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Identifying selection signatures  can provide valuable insights into genomic regions that are under positive selection, which in turn leads to a better understanding of genotype-phenotype relationships Over the past few decades,, selection programs in broiler chicken have been based on fast growing and increased feed efficiency. On the other hand, this selection for rapid growth has been resulted an accumulation of fatty tissue and decrease of chicken meat quality, it has been new challenges in poultry breeding due to genetic correlation between rapid growing and fat deposition. The aim of the present study was to identify genomic regions under positive selection associated with body fat deposition in seven-week-old broiler chickens  using a statistical method based on linkage disequilibrium.

In the present study, a total 475 chickens from two chicken lines divergently selected were obtained using the Illumina chicken 60 K SNP chip. The broilers used in this study were from two Chinese broiler lines. In the first step, for the detected regions of the genome were evaluated using the XP-EHH method based on linkage disequilibrium using Selscan software v.2.0. Candidate genomic regions and genes were identified by SNPs located at 1% upper range of XP-EHH values in ten creeping windows. Finally, GeneCards and DAVID databases were also used to interpret the function of the obtained genes. Additionally, the latest published version of Animal genome database was used for defining QTLs associated with fat deposition traits in identified locations.

Candidate genes STAB2, TAPT1, JDP2, FNDC3B, PTPN11, ADIPOR1 and SLC44A3 obtained these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with lipid metabolism, fatty acid transport, lipoprotein receptors, glucose metabolism and homeostasis. Various genes that were founded within these regions can be considered as candidates under selection based on function. Also, a survey on extracted QTLs showed that these QTLs involved in some economically important traits in chicken such as abdominal fat weight and carcass fat weight traits.

However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in poultry breeding programs. The results of our research can be used to understand the genetic mechanism controlling fat deposition trait and using these findings could potentially be useful for genetic selection in chicken for increasing body weight while reducing body fat deposition during a broiler breeding.

The selection of novel mutations beneficial only in some subpopulations leads to the retention of signatures across the genome. This study aimed to identify genomic regions, candidate genes, and biological pathways associated with fat deposition in some Asian and African sheep breeds based on selection signatures method and gene set enrichment analysis. A total of 49,034 SNP markers data obtained from 404 animal samples, including 13 fat-tailed and 7 thin-tailed sheep breeds with relatively similar tail and fat-tail dimensions distributed across different regions of Asia and Africa, were used. Principal component analysis (PCA) was utilized for assessing the clustering of animals into their true population, and FST (Theta) statistics was employed for detecting of positive selection signatures. Subsequently, genes reported in the selected regions were identified, and gene set enrichment analysis was performed to identify biological pathways (and candidate genes) associated with fat deposition. PCA analysis showed that all animals clustered into their respective breed groups, and thin and fat tailed sheep breeds could be separated based on different components. In this study, 19 genomic regions were identified to be under selection between thin and fat tailed sheep breeds. Investigation of reported genes in these regions led to the identification of several biological pathways (and candidate genes) directly or indirectly associated with tail morphology (NDUFB, ANO4, ASXL2, ABHD2, and NID2), fat-tail size (ACADL), skeletal or body size (PDGFD, ACAN, HOXC, HOXB, BMP2, and BMP4), immune response (ATG5, IL4, IL5, and IL13), and melanocyte regulation (KITLG). Overall, the findings of this study could play an important role for identifying the genomic regions associated with distinctive phenotypic traits of these breeds, especially fat deposition traits in tails, immunity, and adaptability, which could be of great economic importance in the future considering the observable climatic changes in recent years in various countries.

In order to protect native breeds in order to maintain genetic diversity, it is necessary to keep the animal in its place of residence because the cost of protecting genetic resources is high and it is not possible to maintain all genetic resources in laboratories and research institutions. The aim of this research was to identify selection traits in Holstein, Najdi and their hybrids in the herds of Khuzestan province.

