hossein moradi shahrbabak

Due to the increasing demand for animal products, reproductive efficiency considered as one of the main objectives of sheep breeding, even in cases where the main emphasis is on milk or wool production. In cases the meat production is the main breeding objective, increasing reproductive efficiency is the most important goal of breeding programs. Although increasing fertility in ewe is possible in different pathways, ovulation rate and liter size are the main goals in breeding programs to achieve high fertility. Then, this study was performed to detection selection signature between Iranian native (as a genetic group with low reproductive performance) and Icelandic (as a genetic group with high reproductive performance) sheep breeds, and identify genes related to fecundity and litter size in sheep.

In this regard, the genomic information of 154 samples including 11 Iranian sheep breeds (Kermani, Baluchi, Afshari, Karakul, Sanjabi, SiahKabud, LoriBakhtiari, Shal, Ghezel, Chios, GrayShiraz) and 54 Iceland sheep breeds, were used. The genomic data related to these genetic groups including Icelandic and Iranian sheep breeds were obtained from the iSheep database and the address https://disk.yandex.ru/d/3N2wEv0-9_NL0w, respectively. Quality control of genomic data and filtering was performed using the PLINK software. The individuals and SNP with more than 5% missing genotypes were excluded. Then, the data were screened based on Minor allele frequency (MAF) less than 1%, and Hardy-Weinberg equilibrium (HWE). From the total available data, including 552,847 SNP markers related to autosomal chromosomes with known locations from 204 animals, finally 527,292 SNP markers from 204 animals, with about 0.999376 genotyping rate, was remained for inter-population genetic differentiation and structure analyses. Then, data filtering was done for seprate genetic groups. In this edition of the data, 527,284 SNP markers related to 174 animals were endured to selection signature analysis. Genetic differentiation index analysis (FST) and principal component analysis (PCA) were performed to determine genetic groups using PLINK 1.9 software. Ubiased FST (θ) estimator statistic were used to explore the signs of selection. In order to better identify the selection signals, numerical values of SNP markers were averaged using the creeping window method up to a maximum length of 100 kb for adjacent SNPs. Only 0.1% of the genome regions with the highest values, were identified and determined as selection signatures. The genes related to selected genomic regions was extracted using the BIOMART online database corresponding areas in the sheep genome assembly (Oar 3.1). The detected genes, related to the selected regions, were surveyed by DAVID 2021 (The Database for Annotation, Visualization and Integrated Discovery) and STRING (Version 12) to identifying biological pathways and probably gene interaction networks.

According to the principal component analysis (PCA) results, the group with high reproductive performance (Icelandic sheep) is completely separate from the genetic group with low reproductive performance (Iranian sheep breeds). The complete differentiation between two groups with low and high reproductive performance can be related to the regional separation of these two groups. Kermani and Chios breeds (from the Chios breeding center in Kerman province of Iran) are seprated from other Iranian breeds with the second component. It was confirmed by further population structure analysis, with FST analysis and phylogeny tree extracted from the genetic distance determination information. The Icelandic breed had the greatest genetic distance with other studied breed. The GrayShiraz (SDK) and Kermani had the lowest and the highest genetically distance with Icelandic breed, respectively. In order to reduce the bias in selection signatures analysis, Kermani and Chios breeds was excluded from the further analysis. The results of principal component analysis (PCA), four distinc genetic groups was detected based on the information of the 1th component with one of the 2th to 6th components. According to the obtained results, the group with high reproductive performance or litter size (Icelandic) is completely separate from the genetic group with low reproductive performance (Iranian sheep breeds). The 2th to 6th components could demonstration differences among Iranian sheep breeds, and Kermani and Chios sheep breeds (raised in the Chios breeding center in Kerman province) were separated from the Iranian other sheep breeds. In the identified regions as selection signatures (N=55), including 0.1% of all studied markers, the number of 391 genes were identified. Of all detected genes, at least 13 genes including BMPR2, SLC26A4, WNT16, CREB3L4, PRLR, ACVR2B, PRKCSH, HOXA9, HOXA10, Dkks, KATNAL1, OSBP2 and W5PHY6_SHEEP genes were related to reproductive performance and probably litter size in sheep. Although no significant biological pathways (with high significance) related to litter size in sheep were identified, some of the identified genes have major effects on reproductive performance. Detected genes from this study and other complementary studies about involved genes on litter size in sheep, could be effective in designing breeding programs to improve reproductive performance.

Survey on identified biological pathways related to genomic differences between Iranian native and Icelandic (which is considered one of the most significant multi-twin breeds in the world) sheep breeds, was shown that, the significant biological pathways involved in immunity, smell, and hemoglobin construction. Despite of the identification a large number of genes related to The reproductive performances, these genes did not involved in a significant biological pathways. However, although no significant biological pathways related to litter size in sheep were identified, some of the identified genes have major effects on reproductive performance. Detected genes from this study and other complementary studies about involved genes on litter size in sheep breeds could be effective in designing breeding programs to improve reproductive performance.

In recent years, wide access to molecular polymorphism data has increased attention to identifying patterns within the genome that indicate positive selections occurring continuously in populations. The basic view about positive selection is the phenomenon of Genetic Hitchhiking. When a beneficial allele is the target of positive selection during different times, it creates signs at the genome level and these signs can be identified and tracked by different methods. The meta-analysis of different methods of selection signature at the genome level can lead to a much more accurate identification of these signature, because each of the different methods of identifying selection signature follow different criteria for identifying marks in the genome of organisms. In fact, the purpose of performing different methods of identification of selection signature is to improve the discovery and identification by using the combination of information and increase the accuracy and precision of the results.

