علی اسمعیلی زاده کشکوئیه

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.

Litter size is a key economic trait in sheep, significantly influencing the reproductive efficiency of flocks. This study aimed to refine the genetic understanding of the ESR2 gene using a combination of ARMS-PCR and PCR-sequencing methods in a cross between Lori Bakhtiari ewes and Romanov rams. The primary objective was to identify beneficial mutations in the ESR2 gene associated with litter size in these crossbred lambs. A total of 114 whole blood samples were collected from the crossbred population. The study was conducted in two phases. Initially, a 500-bp region of the ESR2 gene was amplified via PCR, followed by molecular analysis using ARMS-PCR and direct sequencing according to standard laboratory protocols. Genotypic and allelic frequencies were analyzed using software tools such as POPGene, FinchTV, and MAFFT to confirm the presence of mutations and assess alignment consistency. For the first time, two specific primer sets were designed to amplify overlapping regions of the ESR2 gene. Two distinct bands (500 bp and 300 bp) were successfully observed, and the larger band was sequenced. Sequencing data were aligned using MAFFT software, confirming the presence of a nucleotide mutation, g.73383249T>C, in the intergenic variant region of the ESR2 gene. This mutation involves a transition from the wild-type T allele to the mutant C allele, previously associated with litter size in sheep. The study achieved two major outcomes: (1) the successful conversion of a GWAS-reported marker into a simple PCR-sequencing marker and (2) the development of specific primers enabling the detection of the mutation without the need for PCR sequencing. Genotypic analysis revealed frequencies of 0.74 for the TT genotype and 0.26 for the TC genotype. A significant association was found between genotype and multiple births (P < 0.001). The additive substitution effect of the C allele for the T allele on litter size was estimated at 0.904 ± 0.0771 (P < 0.001). In conclusion, the use of this marker for pre-selection of Romanov rams carrying the CC allele associated with increased litter size represents a practical strategy for improving reproductive performance in sheep. This approach could help farmers increase economic returns by enhancing lambing rates.

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.

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.

The BRCA1 gene, which is called “gate keeper” It plays an important role in the process of repairing DNA damage, regulating the cell cycle, regulating the transcription process, maintaining chromosome stability, and other important pathways for the maintenance of genome stability. The current research was conducted with the aim of bioinformatic analysis and comparison the genetic diversity and phylogenetic structure of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 6 geographical regions: Western Asia, Europe, China, North Africa, South Africa and wild (Iran) using the NCBI genome databas.

The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. Also, the number of mutations, nucleotide diversity, haploid diversity, the number of positions in which similar or non-similar substitutions occurred, the percentage of gene differentiation, gene conversion were also analyzed using Dnaspv5 software.

The analyzes related to the comparison of breeds in 6 geographical regions showed 112 polymorphisms, which led to the creation of 19 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences (k) among breeds were estimated as 0.205 and 0.052, respectively. The genetic differentiation between the Chinese sheep population and the wild sheep population was the lowest. The average genetic distance between all geographical regions was calculated to be 0.29. The average nucleotide ratio (A+T):(G+C) was equal to 38:62%, which indicates the predominance of cytosine and guanine bases. The amount of conserved sequence (c) in this research was 0.313 on average, which indicates the high polymorphism of this gene and the creation of new proteins as well as new functions to adapt to different homeostasis conditions. The effective number of codons (ENC) in this research was calculated to be 56.41. The value of D in the Tajima neutrality test was 0.478, which indicates that the selection pressure is balanced.

The high genetic diversity in the wild population, the reasons for which are the presence of forest and open environments, prevention of genetic drift and reduction of inbreeding, which affects muscle strength, eating habits, aggressive behaviors, defense responses, sensory perception of confrontation with environmental conditions and stress that related to BRCA1 gene expression in these populations.