For this purpose, the genomic information of 209 cattle samples including 21, 128 and 60 samples from Holstein, Najdi breeds and their Holstein-Najdi hybrids were used, which were genotyped using Genotyping Array 30K arrays. First, animals with more than 5% missing genotype were excluded from the next steps, and monomorphic genotypes and genotypes with a minimum allelic frequency of less than 5%, as well as loci with more than 5% missing genotype, were excluded. Hardy-Weinberg equilibrium was checked in all loci and loci with P-value less than 6-10 were excluded from the data set. In this study, the signs of selection were investigated using two series of methods, two of which are multi-population (FST, hapFLK ) and the other one is single-population (iHS, nSL). To determine the signs of selection in the studied cattle breeds, FST values for each SNP marker were calculated using the unbiased theta estimator method by Plink and R software. Also, in order to identify the signs of selection in the studied breeds, the FLK Single Marker haplotype expansion method called the hapFLK test was also used. iHS and nSL statistics have been used as intra-population statistics in order to investigate the areas carrying selection signs. To calculate these statistics for each SNP, VCFtools and Selscan version 2.0 were used, respectively.

After data editing and imputation of 662,428 SNPs from 329 Najdi, Holstein and their hybrids, and after removing 3,129 SNPs with Hardy-Weinberg 6-10 test and 68,116 SNPs with MAF 0.05, 591,181 SNPs remained for further analysis. In order to identify selection signals at the genome level, the numerical value of fixation index (FST) was used. Only 0.1% of the regions of the genome where all markers had high values. Finally, three regions on the genome were selected for further analysis that passed the threshold. Three regions were located on autosomal chromosomes. These three regions, where the stabilization index had a higher numerical value of 0.38, were located on chromosomes 16, 21, and 8, respectively. A threshold of 0.1% of the high hapFLK value of the population was used to identify the regions under selection by the hapFLK method. Finally, the region of 22774764 to 23377643 base pairs of chromosome 14 and the region of 33981177 to 34039961 base pairs of chromosome 26 had a selection mark at the specified threshold, which was used to identify genes in the next step. The iHS statistic was used to identify signs of selection for alleles that are polymorphic in the population, but have not yet reached the fixation stage. iHS less than zero indicates that the respective haplotype carries the derived allele, and iHS greater than zero indicates that the haplotype in question carries the ancestral gene. In this research, the markers with the highest amount of iHS on chromosomes 3, 7 and 10 were identified as selection markers. By using the nSL statistic which was calculated by Selscan software in the Linux environment and drawing the Manhattan plot diagram of this statistic by R software, it was determined that in the Holstein and Holstein*Najdi hybrids population on chromosome 3 and in the Najdi population 4 and 15 regions have been selected. Some of the areas identified with these statistics are directly and indirectly related to growth traits, reproduction, immune system and other traits related to them.

In this research, four statistics, FST, hapFLK, iHS and nSL, were used to identify the signs of selection in Holstein, Najdi cattle populations and their hybrids. The results of FST and hapFLK statistics, which examine the populations in a multi-population way, showed that the signs of selection detected by these two statistics were on chromosomes 8, 14, 16, 21 and 26, and chromosome 16 was common in each of the two strains. Among the areas identified with these statistics, they are directly or indirectly related to the characteristics of milk production and reproduction in cows. The results of the iHS and nSL statistics, which examine the populations as a single population, showed that the signs of selection detected by these two statistics were on chromosomes 3, 4, 7, 10 and 15, which is the chromosome No. 3 was common in every two races. Some of the areas identified with these statistics are directly and indirectly related to growth traits, reproduction, immune system and other traits related to them. Considering that the statistics used are different in terms of the implementation method and the parameters used (the first two are multi-population based on allele frequency and the second two are single-population based on linkage disequilibrium), consequently their results did not match. But from the total of 59 genes identified by the four methods used, two genes, IQCA1, ACKR3, were jointly identified by iHS and nSL statistics. In addition, it can be concluded that the selection during the past years has been generally focused on traits that have been effective in increasing the production efficiency in addition to increasing the resistance of livestock to the environmental conditions of the place of residence.

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.

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.