The number of samples in this study included 111 Thoroughbred and Turkoman horses (44 and 67 respectively). Blood samples were obtained from the veins of the vedic and subcaudal veins of horses. In this research, single nucleotide polymorphism data (SNP chips, 60k) were used. Genotyping of the samples was done using 60 K arrays from Illumina company at the University of Kentucky. To ensure the quality of the genotyped genomic data, quality control analyzes were performed with a series of filters including MAF, SNP-CR, Animal-CR, HWE test. One of the important points in identifying signature of selection is to consider subpopulations in each population, for this reason, the principal components in this section was obtained based on the kinship matrix. Principal components analysis was done in R software. In this research, Fst, iHS (EHH), Rsb methods were used to identify the selection signature, and finally meta-analysis was performed. The regions under genome selection and the genomic positions obtained from whole genome linkage studies were further investigated to find the genes present in these regions. The genes reported in these regions in horses and related regions in cattle were identified using the ENSEMBL database and based on the assembly of the latest horse genome version available from the NCBI and BioMart databases. The identification code related to the identified genes was done in DAVID software to check the biological pathways related to the selected regions.

Primary quality control was performed on 111 animals from 2 populations (67 Turkoman and 44 Thoroughbred). 3 Turkoman animals were excluded from further analysis due to the missing genotype rate of more than 9%, and finally 108 samples remained. A total of 59,349 SNP markers, 52,036 markers remained after quality control. A total of 118 SNPs were excluded due to the minimum allelic frequency of less than 1%, 704 SNPs out of Hardy-Weinberg equilibrium, 6493 SNPs with a missing genotype rate greater than 5%. The results of PCA analysis show that the samples examined in this study were placed in two completely separate groups. Finally, 5 regions on the genome were selected for further investigation. 5 regions with theta value higher than 0.28 between Turkmen and Thoroughbred horse breeds are located on chromosomes 4, 5, 10, 13, and 15, respectively. The highest number of selected markers were located on chromosome 5, and the lowest number of identified markers were located on chromosomes 13 and 15. According to the results obtained from the iHS analysis, the number of 8 and 23 snps, in Thoroughbred and Turkmen breeds had the highest iHS value respectively, and the number of 3, 2, 2, 1 snps were respectively on chromosomes 28, 21, 1 and The highest iHS value is for the BIEC2_548092 snp located on chromosome 21 of this breed. The results of meta-analysis showed that these regions are located on chromosomes 10, 12, 14, 15, 16, 17, 32. Rsb analysis was performed between two populations of Thoroughbred and Turkoman horses, and the results showed that selection markers are located on chromosomes 12, 16, 17, 31, 32. After examining the genes in the obtained regions, the most important genes were involved in glycosylation, cellular response to stress, metabolic process of cellular macromolecules, repair of broken peptides.

The present research, taking into account the various methods of identifying selection marks in Turkmen and Thoroughbred horses and combining the results of each of the methods, implements a new approach to infer the positive points of selection marks in the horse genome. From the results of this research, it can be concluded that the combination of methods to identify the signs of selection increases the strength and accuracy of the results. Also, the genes identified in this research are involved in important pathways such as glycosylation, cellular response to stress, metabolic process of peptides and organization of protein subunits, cellular macromolecules catabolic process and extracellular transport.

In order to identify genes related to reproductive performance under divergent selection in Iranian indigenous and high reproductive performance Romanov sheep breeds, the genomic data of 233 sheep were used. The genomeic data of Romanov sheep were obtained from the iSheep database and the genomic data of Iranian sheep was achieved from the database at https://disk.yandex.ru/d/3N2wEv0-9_NL0w. Data filtering and quality control, genetic differentiation index analysis (FST) and principal component analysis (PCA) were performed to determine genetic groups using PLINK 1.9 software. Following the final filtering, the genomic information of 488,752 common SNPs from autosomal chromosomes of 79 Romanov heads compared to 120 heads of nine Iranian indigenous sheep breeds to screening signature of selection. The ubiased FST (θ) estimator and XPEHH statistic were used to explore the signs of selection. The genes related to selected genomic regions were extracted using the BIOMART online database corresponding to areas in the sheep genome assembly (Oar 3.1). A total of 489 genes associated with the selected genomic regions (consisting of 0.1% of the studied markers) were identified. Investigation of the genomic regions under selection showed that out of all the identified genes related to the difference between the two studied groups, 7 genes were involved in biological pathways related to steroid synthesis and ovarian steroidogenesis that may be associated with litter size. Identifying this pathway and other complementary studies about genes involved in reproduction could be effective in designing breeding programs to improve reproductive performance.

One of the principal and challenging animal studies in population genetics is to identify the signs of selection to improve economic traits and reduce diseases. Johne's disease is an incurable chronic bacterial infection that primarily affects the lower parts of the small intestine of ruminants, although its pathology and symptoms vary among species. The economic consequences of Johne's disease include reduced production, loss of genetic value, increased sensitivity to other diseases, increased interval between calving, weight loss, reduced carcass value, reduced fertility (due to reduced serum progesterone formation and corpus luteum), decreased quality and quantity of milk (decreasing fat and protein and increasing somatic cells in milk), and premature elimination. According to the results of new research, this bacterium may be a zoonotic pathogen that plays a role in causing Crohn's disease (a chronic inflammatory bowel disease (IBD)) in humans. Even after milk pasteurization, this pathogen remains alive and is therefore a threat to the health of society. This disease is one of the main diseases economically and one of the most prevalent diseases, causing great economic damage to the livestock industry worldwide. In this study, an extensive genome-wide scan was performed using single nucleotide polymorphisms (SNPs) to identify the signs of selection between populations of Holstein cows affected by Johne's disease and healthy animals.

