by DCAD of flushing diet. Whereas, feeding anionic diet around mating decreased plasma concentration of total cholesterol and triglyceride and increased urea nitrogen (P<0.05).

 According to these results, feeding flushing diet with different DCAD around mating had no effect on lamb sex ratio in Kurdish ewes.

Birth weight is the most important factor affecting lamb survival, but even when birth weight is appropriate, some lambs are lost to weaning. Infectious diseases are the most important factors affecting the mortality of lambs before weaning. Therefore, any factor that reduces the prevalence of these infections has a positive effect on the survival of lambs and improves the reproductive performance of the flock. The structure of the placenta in ruminant animals prevents the transfer of immunoglobulins from maternal circulation to the fetus. Therefore, newborn ruminants are completely dependent on the absorption of immunoglobulins from the mother's colostrum after birth. Consuming a sufficient amount of high-quality colostrum at the right time is the most important management factor affecting the survival and health of newborn ruminants. Colostrum also affects the survival of lambs by providing nutrients necessary for metabolism and heat production. Fat-soluble vitamins (A, D3, and E) are among the important components of colostrum and their concentrations are higher in colostrum compared to milk. These vitamins play an important role in improving the immune system of ruminant animals. Many genetic and non-genetic factors such as animal breed, mother's age, nutrition of dam in late pregnancy, herd vaccination program, colostrum volume, and colostrum collection time after parturition affect the quantity and quality of colostrum in ruminant animals. Nutrition status in late pregnancy is the most important factor affecting the quantity and quality of colostrum produced in these animals. Therefore, an insufficient supply of vitamins in pregnant ewes is one of the reasons for reducing the survival and mortality of newborn lambs. Much research has been conducted regarding the effect of dietary or injectable vitamin A, D3, and E supplements in late pregnancy on the maternal immune system and the survival of newborn ruminants, although, they have mainly focused on vitamin E and selenium supplements. To our knowledge, there is no information on how the timing of the use of these vitamins in late pregnancy affects the metabolic responses of ruminants. Therefore, this experiment aimed to investigate the effect of time and amount of vitamin AD3E injection in late pregnancy on colostrum quality and plasma metabolites of Afshari ewes and their lambs. Forty Afshari mature ewes with an average of 45 kg and 2-3 years of age were used. One month before the expected lambing, animals were divided into four groups and randomly assigned to experimental treatments. Experimental treatments were: 1. No injection of vitamin AD3E (Control; C), 2. Injection of 10 mL of vitamin AD3E four weeks before the expected lambing, 3. Injection of 10 mL of vitamin AD3E two weeks before the expected lambing, and 4. Injection of five mL of vitamin AD3E four weeks and five mL two weeks before the expected lambing. Blood samples of ewes and lambs were collected four and one week before the expected lambing and three days after colostrum consumption, respectively. Plasma was separated and stored at -20 ◦C for metabolites’ measurement. Samples of colostrum from all animals were collected and stored at 3-5 ◦C for determining chemical composition and BRIX index. Results showed that the greatest plasma concentrations of glucose and malondialdehyde (MDA) on day 7 before lambing were observed in ewes of the C groups (P<0.05). Experimental treatments did not affect plasma total cholesterol (TCh), triglyceride (TG), and magnesium (Mg) concentrations of ewes on day 7 before lambing (P>0.05). Plasma concentration of total protein (TP), calcium (Ca), and BRIX index on day 7 before lambing were higher in ewes who received vitamin AD3E compared to the C group (P<0.05). Ewes received 10 mL of vitamin AD3E two weeks before the expected lambing had the highest plasma glutathione peroxidase (GPX), superoxide dismutase (SOD), and total antioxidant activities on day 7 before lambing (P<0.05). Colostrum fat and lactose percentage were not influenced by experimental treatments (P>0.05). Whereas, colostrum protein percentage tended to be lower for ewes in the C group (P=0.08). The lowest colostrum BRIX index was observed in the ewes of the C group (P<0.05). The lowest plasma glucose concentration was observed in lambs born from ewes of the C group (P<0.05). Experimental treatments did not affect plasma TCh, TG, Ca, and Mg concentrations of lambs (P>0.05). Lambs born from ewes received 10 mL of vitamin AD3E two weeks before lambing had the highest plasma GPX, SOD, and total antioxidant activities compared to other groups (P<0.05). Vitamin AD3E injection increased the plasma BRIX index of lambs compared to the group without injection (P<0.05). The results showed that injection of vitamin AD3E two weeks before lambing increased plasma TP concentration and antioxidant activity of ewes, as well as colostrum TP content, and consequently increased plasma TP concentration and antioxidant activity of lambs. Therefore, this can be an effective strategy to improve lamb survival and performance.