Selective signatures provide information about the stages of evolution of different species, including sheep, which lead to changes in their genome over many years. The aim of this study was to detect signatures of selection in the genome of Iranian sheep in the highlands. A total of 58 sheep from 4 breeds, two breeds scattered in the highlands and two breeds scattered in the lowlands, were genotyped using Illumina ovine SNP600K BeadChip genomic arrays. Two statistical tests of unbiased FST (Theta) and hapFLK were used to identify the selection signatures. The results of Theta revealed 22 genomic regions and the results of hapFLK revealed 15 genomic regions. Bioinformatics analysis demonstrated that many of genes had important effects on adaptation to hypoxia conditions e.g. rheumatoid arthritis (TXNDC5), hematopoiesis (FANCA), immunity and fighting infection (LEF1, NMUR1, PTMA and COPS7B), regulating blood pressure and responding to pain and inflammation (NMUR1) and suppressing cancer (CD82, GAS8, PRMT1, B3GNT7). For example, TXNDC5 and FANCA functional genes, which are located on chromosome 13 and 14, were related to reacts to hypoxic conditions and hematopoiesis. Also, genes such as LEF1, NMUR1, PTMA and COPS7B are effective in immunogenicity and fighting infection. Study of the reported QTL in these regions of the sheep genome showed that they overlapped with QTL of economically important traits such as corpuscular hemoglobin concentration, hematocrit, traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born. Due to the fact that little research has been done regarding adaptation to altitude in sheep, the results of this research may facilitate the identification of genes affecting adaptation to altitude. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

 Iranian sheep breeds, due to the climate diversity of country, show high diversity and have acquired high adaptability. Compromise with poor quality feed, tolerance of adverse weather and manageable body size are among the factors that probably caused sheep to adapt to different climates. Heretofore, several studies have been carried out in the field of identification of selection signatures in the different native breeds based on SNP-chip data. However, the use of whole genome data can provide researchers with more information about the differences between breeds and their genetic capacities. Identifying and evaluating the effects of climate on the genome of native breeds of Iranian sheep can be effective in designing breeding and conservation strategies. The aim of the present study was to identify the signs of selection related to Iranian sheep compared to the Romanov breed at the genomic level.

 For present study, we used the whole-genome sequencing data related to 43 Iranian and non-Iranian sheep available in the NCBI database. These reads, after performing quality control, were aligned to the sheep reference genome by BWA program. Here, RealignerTargetCreator and IndelRealigner commands available in the GATK program were used to realign around insertions and deletions. Then, the HaplotypeCaller algorithm was used to identify the variants of all samples in ERC GVCF mode. Further, using GenotypeGVCFs module, the variants of all samples were simultaneously identified and finally a VCF file containing raw variants was created. Using the SelectVariants command of the GATK program, all SNPs were separated from other variants. After applying multiple quality filters, high-quality SNPs were extracted and only bi-allelic SNPs present in autosomal chromosomes were used for downstream analysis. Putative selection signatures were identified by using two methods including Fst and XP-EHH. Genes located in positively selected genomic regions were extracted using BEDtools program and the GTF file related to the sheep genome. Gene ontology (GO) analysis was performed on selected genes by "g:Profiler" web-based tool.

Here, Fst and XP-EHH methods were used to identify the signatures of selection related to Iranian sheep in comparison with Romanov sheep. After converting Fst values ​​to ZFst, 958 genomic windows containing 907 protein-coding genes were detected that had scores above the threshold (ZFst > 3.35). GO analysis on 907 genes identified by the ZFst method led to the identification of 157 significant GO terms in the field of biological processes. In addition, 26 significant terms related to molecular functions and 5 significant terms related to cellular components were also identified. The number of genomic windows identified by the XP-EHH method was 953, which contained a total of 311 protein-coding genes. Among identified genes for each method, 29 genes were detected by both methods as signatures of selection for Iranian sheep. From the GO analysis of 29 common genes, no significant term was obtained. However, these genes were involved on traits related to improving milk fat quality (PCCB), fertility (SPATA5, RAB35 and DICER1), muscle growth and development (NF1, AKAP6 and HDAC9), body weight (FBXL3, GRID2 and ADAMTS17), adaptability to harsh desert and mountain condition (BMPR2 and NF1) and also, milk related traits (EXOC6B).

The results showed that Iranian sheep were probably selected to adapt to dry desert areas and improve the quality of meat and milk. The gradual accumulation of such information in different populations will improve the understanding and knowledge of researchers and breeders and will help them to implement efficient breeding programs.