In this study, 145 Holstein cows of the Feka cattle farm in Isfahan were genotyped based on Illumina 30K chips. Cows were grouped into two sick and healthy groups, with 45 and 100 cows, respectively. Quality control indicators included the animal read rate (mind), SNP read rate (geno), rare allele frequency (MAF), and Hardy-Weinberg equilibrium. To identify important metabolic pathways, ClueGo (version 2.5.6) was used in Cytoscape software, which provides biological interpretations of genes. In this study, two statistics, iHS and RSB, were used to identify the signs of selection.

Using iHS statistics, 63 and 70 genes were identified in the diseased and healthy populations of Holstein cows, respectively. The important genes identified by iHS statistics included HCN2, DOCK4, ITGA8, and STAG1 in the patient population, and CAV2, CNTNAP4, MIB1, and TTC23 in the healthy population. After examining the selected regions, 39 and 53 genes were identified in the diseased and healthy populations of Holstein cows with RSB statistics. The important genes identified by RSB statistics included GRID2, PPIP5K2, and CTNNA2 in the patient population, and  DOCK1, PCDH9, and AK1 in the healthy population.

In the present study, the results of the iHS statistics showed that 84 and 96 genomic regions were under selection in the healthy and patient populations, as well as 152 and 129 genomic regions in the healthy and patient populations using the RSB statistics. Most of the genes identified in this study were related to immunity, cancer, bacterial invasion of cells, cell aging, cell response, growth, and cell adhesion, which are among the important biological traits and characteristics of living organisms. By identifying possible candidate genes related to and resistance to Johne's disease in cattle, this information can be used in breeding programs (selection to reduce or increase the expression and frequency of important genes) for Holstein cows in Iran. However, due to the incomplete information related to the function of the genes in cattle species and the small population used in this study, more extensive studies with more samples and the analysis of several separate populations will provide a better understanding of candidate genes for Johne's disease in the cattle population.

Nowadays, with the progress obtained in molecular genetic techniques and bioinformatics, alternative methods have been invented to increase the speed and efficiency of DNA sequencing and their roles in genome level.  In the whole-genome sequencing method, the whole genome sequence of organism (nuclear-genome with mitochondrial DNA) is sequenced. One of the important topics in genomics is genome differences, including single-nucleotide polymorphisms and INDELs for the relationship between genotype and phenotype. Polymorphisms are powerful tools for molecular analysis of economic traits and are important in breeding programs. For this purpose, whole-genome variations of Mazandarani buffaloes were identified and classified. In this study, the whole-genome of 4 Mazandarani buffaloes was sequenced with the Illumina platform. Data quality was measured by FastQC software. BWA-MEM was used for alignment with reference genome. Finally, the variants were obtained using freebayes and the SnpEff was used to calculate the effects of the variants. The result of aligning led us to identification of 56537534 SNPs, and 6128529 indels with an average coverage of x4 to x13. The most number of variants were observed on 1 and X chromosomes, and the least number were in 23 and mitochondrial chromosomes. The transition, transversion and rate of transition/transversion mutations were 236549743, 108015966 and 2/19 respectively. Also, the mutations was calculated. The frequency of variants in intergenic regions was estimated to be 52746727, intron 23560994, downstream 3713594, upstream 3571409 and exon 574093. Considering that this research is the only one that carried out to identify the genomic variations of Mazandarani buffalo, the identified genomic variations can be used for the development of SNP-arrays for Iranian breeds.

Bovine Leukemia Virus (BLV) infection is more common in dairy cattle herds. The main cause of leukosis is the disease that leads to the creation of cancerous lymphocytes in different organisms of the body and affects different species, including cattle. This disease reduces milk production and causes reproductive diseases, and finally the removal of infected animals. Due to trade restrictions and deaths caused by lymphosarcoma, it causes direct economic losses, which is also related to the decrease in milk production and the increase in the elimination rate. No treatment or vaccine is known for this disease so far. Therfore, studying the genomic regions related to susceptibility to BLV infection can be effective in controlling and treating this disease and genetic improvement of animals. This research aimed to perform a whole genom-wide association study (GWAS) study of cattle to identify genomic regions and candidate genes associated with BLV infection.

Material and Methods:

 This study was conducted using Holstein cows that were naturally infected with BLV. For this purpose, blood samples of 150 Holstein cows in an industrial dairy cattle farm in Isfahan were collected, and DNA and serum of them were extracted. The prepared DNA samples were genotyped using k30 microarrays (SNPchip30k) (by Illumina). Quality control of sequences for rare allele frequency components (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1×10-6) and significance test was performed by PLINK software. Analysis of the ontology of genes was done by the online database https://www.Uniprot.org and finally, the ontology diagram of genes was drawn and analyzed by the online database PANTHER.

After control analyzing, 145 cows (77 cases and 68 controls) and 22868 markers were left for further analysis, finally 8 markers higher than the significant threshold were identified, and most significant markers were located on chromosomes 17 and 21. Using ensemble sites and genecards, genes associated with significant selected markers were identified. The most important of them were GRK4, TP53BP1, SCAPER, GLRB, PDGFC, TNIP2, PSTPIP1, CEP350, MR1, TOM1L2, SREBF1, COPS and TNFRS13B. Gene Ontology (GO) analysis showed that these genes are more involved in protein-coding and play a role in regulating enzyme activities, intercellular exchanges, DNA stability, calcium activity, nervous system, and lipid activity. Also, according to other research, these genes played a role in cases such as infectious poison lesions, subclinical ketosis disease, BCS of cattle, fatty acid metabolism and fat deposition, various infections such as mastitis, and in meat traits and muscle stiffness in beef cattle. It should be noted that some of these genes were related to the pathways of innate immunity, humoral immunity, and cancer tumors.

Therefore, it can be concluded that whole genome wide association study analysis as well as gene ontology analysis to identify genomic regions related to viral infections such as leukemia can be effective in designing treatment methods and prevention methods and in choosing Genomics and breeding programs in Iranian dairy cows.