Genomic selection has provided the dairy industry with a powerful tool to increase genetic gains on economically important traits such as milk production (Taylor et al. 2016). One way to identify new loci and confirm existing QTL is through genome-wide association analysis (GWAA). In addition identifying of genes loci with large effects on economically important traits, has been one of the important goal to dairy cattle breeding. QTL assisted selection and genomic regions affecting the production traits have been considered to increase the efficiency of selection and improve production performance. Genome wide association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. A solution to tackle the aforementioned problems, and deepen the understanding of the genetic background of complex traits, is to move up the analysis from the SNP to the gene and gene-set levels. In a gene-set analysis, a group of related genes that harbor significant SNP previously identified in GWAS, is tested for over-representation in a specific pathway.

The present study aimed to conduct a genome wide association studies (GWAS) based on Gene-set enrichment analysis for identifying the loci associated with milk protein composition traits. For each cow, a total of eight traits including protein yield, protein percentage, αs1-casein, αs2-casein, β-casein, κ-casein, α-lactalbumin and β-lactoglobulin were recorded using plink software and no any correction to adjust the error rate. The gene set analysis consists basically in three different steps: (1) the assignment of SNPs to genes, (2) the assignment of genes to functional categories, and finally (3) the association analysis between each functional category and the phenotype of interest. In brief, for each trait, nominal P-values < 0.05 from the GWAS analyses were used to identify significant SNP. Using the biomaRt R package the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 kb up- and downstream of the gene, to include SNP located in regulatory regions. For the assignment of the genes to functional categories, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases were used. The GO database designates biological descriptors to genes based on attributes of their encoded products and it is further partitioned into 3 components: biological process, molecular function, and cellular component. The KEGG pathway database contains metabolic and regulatory pathways, representing the actual knowledge on molecular interactions and reaction networks. Finally, a Fisher’s exact test was performed to test for overrepresentation of the significant genes for each gene-set. The gene enrichment analysis was performed with the goseq R package. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in BioMart, Panther, DAVID and GeneCards databases.

Gene set enrichment analysis has proven to be a great complement of genome-wide association analysis (Gambra et al., 2013; Abdalla et al., 2016). Among available gene set databases, GO is probably the most popular, whereas KEGG is a relatively new tool that is gaining ground in livestock genomics (Morota et al., 2015, 2016). We had hypothesized that the use of gene set information could improve prediction. However, neither of the gene set SNP classes outperformed the standard whole-genome approach. Gene sets have been primarily developed using data from model organisms, such as mice and flies, so it is possible that some of the genes included in these terms are irrelevant for milk production. It is likely that a better understanding of the biology underlying milk production specifically, plus an advance in the annotation of the bovine genome, can provide new opportunities for predicting production using gene set information. According to gene set enrichment analysis, 20 categories from gene ontology and KEGG pathway were associated with the related to traits (P˂0.05). Among those categories, the Oxytocin signaling pathway, Glycerolipid metabolism, Response to progesterone, detection of calcium ion, Complement and coagulation cascades and amino acid binding including candidate genes CDH13, P4HTM, SPP1, CSN1S1, CSN2, SERPINA1, SLC35A3, ODC1 and PAEP have significant association with protein yield and content, phosphorylation of glycoproteins, coagulation and curd firming milk and lactose synthesis. Some of these regulatory regions, such as enhancers, are located far from the genes. Therefore, although the gene might be part of the analysis, the relevant variant would probably not be included in the gene set SNP class. Finally, linkage disequilibrium interferes with the use of biological information in prediction because irrelevant regions (regions without any biological role) capture part of the information encoded in relevant regions, causing both regions to exhibit similar predictive abilities. The use of very high density SNP data or even whole genome sequence data could alleviate some of these issues.Finally, it is worth noting that our gene-set enrichment analysis was conducted using a panel of SNP obtained from a single marker regression GWAS, which relies on a simplified theory of the genomic background of traits, without considering for instance the joint effect of SNP. Hence, other approaches (e.g., GWAS exploring SNP by SNP interactions) might provide a better basis for biological pathway analysis.