The principal aim of the sheep industry worldwide is to produce high-quality meat. In addition to the meat, milk, and wool production are the economic traits in sheep breeding programs. Wool production is one of the most important economic characteristics of sheep with a complex physiological and biochemical process that is influenced by genetics, environment, and nutrition. Almost all Iranian sheep breeds are double-coated and produce carpet wool. Therefore, considering the role of wool on the country's economy, it is necessary to conduct a study to identify the genetic factors affecting this trait. Identifying the genomic regions under selection is effective in understanding the processes involved in the evolution of the genome and also in identifying the genomic regions involved in the emergence of economic traits. Selective signatures in the whole genome can help us to understand the mechanisms of selection and to identify the genomic regions that have been under natural or artificial selection for many years. Since Selective signatures are usually associated with major effect genes and important economic traits, they can provide suitable information sources to improve the performance of selection programs in the future. The objective of this study was to identify the genomic regions that have been under selection in skin and wool sheep breeds.

 In the present study, Illumina ovine SNP600K BeadChip genomic arrays of 80 sheep from six breeds were used, three breeds were bred for their skin (Karakul, SiahKabud, and Gray Shiraz) and three breeds were bred for their wool (Sanjabi, Kermani and Baluchi). Unbiased methods of Weir and Cockerham’s FST (Theta) and hapFLK were used to detect the selection signatures. Also, to check the genes and QTLs in the selected regions, the Biomart database, OAR 3.1 version of the sheep genome, was used, and the function of the identified genes was analyzed through a wide search in different databases such as Genecards and OMIM. Finally, the list of genes related to the selected regions was reported. For this purpose, the chromosomal position of SNPs with high numerical values of theta and hapFLK, as well as the 250 kbp region around these markers, were further investigated. Then, the DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology. Finally, Cytoscape software was used to determine gene networks.Then, DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology.سپس از جستجوی آنلاین پایگاه داده DAVID برای بررسی فرآیندهای بیولوژیکی و عملکردی ژن ها و مطالعه هستی شناسی استفاده شد.Then, to investigate the biological and functional processes of genes and to study the ontology, DAVID database was used to search online. سپس برای بررسی فرآیندهای بیولوژیکی و عملکردی ژن ها و مطالعه هستی شناسی از پایگاه داده DAVID برای جستجوی آنلاین استفاده شد. Can't load full results Try again Retrying…

 The results of the Theta analysis revealed 26 genomic regions on 1, 2, 6, 19, and 24 chromosomes, and the results of hapFLK revealed seven genomic regions on 6 and 19 chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with known genes related to pigment traits and characteristics of wool (KIT on chr 6, MITF on chr 19, IGSF10 on chr 1, PDGFRA on chr 6), muscles (MICALL2 on chr 24), vasodilation and immune response (P2RY on chr 1) and cancer (MIR339 on chr 24, ELFN1 on chr 24, MAD1L1 on chr 24, GPR87 on chr 1). The investigation of reported QTLs showed that these regions are related to QTLs of important economic traits, including traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born. Also, the analysis of Gene Ontology and Enriched pathway terms in regions under positive selection were related to the pathways involved in the differentiation of melanocytes and pigments, differentiation of stem cells, cellular processes, development of the immune system, blood system, reproductive and cellular processes. The results of the gene networks with the information obtained from Theta and hapFLK statistics showed that the genes identified were significantly active in the development and morphogenesis networks of the embryonic digestive tract, the networks related to pigment and melanocyte differentiation, and the networks related to Purine and G protein. However, to identify the exact function of the identified genes and QTLs, it is recommended to carry out more investigations.نتایج شبکه های ژنی با اطلاعات به دست آمده از آمار تتا و hapFLK نشان داد که ژن های شناسایی شده به طور معنی داری در شبکه های رشد و مورفوژنز دستگاه گوارش جنینی، شبکه های مربوط به تمایز رنگدانه و ملانوسیت و شبکه های مربوط به The results of the gene networks with the information obtained from theta and hapFLK statistics showed that the genes identified were significantly in the development and morphogenesis networks of the embryonic digestive system, the networks related to the differentiation of pigment and melanocytes and the networks related to نتایج شبکه های ژنی با اطلاعات به دست آمده از آمار تتا و hapFLK نشان داد که ژن های شناسایی شده به طور معنی داری در شبکه های رشد و مورفوژنز دستگاه گوارش جنینی، شبکه های مربوط به تمایز رنگدانه ها و ملانوسیت ها و شبکه های مربوط بهCan't load full results Try again Retrying…

 The results of the present study and the identified genomic regions can play an important role in the study of the effect of the selection on population differentiation in two sheep breeds that bred for skin and sheep production. Subsequently, this would direct us to identify the genomic regions associated with traits that differentiate these groups. However, these areas need to be confirmed in other independent studies with more samples. In general, the data of this research can be used in research related to genomic selection, design of mating systems, and additional reviews and evaluations to improve skin and wool production in sheep.