Selection as a factor increases the frequency of positive mutations in some subpopulations and creates selection signatures in the genome. Identifying the selection signatures in animals aimed at promoting economic traits and reducing diseases is one of the main and most challenging research areas in population genetics. This study aimed to conduct an extensive genome scan using single nucleotide polymorphisms (SNPs) to identify genomic regions under positive selection between diseased and healthy Holstein cattle populations. The data included 145 Holstein cows from Foka. These cows were genotyped using Illumina 30K chips. The cows were divided into diseased (45 cows) and healthy (100 cows) groups. FST and XP-EHH statistics were used in this study to identify genomic regions under selection. The genes identified by FST statistics in both diseased and healthy populations included RAB37, ZC3H10, ESR1, HSD17B6, KCNC4, and ERBB3. Genes identified by XP-EHH statistics in both diseased and healthy populations included AK1, ATP8A1, BTBD1, C1GALT1, CCDC6, CEP295, CLGN, CLSTN2, EHHADH, ERBB4, FRK, GRID2, GRIP1, and LRP6. Most of the genes identified in this study were related to immunity, diseases such as cancer, lactation, skeletal muscles, estrous cycle, feed consumption, sperm adhesion, and growth, which are among the important biological traits and characteristics of living organisms. Further research using an increased sample size in the population will provide a better understanding of candidate genes for ion disease in cattle. Moreover, the design of successful breeding programs will help reduce the costs associated with this disease.

First lambing age and lambing interval are among the most important reproductive traits affecting profitability of sheep breeding systems. The present study aimed to conduct a genome wide association studies (GWAS) for identifying the loci associated with first lambing age and lambing interval in Zandi native sheep using the 50K arrays.

For this purpose, phenotypes records and genotypic data related to first lambing age and lambing interval were obtained from 96 Zandi sheep. Different steps of quality control and identification of independent SNP markers were performed by PLINK software. After quality control, 94 animals and 36070 markers were identified for further analysis. Genome wide association study was performed with reproductive traits using GEMMA software. Using the Genome Data Viewer software from NCBI database based on last assembly (ARS-UI_Ramb_v2.0) the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 300 kb up- and downstream of the gene. Finally, from online bioinformatics databases for the assignment of the genes to functional categories, DAVID and PANTHER databases were used.

In this research, seven SNP markers on chromosomes 1, 2, 3, 6, 11 and 23 were identified. Also, we identified different sets of candidate genes related to reproductive traits: UMPS, ITGB, SMARCAL1, APAF1, UGT8 and ST8SIA5 in Zandi sheep. Some of the found genes, are consistent with some of the previous studies related to reproductive traits. Some of the genes were found are consistent with some previous studies and to be involved biological pathways related to fertilization, ovulation rate, estrogen biosynthesis, conception rate, skeletal muscle development, early development of the fetus and puberty.

The results of our research can be used to understand the genetic mechanism controlling reproductive traits and considering, this study supported previous results from GWAS of reproductive traits, also revealed additional regions, using these findings could potentially be useful for genetic selection in sheep for age at first lambing.

When continuous selection is carried out over years, it creates effects on the genome level, which can be detected by using some strategies. This study was carried out with the aim of scanning the whole genome to identify regions of the genome in Thoroughbred and Turkoman horses that have been targeted by natural or artificial selection.

DNA was extracted from blood samples using the optimal salt method. The quality and quantity of extracted DNA of all samples was determined by nanodrop device with absorption ratio on DNA solution. For this purpose, 44 Thoroughbred horses and 67 Turkoman horses were genotyped by genomic arrays of 60k SNP chips. By two general methods of population differentiation and linkage disequilibrium methods, the selection signatures at the genome level were looked into. In order to identify the population genetic structure of the studied animals, principal component analysis was done in R program.

The study of population differentiation using the fixation index method (Fst) corrected for the sample size (θ) showed that there are evidences of selection in several loci in these two breeds. A number of five genomic regions were identified in which there were signatures of selection. These areas are located on chromosomes 4, 5, 10, 13 and 15. In order to evaluate the signatures of selection based on linkage disequilibrium methods, the extended haplotype homozygosity test (EHH) was used. The results confirmed the existence of population segregation in these genomic regions. Finally, the investigation of QTLs in the bovine orthologous regions showed that these regions are related to the traits of body length, body weight, chest depth and other important economic traits in horses.

The present research was effective in identifying regions of the genome of the two breeds of Turkoman and Thoroughbred horses being divergently selected, and identifying the genes that exist in these regions. Also, useful information was obtained on the existence of genetic diversity and signatures of selection between these two horse breeds.

Paratuberculosis  known as Johne's disease, is a contagious, chronic, intestinal disease in ruminants, which is caused by Mycobacterium avium paratuberculosis subspecies (MAP) and causes a huge economic damage to the livestock industry. There is no effective treatment nor vaccine for MAP infection. Thus, investigating the genetic regions associated with susceptibility to MAP infection can provide a better understanding of paratuberculosis mechanisms and contribute to the genetic improvement of animals. The aim of this study was to identify genomic regions and candidate genes associated with susceptibility to MAP infection in Holstein dairy cattle using a genome-wide association study (GWAS). For this purpose, blood samples of 150 cows were collected, and DNA and serum of them were extracted.The prepared DNA samples were genotyped using bovine SNPchip30k (Illumina). Quality control of genotypes was performed based on the minor allele frequency (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1) 10-6) using PLINK software. The association was performed using a mixed linear model in PLINK software. After quality control, 28749 markers on 142 cows (99 cases and 43 controls) were remained for the further analysis. Associations analysis showed that 16 markers located in chromosomes 30 and 6, were associated with  Johne's disease. Positional candidate genes for Johne's disease were identified. The most important identified genes were LMX1A, THSD7A, ELMOD2, ATP6AP2, RNF150, SLIT3, SDE2, PARP1, PBX1, TFB2M, SMYD3 and PYCR2. Gene ontology analysis showed that most of the identified genes are involved in the nervous system, cytoskeleton system, regulation of cytokines, Golgi apparatus, catalytic activity, calcium ion transport, and resistance to diseases. Whole genome-wide association study (GWAS) and ontology analysis (GO) can help to identify candidate genes and regions related to sensitivity to MAP in dairy cows, which can play an important role in the treatment and prevention of Johne's disease.