Our finding showed a genetic selection potential for improving milk quality to milk protein composition per animal. Since genetic improvements are heritable, cumulative, and permanent, this improvement would be permanent and beneficial.Keywords: pathway analysis, casein, α-lactalbumin, β-lactoglobulin, candidate gene

Identifying of genes with large effects on economically important traits, has been one of the important goal to sheep breeding. Over recent years, advances in DNA-based marker technology have made it possible to identify genomic regions or quantitative trait loci (QTLs) underlying complex traits, such as fleece traits, in sheep. The present study aimed to conduct a genome wide association studies (GWAS) based on gene-set enrichment analysis for identifying the loci associated with wool traits in native Zandi sheep using the 50K arrays.
A total of 300 Iranian Zandi sheep used in this study came from the Zandi sheep breeding station. Wool sampling coincided with the maximum wool growth prior to the shearing of wool. In order to facilitate sampling, sheep were restrained in a lateral position and true wool from the left mid-side site was cut from a 5×5 cm2 close to the skin using regular scissors. Each sample was separately packaged and labeled with ear tag number of the sheep. We measured and recorded four wool production traits: staple length (SL), mean fiber diameter (MFD), fiber diameter coefficient of variation (CVFD), and the proportion of fiber that are equal or more than 30 µm (PR), kemp percentage (KEMP%) and outer coat fiber (OCF) were measured. Genomic DNA extraction from sheep blood was performed by the applying a modified salting out protocol and genotyping of the Sheep SNPChip 50 K SNP Bead from Illumina Inc. The gene set analysis consists basically in three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories, and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study was performed with wool traits using GEMMA software. Using the biomaRt2 R package, the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 50 kb up- and downstream of the gene and bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases. The GO database designates biological descriptors to genes based on attributes of their encoded products and it is further partitioned into 3 components: biological process, molecular function, and cellular component. The KEGG pathway database contains metabolic and regulatory pathways, representing the actual knowledge on molecular interactions and reaction networks. Finally, a Fisher’s exact test was performed to test for overrepresentation of the significant genes for each gene-set. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in GeneCards databases.
The result from genomic control showed weak population stratification with for woot traits among Zandi sheep population. We identified different sets of candidate genes related to wool traits including: CEP290, PRKCZ, TMTC3, RHPN2, TNFSF4, NLGN1, SPHKAP, PLCE1, FAT1 and PIK3R4 in Zandi sheep. Some of the found genes, are consistent with some of the previous studies related to reproductive traits. According to pathway analysis, 21 pathways from gene ontology and biological pathways were associated with the wool traits (P˂0.05).  Some of the genes were found are consistent with some prior studies and to be involved biological pathways related to hair follicle development, keratinocytes differentiation, synthesizes an enzyme of threonine kinases, development of epidermal and Wnt signaling pathway.
In total, this study supported previous results from GWAS of wool traits, also revealed additional regions in the sheep genome associated with these economically important traits. These findings could potentially be useful for genetic selection in the breeding programs and can be used to understand the genetic mechanism controlling this trait.

The number of teat is an important trait in relation to the maternal ability of high litter size sheeps, it is important to know the genetic function and controlling positions of this trait in the genomes of different species. High litter size domestic animals are potentially dependent on colostrum-derived immunoglobulins due to placental structure in the early hours of life. Therefore, the number of teat plays a critical role when there are more offspring born at birth than the number of teats. In some cases, particularly the number of the extra teat and even their position is very important. A method to identify new loci and confirm existing QTL is through genome-wide association studies (GWAS). QTL assisted selection and genomic regions affecting the production traits have been considered to increase the efficiency of selection and improve production performance. Genome wide association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. A solution to tackle the aforementioned problems, and deepen the understanding of the genetic background of complex traits, is to move up the analysis from the SNP to the gene and gene-set levels. In a gene-set analysis, a group of related genes that harbor significant SNP previously identified in GWAS, is tested for over-representation in a specific pathway. The present study aimed to conduct a genome wide association studies (GWAS) based on Gene-set enrichment analysis for identifying the loci associated with teat number trait using the high-density SNPs.