The goal of nutrigenomics is to study nutrients as signals that are received by cellular receptors, which can affect the genome, gene expression and metabolite production. In this research, to investigate the effect of cannabis seed on the fold change of carnitine palmitoyl transferase-1-B (CPT1B) expression in Baluchi sheep, 12 five-month-old male lambs were divided into two groups in a completely randomized design. The groups were fed with a control diet without cannabis seed and with a diet containing 10% cannabis seed. After the fattening period of 110 days, samples were taken from the heart, liver, testis, subcutaneous back fat and Longissimus dorsi muscle. Total RNA was extracted for Real Time PCR reaction and measurement of CPT1B gene expression change between groups. The change of CPT1B gene expression in liver tissue was significant between control and treatment groups (P<0.05). The expression of CPT1B gene was 5.74 times higher in liver of lambs treated with Cannabis seed compared with the control group. The CPT1B gene expression in heart, subcutaneous back fat, Longissimus dorsi muscle, and testis decreased by 3.1, 2.36, 2.12 and 2.47 times, respectively compared to control group. Cannabis seeds contain unsaturated fatty acids and these compounds can change the fat metabolism in the liver through the expression of genes such as CPT1B. Therefore, it can be stated that, CPT1B is one of the effective genes in fat metabolism and the addition of cannabis seeds to the diet can have a beneficial effect on the animal's production performance by increasing the activity of the liver tissue.

The Helmeted Guineafowls were originated from West Africa and spread widely across the world, due to their ability to adapt to different environmental conditions. The main goal of this investigation was to identify the single nucleotide variations (SNVs) in order to explain the genetic structure of Helmeted Guineafowl in Iran. The whole genome of six Guineafowl ecotypes (18 samples) including Tabriz (blue and grey), Rasht, Tabriz (white), Rasht×Tabriz cross, Shiraz and Lar were sequenced. Paired-end libraries with 125 bp of Guineafowl samples were sequenced by whole genome Illumina platform. The phylogenetic tree analysis based on the maximum likelihood and neighbor joining was constructed. Runs of homozygosity (ROHs) were detected across all individual genomes by PLINK software. In the current study, around 14.48 million SNVs were detected. To evaluate the phylogenic relationships among all Guineafowl ecotypes, we applied two different phylogenic methods based on neighbor-joining and maximum-likelihood methods. Similar results were reported by these methods, all Helmeted Guineafowl ecotypes were classified separately except Shiraz and Lar ecotypes, which showed the most amount of genetic similarities. The results of runs of homozygosity (ROH) analysis indicated that the highest level of inbreeding at all levels of ROH were observed in the white Tabriz ecotype, in contrast Tabriz (blue and grey) ecotype showed the lowest level of inbreeding at all levels of ROH. These findings can provide new insight into genetic structure of Helmeted Guineafowl ecotypes in order to develop the breeding programs.

Insertions and deletions (INDELs) are one of the main events contributing to genetic and phenotypic diversity, which have received less attention than SNPs and large structural variations. A total of 287.5 GB of data resulting from whole genome sequencing of six dog and wolf genomes with mean depth and coverage (percentage of mapping to genome reference) of 16X and 99.47, respectively, were analyzed to detect INDELs and assessment of their related functional groups, More than three million INDELs (1-73 bp) were detected. In this study, powerful algorithm (HaplotypeCaller) was used to increase precision and accuracy of detected INDELs. Most of the INDELs (95.179.9%) were smaller than 10bp. Results of INDELs annotation showed that the percentage of INDELs in exon and 3´ utr regions in dog genome was more than that in wolf genome, indicating that the domestication process has targeted the genomic variation in the exon and utr'3 regions.

This wok was conducted to identify polymorphisms in the region of the exon 1 in 5'UTR of myostatin gene and their relationships with the growth traitsin Raeini cashmere goats. Myostatin gene has been identified as a factor causing a phenotype known as double-muscling in which a series of mutations render the gen inactivity; therefore, able to increase muscle growth. Blood samples were randomly taken from 150 Raeini cashmere goats. Total genomic DNA was extracted and a 701 bp fragment was amplified from the exon 1 of myostatin gene using PCR-RFLP method. The analysis of band patterns indicated three genotypes including AA, AB and BB with frequencies of 0.56, 0.33 and 0.11, respectively. The A and Balleles had a frequency of 0.72 and 0.28, respectively. The analysis of additive and dominance gene actions revealed that the effect of the myostatin gene on growth traits and body size of Raeini cashmere goats is via the dominance mechanism. The results showed that all growth traits except weaning weight were significantly associated with the identified polymorphisms, thus this gene can be used as a molecular marker in Raeini cashmere goats breeding.