In order to determine the effects of sodium acetate and conjugated linoleic acid (CLA) on dry matter consumed, feed digestibility, milk yield and milk fat profile, 33 Holstein cows several calving times during days 5-31 after calving in a completely randomized design with Three treatments and 11 replications were used. The experimental diets included 1- basic diet (control), 2- diet containing 300 gr of sodium acetate , 3- diet containing 100 gr of CLA. Daily dry matter intake and milk production, body weight and body condition score were measured at the beginning and end of the experiment. milk samples were taken at regular intervals to determine the amount of milk compounds. Also, on the last day, a sample was taken to determine the profile of fatty acids. Dry matter intake was not significant among dietary treatment (P>0.05). Milk production was increased by supplementing diets with sodium acetate (3.16 kg/d) and CLA (2.46 kg/d) compared to control treatment. CLA supplementing decreased milk fat content significantly and sodium acetate increased it. The yield and content of milk protein and lactose were not significantly different between the treatments. With the consumption of sodium acetate, the amount of milk fat and milk production increased, as probably the hypothesis that sodium acetate is lipogenic for adipose tissue was ignored and Acetate partition nutriunt toward milk fat production. CLA consumtion, negative energy balance did not change between as spared energy partition toward more milk yield. The use of CLA could be beneficial for the health of consumers by increasing the trans-10-cis-12 CLA isomer transfer to milk and reducing thrombogenic and atherogenic indicators.

Advances in next generation sequencing technologies have created the ability to efficiently and economically sequence the whole genome more than ever and provide the opportunity to discover and introduce multiple polymorphisms throughout the genome of organisms. Azeri buffalo is one of the most important breeds of Iran and it is scattered in the north to the northwest of the country and is completely adapted to the environmental conditions of this geographical region. The main purpose of this study is to introduce the genomic diversity of Iranian buffaloes and categorize them. Also, introducing the effects of these variations on different genomic regions of Azeri buffaloes have potential applications in breeding programs.

In this study, whole genome sequencing of 5 heads of Azeri buffaloes native to Iran was done by Illumina sequencing platform. Data quality was measured by FastQC software. BWA-MEM software was used for alignment with the reference genome. Finally, the variants were identified using freebayes and the SnpEff program was used to calculate the effects of the variants by mentioning their type, location and number. The alignment result of high quality reads with the reference genome showed that the alignment percentage for all 5 samples was over 97.5%, which indicates the high quality of short reads.The coverage in the sequenced samples was determined between 4x and 12.8x.

finally, 76,298,858 million variants were identified, including 57,921,822 SNPs, 6,162,328 indels, 10,534,042 MNPs, and 1,680,666 MIXEDs. Small deletions and insertions with a minimum length of 1 bp, a maximum length of 28 bp and an average of 1.39 bp were identified. From the total number of variants, the highest frequency of variants was observed in intergenic regions, 53,789,879 (62.022 percent), intron 24,003,682 (27.677 percent), respectively, and the variants detected in exons had the lowest number.

Identification of genome-level variations such as snps, small insertions and deletions, and multi-nucleotide polymorphisms in different populations are a valuable resource in genetic research and can be useful in locating genomic segments responsible for important economic traits. Also, the large volume of SNPs enables genome-wide association studies in animals. In addition, the genomic variations identified in the present study can be used to develop high-density SNP arrays in Iranian breeds for genetic and breeding applications.

The rapid development of sequencing technologies and bioinformatic tools has made it possible to sequence the entire genome of many species, providing a starting point for exploring the genome-wide genetic diversity of organisms. The buffalo is one of the most important domesticated animals in the world and has great economic value for humans, being used for milk, meat, leather and most importantly as labor. Khuzestani buffalo are among the most important buffalo in Iran. These animals are scattered in western and southwestern Iran. The largest population of this breed is in the Khuzestan province and they are fully adapted to the geographical features of this region

In this study, whole genome sequencing of the Khuzestan buffalo was performed in paired-end format using Illumina technology. Quality control of the readings obtained met all quality parameters and processing of the readings showed that all samples were of high quality. The BWA-MEM software package was then used to match the data to the reference genome. Genome variants were obtained with the Freebayes software. The final filtering of the variant file then took place. This filtering serves to increase the quality of the analysis and to sort out inferior variants.

The alignment percentage for all samples was over 97.44% and also the coverage in the sequenced samples ranged from x 4.3 to x 9.12, indicating reasonable quality of the reads. Also, in this study we identified 76,676,529 million variants fairly evenly distributed on the chromosomes of the Khuzestan buffalo. The highest and the lowest number of variants were observed on chromosome 1 chromosome 28, repectively. In this study, the total number of translocation and inversion mutations in the genome level was 298,193,017 and 135,694,466, respectively. In addition, the ratio of transitions to transversion was estimated at 2.1989 (Ts/Tv).

The presence of genetic diversity in the native population of Iranian buffalos are valuable parameters that can be studied to evaluate the genetic potential of economic traits in these populations in order to design suitable breeding programs.

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. Also, selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these regions are often control economically important traits, identifying and tracking these regions is the most important subject in the animal genetics.