Hu sheep, a descendant of Mongolian sheep, is a famous lambing breed in China. In ewes of the Hu sheep, TT (individuals with two normal teats) and MT (individuals with two normal teats and one or two supernumerary teats) account for 76–62% and 38–24% respectively. For MT ewes, the supernumerary teats are smaller than the normal teats, but some can produce milk. In the current study, we analyzed the complex genetic mechanism of differences in teat number using single-locus GWAS in a total of 160 Hu sheep. The gene set analysis basically consists of three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories, and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study was performed with birth weight and biometric traits using GEMMA software. Using the biomaRt2 R package, the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 25 kb up- and downstream of the gene. For the assignment of the genes to functional categories, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases were used. The GO database designates biological descriptors to genes based on attributes of their encoded products and it is further partitioned into 3 components: biological process, molecular function, and cellular component. The KEGG pathway database contains metabolic and regulatory pathways, representing the actual knowledge on molecular interactions and reaction networks. Finally, a Fisher’s exact test was performed to test for overrepresentation of the significant genes for each gene-set. The gene enrichment analysis was performed with the goseq R package. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in BioMart, Panther, DAVID and GeneCards databases.

Gene set enrichment analysis has proven to be a great complement of genome-wide association analysis (Gambra et al., 2013; Abdalla et al., 2016). Among available gene set databases, GO is probably the most popular, whereas KEGG is a relatively new tool that is gaining ground in livestock genomics (Morota et al., 2015, 2016). We had hypothesized that the use of gene set information could improve prediction. However, neither of the gene set SNP classes outperformed the standard whole-genome approach. Gene sets have been primarily developed using data from model organisms, such as mice and flies, so it is possible that some of the genes included in these terms are irrelevant for meat production. A better understanding of the biology underlying meat production specifically, and an advance in the annotation of the ovine genome, can provide new opportunities for predicting production using gene set information.In this research, 7 SNP markers on chromosomes 3, 5, 7, 8, 12, 14 and 17 located in CDH11, NUMB, FGF2, ESR1, LGR5, INSR and PTGS2 genes were identified. Some of the found genes, are consistent with some of the previous studies related to teat number traits. According to pathway analysis, 11 pathways from gene ontology and biological pathways were associated with teat number (P˂0.05). Among these pathways, Blastocyst development, Mesenchymal cell development, Developmental growth involved in morphogenesis, Muscle cell differentiation and AMPK signaling pathway have important functions in development of mammary gland and activation of the AMPK signaling pathway. Finally, it is worth noting that our gene-set enrichment analysis was conducted using a panel of SNP obtained from a single marker regression GWAS, which relies on a simplified theory of the genomic background of traits, without considering the joint effect of SNP. Hence, other approaches (e.g., GWAS exploring SNP by SNP interactions) might provide a better basis for biological pathway analysis.

In total, this study supported previous results from GWAS of teat number, also revealed additional regions in the sheep genome associated with these economically important trait. Using these findings could potentially be useful for genetic selection in the breeding programs.

The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Run of homozygosity one of the most methods were used to detecting the genomic inbreeding. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable.

In this research, the amount of genomic inbreeding and the effective size of the population were investigated using the information obtained from 879 goats of different breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. 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 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 827 goats were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. The effective population size (Ne) was calculated from linkage disequilibrium data with SNeP software (version 1.1). GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.

The lowest and highest inbreeding coefficient calculated by three methods (FGRM, FHOM, and FUNI) were related to Beetal and Barbari breed, respectively. The highest (0.159) and lowest (0.028) amount of FROH was estimated in the Barbari and Pothwari breeds, respectively. The average length of ROH ranged from 70.2 to 391.4 Mb, and the average number of ROH fragments varied between 8.19 and 48.65. Also, the highest and lowest number of ROH were observed on chromosome 2 and 29, respectively. The size of Ne in in the current generations (fifth generation) of the studied breeds was ranged from 35 to 365. The highest Ne was estimated in the Beetal breed (365 heads) and the lowest in the Barbari breed (35 heads). The average inbreeding coefficient in Beetal, Teddi, Pahari, Nachi, Barbari, Daira Deen Panah and Pothwari breeds was obtained 0.035, 0.081, 0.031, 0.052, 0.15, 0.11 and 0.02, respectively. In addition, the Ne of most of the studied populations has been decreased. The results of this study revealed that, the selection processes in different goat breeds for economic traits during several years, has led to the formation of many ROH islands in goat genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.

our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study goat breeds. Therefore, it is necessary to economize production and planning a suitable mating scheme to control inbreeding and genetically conserve the remaining pure animals of these breeds.