The aim of this study was to map loci affecting live weight and body size in Lori-Bakhtiari sheep and identification of biomarkers linked to growth rate in sheep. Quantitative trait loci (QTL) linkage analysis in a Lori-Bakhtiari sheep population was conducted using the regression-based interval mapping method. The mapping population consisted of 162 animals related to 5 paternal half families. Phenotypic data were measurements of birth weight (BW), weight at one month of age (W1), weaning weight (WW), weight at six months of age (W6), chest circumference (HG6), body length (BL6), wither height at six months of age (HT6), weight at nine months of age (W9) and yearling weight (W12). Five sires and their progeny were genotyped for microsatellite markers in a candidate region on sheep chromosome 1. Data were analyzed in two phases, individual family analysis and combined family’s analysis using a single-QTL model. Analysis based on individual families revealed QTL related to W1 (210.6 cM), near INRA011 marker segregating in the second family. In the third family, QTL affecting W1 and WW were identified at 252.6 and 223.6 cM, nearby MCM137 and LSCV105 markers, respectively. In addition, in the fourth family, a QTL underlying W1 was detected at 256.6 cM near LSCV105 marker. Combined analysis of all the families resulted to the identification of a QTL associated with W1 at position 254.6 cM relative to the centromere near the LSCV105 marker. There were two strong candidate genes close to the location of the detected QTL, the transferrin and PIT1 genes, thus these genes may account for the observed QTL effects for growth traits in Lori-Bakhtiari sheep.

For genetic analyses of growth traits of Kermani sheep including body weight at birth, three, six, nine and twelvemonths of age, 10, 459 body weight records measuredon 3132 animals originated from 78 sires and 1163 dams were used. The data were collected at Kermani sheep breeding station during 1988 to 2010. The data were analyzed using a multivariate animal model. In the model, animal age, sex, type of birth, year and season of birth were fitted as fixed effects. Maternal genetic effects as well as the direct additive genetic effects were fitted as the random effects. Heritability estimates of the body weight measured at birth, 3, 6, 9 and 12 months of ages were 0.14, 0.33, 0.34, 0.12, and 0.16, respectively. The genetic correlations between the growth traits were in a range of 0.78 to 0.98. These results show that the growth traits can be improved genetically. In the station, the genetic trends of the traits investigated were generally erratic and the genetic progress was low which were mostly due to the lack of an efficient breeding program. The genetic progress can be achieved if the animals are genetically evaluated based on their individual performance records and pedigree information.

A paternal half-sib design was implemented to identify QTL on chromosome 2 affecting growth traits in Japanese quail. Using a reciprocal cross between two strains, white (laying) and wild (broiler) of Japanese quail, 34 birds were obtained in F1 generation and 422 offspring related to 9 paternal half-sib families in 5 consecutive hatches were generated. Progeny from 9 paternal half-sib families were measured for growth traits, and genotyped for four microsatellite markers on chromosome 2. QTL analysis was performed with least squares interval mapping method based on regression in across and individual paternal half-sib families. In addition to the QTL responsible for Kleiber ratio, other QTLs related to growth in positions 13, 51, 53, 54 and 55 cM, (P

This study aims to identify quantitative trait loci (QTL) related to the skeletal traits of Japanese quail on chromosome 2. Eight males and eight females from wild type (W) and white (S)) were selected as the parent generation (F0) and the crossing between them was reciprocal. The population consisted 422 birds of F2 population through random mating of F1 generation (17 progenies (SW) derived from crosses between white male × wild female (14 females and three males) and 17 progenies (WS) derived from crosses between wild male × white female (11 females and six males)), which were slaughtered at the end of a 35-day period of breeding. Subsequently, the phenotypic characteristics of the bone were recorded and blood samples were taken for genotyping four microsatellite markers on chromosome 2. QTL analysis was performed by least squares interval mapping method based on regression; QTL effects were estimated using three different statistical models (additive model; additive and dominance model; additive, dominance, and imprinting model); and 19 QTL were identified with nine traits. The weight of left foot, femur weight, and diameter of left and right feet had significant QTL almost in most of the models. The results of this study showed that there were significant loci on chromosome 2, which could affect some traits of bone at the significance level of P