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

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

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

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

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 associated with significant economic traits. The aim of this study was to identify selection traits related to functional traits in the number of world's sheep using modern methods. For this purpose, genotyping files were used using genomic chips related to 1591 sheep from different breeds of the world, (Dryad ،Frontiresin ،Zenodo ،Animal Genom، Hapmap( including 52 breeds from 20 countries on all continents, and 13 studies were stored in various genomic databases. First, to determine the population mixing between different breeds from regions with different climatic conditions, population structure analysis or population stratification was carried out. Fst, hapflk, iHs, Rsb, XpEHH tests were used to identify the selection signatures, and finally, a meta-analysis of the above methods was used. The population was divided into three groups by PCA analysis: AIT: Asian, Turkish and African breeds, AUNZ: Australian and New Zealand breeds, and EU: European breeds. Based on the meta-analysis test, 10 genus regions were identified on chromosomes 2, 3, 4, 5, 6, 7, 9, 12, 20, 22. For example, the MC1R gene is associated with skin color, the DSG2 gene with the quality and quantity of wool, and the AICDA gene with the production of immunoglobulin. Bioinformatics analysis showed that some of these gene regions are directly and indirectly associated with genes affecting environmental adaptation (ADAMTS9), reproduction (GNAQ), melanocyte regulation (KITLG), and immunoglobulin production (BATF, TNFSF13, AICDA, MZB1), Cell differentiation (TNFSF13, TGFB1), Immune process (AGBL5, ATG7, PRDX1, CCL26, IL17RC, TNFSF12, TGFB2, PTGS1), Cellular response to external stimulation, NKK1, PRF3 (PR) Interferon alpha (DDX58), defense response process (CCL24, FAM13B, LDLR, CLDN7), cellular homeostasis (BAMBI, DVL2), regulation of mitogen-activated protein kinase (PLCE1) and regulation of stress response (FXR2, HSPH1). Comparative analysis of meta-analysis of selection cues based on bioinformatics databases can identify selected genomic regions for traits of economic and biological importance in sheep.

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.

Identification of genomic regions controlling economic traits is one of the most challenging uses of dense markers in animal genetics. Fat storage is economically important for breeding sheep. Therefore, identification of lipid-associated gene positions was the main goals of this study.In this study, 49034 Single Nucleotide Polymorphisms (SNPs) were used to identify the genomic regions affecting fat deposition of 106 sheep individuals include Afshari (n=37), Moghani (n=34) and Qezel (n=35) breeds were used. All samples were genotyped by Illumina OvineSNP50K bead chip. By running the quality control on the raw genotype, from tolal 49,034 SNP markers only 46,676 SNPs remained then genomic relationship principal component analysis (PCA) was used in order to assign correct individual to each breed. Theta and Fst analysis were applied to survey the population differentiation in three breeds, so five regions in 99.99 percentile FST score of the genome distribution were selected for further analysis. These regions are stated on chromosomes number 3, 13 (two areas), 15 and 22 were associated with LDL and HDL receptors Lipolise regulation in fat cells and fatty acid metolism. To verify those regions, Extended Haplotype Homozygosity (EHH) test based on linkage disequilibrium was perform. The results of this study shows that SNP bead chip are useful for population differentiation and GWAS so this can help us to achive an genetic improvement by genomic selection.