In this study, assessed genomic prediction accuracies based on different selection methods (phenotypic and estimated breeding value), evaluation procedures (GBLUP and ssGBLUP),training population (TP) sizes, heritability (h2) levels, marker densities and pedigree error (PE) rates in a simulated population. QMSim software was used to create a reference database of 1000 and number of animals was reduced to 200 (100 males and 100 females) during 95 generations to create LD and mutation-drift equilibrium. The heritability of the trait was 0.1, 0.3 and 0.5 and the marker density was simulated for three strategies of 1, 5 and 10 K. The proportions of errors substituted were 10%, 20% and 30%, respectively.The results of this study showed that, compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection.With increasing reference population size and trait heritability, genomic prediction accuracy increased in all strategies.When errors were introduced into the pedigree dataset from 0 to 30%, the prediction accuracies were only minimally influenced across all scenarios.Our study suggests that the use of ssGBLUP, EBV sThe results of this study showed that, compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection.With increasing reference population size and trait heritability, genomic prediction accuracy increased in all strategies.When errors were introduced into the pedigree dataset from 0 to 30%, the prediction accuracies were only minimally influenced across all scenarios.Our study suggests that the use of ssGBLUP, EBV selection, and high marker density could help improve genetic gainseven in the case of pedigree error in cattle.election, and high marker density could help improve genetic gainseven in the case of pedigree error in cattle.The results of this study showed that, compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection.With increasing reference population size and trait heritability, genomic prediction accuracy increased in all strategies.When errors were introduced into the pedigree dataset from 0 to 30%, the prediction accuracies were only minimally influenced across all scenarios.Our study suggests that the use of ssGBLUP, EBV selection, and high marker density could help improve genetic gainseven in the case of pedigree error in cattle.

Guar gum is a galactomannan compound and is anti-nutrient in high amounts and can have prebiotic properties in low amounts in the diet, β-mannanase enzyme reduces its anti-nutrient state by reducing the molecular weight of this compound. Protein is the most expensive component of the diet, which is mostly provided provided by soybean meal in commercial diets. Due to the high cost and limited soybean cultivation area, numerous studies have been carried out on the use of other vegetable meals such as guar meal in chicken nutrition. Cyamopsis tetragonoloba is a drought-tolerant legume that is used primarily in the chewing gum industry because its seeds contain large amounts of guar gum. Guar gum is extracted from the seeds of the guar plant; it is a natural nonionic branched polymer in which the -D-mannopyranosyl unit is attached to 1-4 and the unit a-half pyranosyl unit is used as the side chain takes place. Guar has been used in many applications such as thickeners, ion exchange resins, suspending agents, pharmaceuticals and paper (Wang and Wang, 2009). In order to produce gums, the guar seeds are split, producing a high protein germ fraction and a low protein shell fraction as by-products. These two fractions are typically recombined to produce guar meal with a crude protein level of 35-47.5%, depending on the relative concentrations of the two fractions (Chenault et al., 2002). In addition, approximately 88% of the nitrogen content is true protein, making it possible to use as a component of poultry feed (Lee et al, 2003a). The purpose of this study was to evaluate the different levels of guar gum and with and without addition of β-mannanase enzyme on the performance and immune response of broilers.

For this reason, 312 Ross-308 broiler chickens from 1 to 42 days of age were used based on a completely randomized design with 6 treatments and 4 replicates (13 broiler chicks in each replicate). The six experimental treatments were as follows: corn–soybean meal basal diet:1) control diet, 2) control diet + supplements Fermacto (0.18%), 3) control diet + low gum (0.35%), 4) control diet + high gum (0.70%), 5) control diet + low gum (0.35 percent) + β-mannanase enzyme, 6) control diet + high gum (0.70 percent) + β-mannanase enzyme. Feed intake (FI), body weight gain (BWG) and feed conversion ratio (FCR) were recorded at the end of the period. Two chicks per dietary replicate were injected (32 d.) with either 0.5 mL of 2.5 % SRBC intramuscularly into each breast muscle. Heparinized blood was collected from the wing vein at (39 d.) by venipuncture 6 and 12 d after immunization with SRBC. Samples were frozen at -20°C until analysis. The hemagglutination assays were performed as described by Cheema et al (2003) for RBC. In order to enumerate the Lactobacilli and Escherichia coli on day 42 of breeding period, one chick was selected from each replicate according to protocol described by Corduk et al (2008). The data were analyzed in a completely randomized design by ANOVA using the General Linear Model (GLM) procedure of SAS Institute.