In order to identify the signatures of selection and ROH Islands, 81 native Zandi sheep including prolific ewes (42 animal) and others with only singleton records (39 animal) were genotyped using the medium-density Illumina Ovine SNP50 array. Theta unbiased statistical method in R software was used to identify selection signatures. Candidate genes were identified by SNPs located at 0.1% upper range of Theta using BioMart software in ensemble 109. Also the detectRUNS package of R was useful to find the proportions of the homozygous genome and one percent of SNP with the highest frequency in ROH were considered as ROH Islands.

Based on the results of obtained Theta values genomic regions on chromosomes 1(3 regions), 2 (2 regions), 5, 6 (2 regions), 8 (2 region), 10 and 25 were identified. A total of 17 ROH Islands with length: 270.46 Kb to 8.25 Mb related to studied trait were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform. The highest number ROH Island was observed on chromosome 1, while the lowest was on chromosome 24. Candidate genes PER2, KCNH7, CLCN3, UTG8 and EPHA5 obtained these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with the genes associated with development of ovarian granulosa cells, ovulation rate, lipid transport in Sertoli cells and early growth fetus.

The results of this study revealed that, the selection processes in different sheep breeds for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

One of the goals of identifying loci related to quantitative traits is to find the genes that affecting economic traits related to growth,  which can be of particular importance in the progress of breeding programs. The aim of the present study was to identify the polymorphisms of GH and GHR genes and their association with carcass traits in Zel sheep using PCR-SSCP.

After collecting blood samples from157 Zel sheep, DNA was extracted using modified salting-out procedure. PCR was done to amplify fragments with length of 214 and 218 bp from exon 4 of GH and exon 10 of GHR genes, respectively.  For detection of polymorphisms in each marker site the SSCP and sequencing methods were used.

The results showed the presence of polymorphism in GH gen site; however, no difference was observed among banding patterns for GHR gene. Genotypes 1 and 2 of GH gene were obtained with frequencies of 43.71 and 56.29, respectively.

The sequencing results showed 5 mutations for GH gene in the studied population. No significant associations of the available genotypes in the exon 4 of GH Gene were observed for any trait. In relation to the third structure of mutated protein for both patterns, the results indicated the predicted protein contains only two chains and consequently lacks of performance, compared with the reference protein. Therefore, the studied marker in the GH gene  can not be considered as an effective marker on carcass traits in Zel sheep breed.

The proportion of adipose depots varies considerably between fat-tailed (FT) and thin-tailed (TT) sheep breeds. FT breeds accumulate majority of body fat in fat-tail depot, whereas TT breeds deposit considerable proportion of body fat in visceral depots. These differences in proportion of adipose depots seem to affect body metabolism due to differences in metabolism of different depots. Hence, the current research aimed to evaluate the response of fat-tailed lambs (FTL) and thin-tailed lambs (TTL) to glucose and insulin challenges during negative energy balance (NEB) and positive energy balance (PEB). Glucose tolerance and insulin challenge tests were conducted on randomly selected lambs from each genotypes at the end of induced NEB and PEB. Glucose injection during NEB caused greater plasma glucose concentration in TTL, whereas in PEB, the enhancement in glucose concentration as a consequence of glucose injection was higher in FTL (P≤0.09). The area under the glucose curve was higher in FT compared to TT lambs during glucose tolerance test regardless of energy balance (EB; P≤0.03). The clearance rates of insulin (P≤0.09) and glucose (P≤0.006) in the respective insulin and glucose tolerance tests were higher during PEB compared to NEB regardless of the genotypes. These results demonstrated that induced NEB can enhance insulin resistance in both FT and TT lambs, severity of which is greater in FT than in TT lambs.

 Selection in animal populations to increase the frequency of ideal alleles causes of remaining some signs in the animal genome, which are usually associated with important traits. Today, with developments in next-generation sequencing and easier access to animal genomic information, some models have been proposed to identify selective signatures based on allelic frequency and haplotype blocks. This research aimed to identify the selective signatures in two horse breeds of Caspian and Kurdish using a k70 SNP chip.

 In this research blood samples from 35 Caspian and 31 Kurdish horses were collected. After DNA extraction and sequencing (by Illumina company), Quality control of the data was performed for minimum allele frequency (PMAF<0.05), genotyping rate (PGENO < 0.5), and deviation from Hardy-Weinberg equilibrium (PH-W<1 ͯ 10-6). Then the theta (θ) test and ensemble site were used for identifying selective signatures and the positions of snaps respectively, and finally, the genes related to these positions were identified.

 After quality control of data and integration of genomic data of two populations based on R package protocols, 61 horses with 52,650 SNPs remained for the rest analysis. Finally, Fst statistical test based on unbiased estimator theta method 31 differentiating markers of the two studied horse breed were identified

The results showed that Caspian and Kurdish horse breeds belong to two separate groups. The Kurdish horse breed has more diversity and variety than the Caspian. The most important genes associated with significant SNPs were INPP5F, HPSE2, R3HCC1, DOCK3, ITGB6, GM6B, PHEX, WDR13, LRCH2, GRIA3 and THOC2. Most of the identified genes were associated with intercellular exchanges, muscle contractions, immunity, membrane support, DNA stability, and the nervous system.

The aim of this study was to investigate the effect of sodium acetate and conjugated linoleic acid on dry matter intake, body weight, activity of liver enzymes and blood metabolites in fresh cows.

This study was performed to investigate the effect of sodium acetate and conjugated linoleic acid on dry matter intake, body weight, liver enzyme activity, milk production and blood metabolites in newborn cows. Materials and Methods In this study, 24 Holstein cows with an average initial weight of 601.47±13 kg and a body condition score of 3.64±0.21 were used for 25 days during days 5-30 postpartum. This experiment was performed in 3 treatments and 8 replications in a completely randomized design by comparing the means by the mean least squares method at a significance level of 0.05. Treatments include 1- control with a source of calcium salt of palm fat, 2- Diet containing 300 g of sodium acetate supplement, 3- Diet containing 100 g of conjugated linoleic acid supplement (50% cis-9 trans-11CLA, 50% trans-10 cis-12 CLA) was. Dry matter intake and milk production were recorded daily, body weight and body condition score at the beginning and end of the experiment. Blood samples were also taken on days 5, 7, 14, 20, 25. The cows were milked in three meals of morning, evening and night, and the record of each meal was recorded. In order to measure milk composition, milk samples were taken on days 5, 8, 11, 14, 17, 20 and 25 after calving.