The Arab horses are famous for endurance riding, jumping and beauty. Kurdish horses are native to hilly regions of west of Iran and they are suitable for Polo tournament. Kurdish horses are shorter and heavier than Arabian horses. In this study, we use the linkage disequilibrium-based method, XP-EHH statistic, for Identification of regions that have undergone selection in the genome of Arabian and Kurdish horses. For this purpose, genomic DNA from blood and hair samples from 38 Arabian and 58 Kurdish horses were extracted. All DNA samples genotyped by the Axiom MNEC670 array. After data pruning, XP-EHH statistic was calculated. We identified 51 genomic regions (85 genes) in Iranian Arab horses and 7 genomic regions (13 genes) in Kurdish horses showing signatures of selection. We found positively selected genomic regions in the Iranian Arab horses associated with immune system related pathways, milk protein formation, muscle growth and development, vision, nervous system and body size whereas in the Kurdish horses associated with G protein–coupled receptors, growth and maturation of muscle fibers, cellular oxygen homeostasis and skin and hair pigmentation.

Selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these areas are often control economically important traits, identifying and tracking these areas is the most important issue in the animal genetics. The aim of this study was to detecting signals of selection in the genome of Turkmen horse using 70K SNP chip. Twenty-three Turkmen horses selected from different areas of Gonbad-e kavuos, were Blood sampled. Then DNA extracted genotyped. To detect footprint of signal selection, some tests based on linkage disequilibrium (LD) such as extended haplotype homozygosity(EHH) and integrated haplotype Score (iHS) was used. First to identify regions of the genome that included the most signals of selection, iHS statistics was used and accordingly 6 genomic regions which were in the 99.99% percentile of iHS values selected for further analysis. These regions were located in 6 areas on chromosomes 4,5,7,8,9 and 10. Results of EHH test with bifurcation diagram of haplotype, confirmed signals of selection in these areas. Based on the results of the EHH test, sharp decay of LD in some regions was observed (chromosomes 7, 9 and 10) while in other regions it wasn’t so significant (chromosomes 4,5 and 8). As studied alleles on chromosomes 4,5 and 8 had long range of LD and had frequency of, respectively, %43, %52 and %37, these regions of the genome of Turkmen horse most likely has been the target of positive selection.

The Arab horse breed is one of the most ancient horse breeds. Arabian horses are famous for endurance riding and flat racing. Moreover, this breed has contributed to the formation of some of the most important horse breeds in the world. Kurdish horses are found in rough terrain and hilly regions and they are suitable for riding in hilly areas and Polo tournament. To investigate the population structure and to find the signatures of selection in the genome of Arabian and Kurdish horses, blood and hair samples from 38 Arabian and 58 Kurdish horses were taken and genotyped using the 670K Axiom Equine Genotyping Array. Principal component analysis (PCA) was carried out on the genotypic data and Fst statistic for each SNP was calculated. Fst values were smoothed over each chromosome. PCA showed that the Arabian horse population is more genetically diverse than the Kurdish horses. We identified six genomic regions showing signatures of selection. The strongest signal of selection was found in ECA8. Annotation of the regions of the genome that showed selection signatures revealed candidate genese.g. CaMKK2, MLXIP and ATP2A2 that may involve in endurance riding and racing. These genes for further studies are proposed.

Identification of selection targeted genomic regions is one of the most challenging areas of research in animal genetics, particularly in livestock. We carried out a genome-wide scan for signatures of positive selection to identify genomic regions that had been under selection in Iranian Khuzestani and Mazandrani buffalo breeds. A total of 148 water buffalo from Khuzestani (N=121) and Mazandrani (N=27) buffalo breeds were genotyped using Axiom® Buffalo Genotyping 90K Array. Unbiased method of population differentiation index (FST) was applied to detect signatures of selection. In total, 23 regions exceeding the 0.1 percent threshold of the empirical posterior distribution were identified as extremely differentiated. These selected genomic regions were surveyed to find encoding putative candidate genes and 64 genes and 27 QTL were extracted from the corresponding areas in UMD3.1 Bos Taurus Genome Assembly. Some of these genes have previously reported as signature of positive selection in the last studies. Some of these genes were also found to be involved in milk production traits and domestication-related changes include sensory perceptions, brain and neural system development, pigmentation, and geographic adaptation. Also, survey on extracted QTLs was shown that these QTLs involved in some economicl important traits in buffalo such as feed conversion ratio, subcutaneous fat, body weight, average daily gain, type, Meat tenderness, milk production conentent, udder attachment, calf size and calving ease traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.