The results showed that the highest feed conversion ratio was seen in high gum 0.70% diet (no- enzyme) and the lowest one was in low gum diet (with enzyme). In agreement with the results of this experiment, Justina et al (2018) showed that chicks fed with high soybean meal and high soybean meal + guar gum diets with added β-mannanase significantly improved blood glucose and anabolic hormone homeostasis, FCR, digestible energy, and digestible amino acids compared to chicks fed with same diets without β-mannanase. The results of this experiment showed that there was no significant difference in IgG and IgM antibody titers between treatments. Unlike our results, the addition of β-mannanase to the enhanced β-galactomannan diet eliminated most of this immune-related signal, indicating that the feed-induced immune response within jejuna was eliminated by the addition of β -mannanase. They also observed changes in specific metabolic and intestinal functional pathways of birds fed β-mannanase. These observed changes in β-mannanase-fed birds may be an enhanced performance and feed conversion mechanism observed in birds given β-mannanase in their diet (Arsenault et al 2017). The reports show that the enzymes be able to accidentally attack the cell wall polymers and thus move to the center of the polymer. Breaking down any polymer chain will significantly reduce the molecular weight of the polymer solution, thereby reducing its anti-nutritional effects (Chacher et al 2017). The dietary β-mannanase had potential to improve daily gain and feed efficiency and apparent ileal digestibility while decreasing digesta viscosity of broiler (Balasubramanian et al 2018). Mannan oligosaccharides bind to type 1 fimbriae to reduce pathogenic bacteria, increase goblet cells, thus, lead to the production of antibacterial mucus and create the conditions for the growth of beneficial bacteria, and eliminates competition. The balance between pathogenic and beneficial bacteria increases the length of the villi and decreases the depth of the crypt, which indicates an improvement in the morphology of the intestine. Improving the morphology of the intestine increases the activity of digestive enzymes and thus increases digestion. In addition, mannan oligosaccharides activate macrophages in intestinal lymphatic tissues, thereby improving cellular and humoral immunity. Mannan oligosaccharides also increase butyric acid production and decrease intestinal pH in broilers. These combined mechanisms promote the growth rate and performance of broilers (Chacher et al 2017).

According to the results, Addition of guar gum and betanamase to the diet had no effect on the performance and immune responses of broilers compared to controls. However, the addition of guar gum with the β-Mannanase enzyme increased the microbial population of jejunum and ileum lactobacilli, therefore, this is also recommended.

This study was performed to evaluate the effect of body condition score (BCS) during dry period and calving season on the incidence of metabolic disorders in Holstein cows in Isfahan province.  About 5138 birth records were extracted from different births since 1395. Data included animal number, year of calving, month of calving, length of dry period, length of gestation period, calf birth weight, calf sex, number of calves born per calving, retained placenta, dystocia, stillbirth and metritis. Data were classified into different classes, for uniformity and were analyzed by SAS software using GLIMMIX procedure. The results showed that effect of BCS changes on the incidence of metabolic disorders (retained placenta, dystocia, stillbirth and metritis) was not significant (P>0.05). The effect of parity on retained placenta, dystocia, stillbirth and metritis was significant (P<0.01). Calf birth weight had significant effect on retained placenta (birth weight less than 35 kg and more than 46 Kg), dystocia and stillbirth (calves with birth weight 46 kg) and metritis (P<0.01). Effect of dry period on the incidence of retained placenta (dry period: less than 45 days, 61-100 days and 46-60 days) and dystocia (increasing dry period from 61to 100 days) and metritis (dry period: less than 45 days, 61-100 days and 46-60 days) was significant (P<0.01). The effect of gestation length on the incidence of retained placenta was significant (P<0.01) but had no significant effect on the stillbirth (P>0.05). The effect of calving season on the incidence of retained placenta and metritis was significant (P<0.01).