The results showed that the mean body weight, body condition score and dry matter intake were not significantly different between treatments. The concentration of non-esterified fatty acids was not affected by the treatments. Also, no significant differences were observed for triglycerides, cholesterol, albumin, total plasma protein and blood urea nitrogen between treatments. Plasma glucose concentration was significantly different between treatments (p<0.05), however, CLA and sodium acetate significantly increased and decreased compared to the control) (p<0.05. Sodium acetate significantly reduced the levels of aspartate aminotransferase and lactate dehydrogenase compared to control and CLA treatment (p<0.05). Daily milk, corrected milk production of 3.5% fat and milk fat percentage were significantly different between treatments, and sodium acetate and CLA treatments significantly increased and decreased milk fat percentage, respectively, compared to the control (0.05). Also, milk fat production increased with sodium acetate compared to control and decreased with CLA (p <0.05).

By consuming CLA due to the reduction of milk fat, the amount of blood glucose increased, as a result of which the intensity of the negative energy balance decreased, which in turn reduced the damage to the liver cells. Sodium acetate also improves energy levels, possibly due to the supply of acetate for milk fat synthesis. It can be concluded that adding sodium acetate is the best way to have a healthy liver along with increasing milk production and milk fat after birth.

Conservation of the genetic diversity of indigenous animals is very important. For the sustainable use of genetic resources, it is necessary to first study the genetic structure of populations. The main goals of this research were to identify the population structure of Turkmen and Darehshori horses using dense SNP markers and to compare the effectiveness of PCA, DAPC, and SPC methods in clustering these populations.

For this purpose, 67 Turkmen and 39 Darehshori horses were genotyped using Illumina EquineSNP70 BeadChip. After applying quality control steps, five Turkmen horses and one Darehshori horse were removed. Then, the structure of populations was identified by three methods of principal component analysis (PCA), discriminant analysis of principal components (DAPC), and superparamagnetic clustering (SPC). These methods do not depend on previous assumptions and make it possible to analyze very large genome databases without prior knowledge of individual ancestry. These methods are also very fast and efficient.

This study compared the efficiency of these three clustering methods in identifying population structures. All three methods were successful in separating the two breeds, and Turkmen and Darehshori breeds were grouped into separate genetic groups. The difference is that the DAPC method only separated the two main populations, but the PCA and SPC methods could identify several subpopulations in each breed. The results of this study showed that the SPC method for studying the population structure of indigenous breeds with unknown information can be more useful than other methods. Therefore, using this method, a suitable program can be designed to conserve and use genetic resources.

PCA, DAPC, and SPC methods were able to successfully identify the genetic structure of Turkmen and Darehshori breeds, and in general, it can be said that the information obtained from dense SNP markers can be a powerful tool for identifying the population structure of indigenous breeds.

Selection to increase the frequency of new mutations useful only in some subpopulations leaves markers at the genome level. Most of these regions are related to genes and QTLs controlling significant economic traits.

In order to detection of genetic differences between Iranian northwestern crossbred and Holstein cattle breed, respectively number of 100 and 60 sample from Iranian north-west hybrid and Holstein populations were used. After ensuring the distinct structure of the studied populations, FST, XP_EHH and Rsb statistics were used to identify the selection signatures and 21, 16 and 24 regions exceeding the threshold were identified as signatures of selection respectively. These selected genomic regions were surveyed and 104 and 135 genes were extracted from the corresponding areas in ARS-UCD1.2 Bos Taurus Genome Assembly for FST and LD based methods, respectively.

Some of detected genes in regions under selection were involved in metabolic pathways related to taste, smell, fat metabolic pathways, resistance to disease and reproduction performance. Some of detected genes were involved with milk production by involving in WNT (Wingless-type) signaling pathway. The selected genomic regions were further examined for further analysis and finding of gene networks. These analyzes were performed by online software related to the genomic database (DAVID). Only one significant network was identified (p<4.5×10-9). This gene network communicates with taste receptors and specially detection of bitter tastes.

In addition to better understanding about natural and artificial selection effects on the Holstein breed and Iraniannorth-west indigenous hybrid, the selected regions can helpus to detecte QTLs and regions associated with important economic traits. In any case, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

Honeybees, as pollinating insects, are an important part of nature. Because behavioral traits are so important in honeybees, comparing brain tissue transcriptomes of the two subspecies with aggressive and calm behavioral characteristics makes it possible to understand this behavioral difference genetically. This study aimed to investigate to gene expression profile and identify the key genes in brain tissue in Italian (Apis Mellifera Ligustica) and African (Apis mellifera Scutellata) honeybees concerning behavioral traits. The Italian honeybee has calm behavioral characteristics, while the African is known as an aggressive honeybee.

RNA-Seq data were obtained from the NCBI  (GEO) database, and after pre-processing of reads, the brain tissue transcriptomes of both subspecies were aligned and mapped on the honey bee reference genome (v A.mel 4.5), and then data qualification, transcriptome assembly, differential expression analysis, and gene ontology were performed.