The aim of this study was to investigate the effect of early nutrition on performance, humoral and cellular immunity in broilers. This experiment was conducted by use of 480 male broiler chicks (Ross 308) were randomly allocated in a completely randomized balanced design with eight treatments and four replicates and 15 birds in each replicate for 42 days. The experimental treatments were included: Normal Water + Base Diet for first 72 Hours, Normal Water + Corn Powder first 48 Hours, Water Sugar 5% + Corn Powder first 48 Hours, Water Sugar 5% + Corn Powder first 72 Hours, Water Sugar 5% + Base Diet first 48 Hours, Water Sugar 5% + basic diet for the first 72 hours, gluplus + corn meal for the first 48 hours and gluplus + basal diet for the first 48 hours. The results showed that nutritional treatments had no significant effect on antibody response against sheep red blood cells on days 21 and 42 (P>0.05). The highest average weights of 6- and 7-week old obtained in gluplus+basal diets by 2699.3 and 2827.9 grams, respectively, which did not have a significant difference with normal water + basal diet (2508.5 and 2693.2 grams) (P>0.05). According to the results of this study, nutritional treatment of water with 5% sugar and base diet is recommended due to higher daily gain, lower mortality and better production index in the first 48 hours of feeding broiler chicks.

In this research total of 288 one- day old Ross 308 broiler chickens were used in a completely randomized design with 6 treatments and four replications for 5 weeks. The experimental treatments included 1) Basal diet without additive and normal temperature conditions (negative control) 2) Basal diet without additive and heat stress conditions (positive control) 3) Basal diet with 0.18 mg/kg sodium selenite and normal temperature conditions 4) Basal diet with 0.18 mg/kg sodium selenite and heat stress conditions 5) Basal diet with 0.18 mg/kg nano-selenium and normal temperature conditions and 6) Basal diet with 0.18 mg/kg nano-selenium and heat stress conditions. The results showed that in normal temperature conditions, nano-selenium caused decrease in feed intake in comparison to sodium selenite however in heat stress conditions, both nano-selenium and sodium selenite increased feed intake when compared with control treatment (P<0.01). Also, the results of feed conversion ratio showed that the highest and lowest feed conversion ratios in all rearing periods were related to the control in heat stress conditions and nano-selenium under normal temperature conditions, respectively (P<0.01). The highest and lowest blood serum malondialdehyde, aspartate transaminase and alanine transaminase, concentrations were observed in control treatment under heat stress conditions and treatment containing nano-selenium in normal temperature conditions, respectively. Generally the results of the present study showed that the utilization of nano-selenium in heat stress conditions in diet of broiler chickens improved feed conversion ratio, increased growth and increased cellular oxidation inhibitory enzymes.

The goal of this research was to clearly elucidate the effects of centrifugation and cholesterol-loaded cyclodextrin (CLC) on a soy lecithin-based extender on post-thaw ram sperm quality. Sperm samples of 5 adult ram of Ghezel were collected for 3 weeks. After the initial assessment, the approved semen samples were combined and divided into 8 equal parts in the Falcon tube. Four samples were combined at 30°C and the seminal plasma was then removed by centrifugation. The semen from the other four tubes was not centrifuged and was diluted with Tris buffer + different concentrations of CLC (0, 0.75, 1.5, and 3 mg / 120 x 106 spermatozoa) and 7% glycerol, similar to the first group.The sample was then cooled to 5 ° C and frozen in a 0.25 ml of straws. After thawing, total motility (TM) and PM, VSL, VCL, BCF, TAC, SOD, MDA, GPX, the integrity of the acrosome membrane and the integrity of the plasma membrane were significantly (P

The use of cryopreserved semen in artificial insemination (AI) has numerous advantages for the animal husbandry, especially when used in breeding programs. Long-term storage of sperm in liquid nitrogen is a valuable technique for genetic resources preservation (Mazur et al., 2008). Animals are transported frequently and widely around the world, and it is necessary to create and maintain suitable conditions during animal transportation (Salamon and Maxwell, 2000). However, the costs, the risks of escape, and the potential for accidental death of animals are unavoidable. On the other hand, cryopreserved sperm can be transported in liquid nitrogen at a markedly lower cost and without the risk of escape or death of animals (Aires et al., 2003). Numerous investigations have been performed to improve the protocols for cryopreservation of sperm. The extenders used for semen cryopreservation protect the sperm against thermal shock, preserving both motility and fertility by promoting the stabilization of the plasma membrane, and providing energy substrates (Amirat et al., 2004). These attributes reduce the deleterious effects of changes in the pH and osmolarity, prevent the growth of bacteria, and protect the sperm cells from the damage caused by refrigeration, freezing, and thawing. For sperm cryopreservation, protocols using egg yolk have been successfully established and applied in various animal species (Aisen et al., 2002). However, the use of egg yolk in cryopreservation has been questioned, because of certain potential negative aspects. Egg yolk contains a wide variety of compounds that are both beneficial and also potentially harmful to sperm. Additionally, egg yolk introduces a risk of contamination by microbes that can subsequently produce endotoxins; and so, the egg yolk and sperm are subjected to quarantine inspection in the case of import or export. Therefore, a replacement for egg yolk with a well-defined chemical composition would be very advantageous. Lecithin, also known as phosphatidylcholine, is a component of egg yolk and is known to prevent cold shock during the freezing and thawing process in sperm cryopreservation. Soybean lecithin in particular has already been used as a replacement for egg yolk in sperm cryopreservation in various animals. Its non-animal origin and minimal sanitary risks make it preferable for this application. Soybean Lecithin can be used as an extender in the cryopreservation process (Akhter et al., 2012). The aim of this study was to evaluate the effects of Soybean Lecithin as extender on the ram semen quality after freeze-thawing. Semen was collected from the indigenous Ghezel rams. Twenty five ejaculates were collected throughout the entire study, with semen being collected twice a week (every Sunday and Tuesday) from each ram, using the artificial vagina. Ejaculates were collected in graduated test tubes, placed in a thermo flask at 34°C, and transported to the laboratory for evaluation within 1h interval. The raw or fresh undiluted semen was then microscopically evaluated for volume, concentration, and sperm motility. The sperm concentration was determined with the aid of a neubauer lam. A Computer Assisted Sperm Analysis (CASA) system was used to evaluate the different sperm motility characteristics. All data were analyzed using the statistical procedure of SAS (version 9.2). The analysis of variance (ANOVA) was used to test for significant differences between treatments. Characterization of the Ghezel ram sperm viability (percentage live/dead) of the semen samples was determined using an eosin/nigrosin stain (50μl eosin/nigrosin and 5μl semen). The volume of the ram ejaculates ranged between 0.75 and 1.5mL. The sperm concentration recorded in this study ranged between 0.9 and 1.3 × 109 sperm/mL. The effect of different soybean lecithin levels on the Ghezel ram semen characteristics following cryopreservation was evaluated. After initial evaluation of the ejaculates, all ram ejaculates were pooled and semen sample was then divided into three portions; then, semen samples were diluted with soybean lecithin (1, 1.5 and 2 %) citrate extender and cooled over a period of 2h to 5°C. The semen samples were equilibrated for 2h and then loaded into 0.25mL semen straws. The straws were frozen in liquid nitrogen (LN2) vapor, then semen straws were plunged into the LN2 (-196°C). The semen straws were thawed 30 days later, in a water bath (37°C) for 30 seconds. The sperm characteristics included motility and motion parameters, viability, plasma membrane and acrosome integrity, sperm abnormality, and lipid peroxidation were evaluated. Motility and velocity were microscopically evaluated using the Sperm Class Analyzer® (CASA) system. This study demonstrated that soybean lecithin (1.5%) containing 7% glycerol can be used to cryopreserve Ghezel ram semen effectively, based on the sperm motility characteristics. The low sperm motility results recorded when semen was cryopreserved in soybean lecithin (2%). The results showed that total motility and some sperm motion parameters (VSL, VCL, VAP and ALH) were significantly higher in 1.5% lecithin soybean treatment group (P <0.05). In terms of survival, the percentage of abnormal sperm, plasma membrane integrity, and lipid peroxidation were not significant between treatments. Acrosome membrane integrity of 1.5% soybean lecithin treatment group was higher than other treatments (P< 0.05). Briefly, 1.5% soybean lecithin treatment had better performance than other levels on the quality of the sperm after freeze-thawing.