Differential gene expression analysis identified 16,701 genes on the honeybee reference genome, of which 22 genes in brain tissue between the two subspecies had significant differential expression (adj p-value <0 .05 and Log2FC>2). As well, some of these genes were first identified. Gene ontology analysis showed that among these 22 genes, such as ITPR, MRJP, HSP70Ab, MBS, GB45410, and Def1 are directly or indirectly involved in the occurrence of various traits such as defensive, health behavior, reproductive, heat, light, and smell sensitivity. In addition, the SNPs encoding the honeybee brain tissue genome were identified in both subspecies, and 99636 SNPs were identified in the Italian, and 92514 SNPs were identified in the African subspecies.

RNA-seq data, due to its high throughput, can provide us with accurate information about the expression of genes in different tissues in various subspecies. In this study, genes involved in honeybee behavioral traits and the SNPs in these genes were identified

Reproductive traits (especially litter size at birth) is one of the most important economic traits in sheep breeding systems. The present study aimed to conduct a genome wide association studies based on Gene-set enrichment analysis for identifying the genomic region, candidate genes and biological pathways associated with Litter size in Zandi sheep breed. 

Prolific ewes with at least one twining record and others with only singleton records were genotyped using the medium-density Illumina Ovine SNP50 array. 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 for litter size evaluated using Plink software method case-control. Using the biomaRt2 R package the SNP were assigned to genes. Subsequently, gene enrichment analysis was performed with the goseq R package and bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases. 

We identified different sets of candidate genes related to litter size: AFP, FOXO3, ESR1, ESR2, RBP4, AURKA, DLG1 and ZGLP1 in Zandi sheep. According to pathway analysis, 11 pathways were associated with the litter size trait. Among biological pathways, the Oocyte differentiation, Ovulation from ovarian follicle, Estrogen signaling pathway and Positive regulation of peptide hormone secretion pathways have significant association with ovulation rate and ovarian steroidogenesis traits. 

Considering, this study supported previous results from GWAS of  litter size, also revealed additional regions in the sheep genome associated with these economically important traits, presented here should be contribute to a better understanding of the genetic control of litter size in sheep and using these findings can accelerate the genetic progress in sheep breeding programs.

The agriculture contribute to 50-60 % of global methane emission and ruminants have a key role in this contribution. Methane has an important role in global warming and it's global warming potential is 25 times greater than CO2. Furthermore, methane is the second most abundant global anthropogenic greenhouse gas after carbon dioxide. The present study aimed to perform genome wide association study to identify genome regions affecting the predicated methane production based on the concentrations of volatile fatty acids of rumen in Iranian Holstein cattle. One-hundred and fifty hair and rumen digesta samples were sampled using the two-tailed strategy based on breeding values of milk. After the measurement of the concentration of volatile fatty acids of rumen, methane emission of each animal was predicated according to these acids. DNA of animals was genotyped using GGP-LD v4 SNP panel (contains 30108 SNPs). Fourteen significant SNPs associated with methane emission trait located on 1, 2, 6, 10, 15, 17 and 18 chromosome were identified. Using annotating some quantitative trait locus (QTLs) were discovered around some of these SNPs. The results showed a genetic selection potential to mitigate methane emission per animal. Since genetic improvements are heritable, cumulative, and permanent, this improvement would be permanent and beneficial.

Bovine viral leukemia (BLV) is one of the deadliest viral diseases that is associated with many economic losses in the dairy industry, such as reduced production capacity and reproductive performance of infected animals and their eventual culling. The aim of this study was to identify the selection signatures associated with resistance to BLV in Iranian Holstein cows. For this purpose, a total of 152 animals were genotyped for 30,105 SNP markers using GGP Bovine LD v4 chips. After quality control of the initial data, 23,513 SNP markers in 140 animals of cattle were finally entered for further analysis. The animals used were classified into two groups consisting resistant to disease or healthy (68 animals) and sick (77 animals) animals, and then the regions of the genome that were divergently selected in these animals were evaluated using the unbiased Theta method. The results of this study showed that four genomic regions on chromosomes 1, 13, 20 and 22 were divergently selected in these groups. Study of the genes reported in these regions revealed that some genes such as the STGA1 on chromosome 1, the STK35, EBF4, and PDYN on chromosome 13 and the SLC38A3, RASSF1, and RBM6 on chromosome 22 were previously reported within or adjacent to these genomic regions. Study the function of these genes showed that the genes are involved in the immune system, the regulation of mitotic and meiotic cycles and cancer suppression. Overall, the results of this study can provide a valuable source of information to identify candidate genomic regions or causal genes associated with this disease.

Genome-wide association studies (GWAS) is a major procedure for studying the genetics of complex economically important traits in sheep. The objective of this study was to determine the genomic regions affecting some growth traits and wool characteristics in Zandi sheep. This study is GWAS implementing a medium-density single nucleotide polymorphism (SNP) panel to determine the putative chromosome area affecting some growth and wool traits in a fat-tailed sheep breed, simultaneously. We used a selective genomic approach sampling DNA from animals at the extreme ends using the estimated breeding values derived from a total population size of over 5,000 animals. The examined phenotypic data included the birth weight, weaning weight, 6, 9, and 12-months after birth weight, pre- and post-weaning average daily gain, fiber diameter (micron), prickle factor (%), staple length (mm), kemp (%) and medullated fiber. Genome-wide association analyses were performed based on the mixed linear model. Twenty-three regions, in which four were associated with more than one trait, located on 12 chromosomeswere associated with the studied growth and wool traits (p < 5×10−6). These genomic regions overlapping with KCNIP4, PPARGC1A, ASAP1, ANK2, WWOX, SYNE1, FBXO5, AKAP6, FABP3, ANGPTL4, ATP6V1B2, PARK2, and KRTAP11-1 genes, were associated with postnatal growth, regulation of metabolic pathways, skeletal muscle differentiation, and bone growth. Gene ontology term enrichment analysis revealed that genes involved in positive regulation of muscle structure, and muscle tissue development were over-represented in the identified candidate genes.