GDF9 gene is one of the most important effective factors on litter size in sheep. Thus, the aim of the present study was to detect single nucleotide polymorphisms (SNPs) available in exon 2 of GDF9 gene in pure and crossbred of Pakistani sheep using PCR-SSCP. Hence, blood samples were collected from 30 Pakistani sheep, 17 crossbred sheep (Pakistani rams × LoriBakhtiari) and 7 crossbred sheep (Pakistani rams × Kermani ewes) and genomic DNA was extracted using salting-out method. A 634 bp fragment was amplified using one specific primer pairs using polymerase chain reaction. After single stranded conformation polymorphism (SSCP) of PCR products, band patterns of GDF9 gene were observed on 8% polyacrylamide gel stained with silver-nitrate method. In total, 4 banding patterns 1, 2, 3 and 4 were obtained with frequencies of 0.193, 0.129, 0.371 & 0.407, respectively. The sequencing results were led to identification of 3 mutations in 443, 477 and 721 nucleotide situations of GDF9 gene in the studied populations.

The purpose of breeding is to rear animals which are biologically and economically important. Among the domestic species, the poultry, due to the large number of offspring per parent and short generation interval, enable researchers to run breeding programs even on small farms. In this regard, quail because of certain characteristics: short generation interval, large numbers of eggs, disease resistance, and low cost farming is of great interest to biologists and commercial growers. Japanese quail (Coturnix coturnix japonica) has been grown for the production of meat and eggs in Asia and for its meat in Europe and America during the recent years. Despite the great diversity of traits in Japanese quail, only a limited number of genes and linkage groups related to the bird have been identified. Japanese quail belongs to the order Galliformes and the Phasianidae family. The considerable phylogenetic similarity between quail and chickens in the number of chromosomes and the genome size makes the quail qualified enough as a model for studies on poultry. Furthermore, the similarities between 9 chromosomes and chromosome Z in quail and chicken have been confirmed and following the divergence, only small numbers of chromosomes of the two species have changed. In recent years, the attempts at mapping of quail genome based on the segregation and identification of microsatellite markers has begun and 50 microsatellite markers were identified in quail. This study examined F2 population of Japanese quail to find the loci for carcass traits on chromosome 5 using microsatellite markers. The population included crosses of two strains of Japanese quail (white and wild strains) and the traits examined included weights of hot and cold carcasses, internal organs and carcass parts.
Polymerase chain reaction (PCR) amplifications of each marker for 472 birds were carried out on a Thermal Cycler (Eppendorf, UK). Afterward, the population was genotyped using AlphaEaseFC 4.0 software for each marker. Parental (P0), F1 and F2 individuals were genotyped with 3 microsatellite markers. A genetic model, line-cross, was applied for QTL interval mapping analyses using the regression method in the GridQTL software. Data analysis was performed with least squares regression interval mapping method. The line-cross analysis employed the models including joint effects of additive, dominance and imprinting. The QTL by sex interaction was assessed to determine whether the effect did differ between the two sexes. The additive QTL effect by hatch interaction was also analyzed.
Significant QTLs were identified for carcass efficiency, breast percentage and breast weight, liver percentage and liver weight, back weight and back percentage, spleen weight and spleen percentage, gizzard and head on chromosome 5. The QTL for breast weight and percentage were identified at 19 cM (in position marker GUJ0100) on chromosome 5. The QTL for head weight and percentage and weight of back were identified at 12 cM (in position marker GUJ049) on chromosome 5. Other QTLs were mapped at 10 cM for carcass efficiency and spleen weight, at 0 cM for Gizzard weight, at 17 cM for head weight, at 15 cM for weight of liver, at 16 cM for liver percentage and at 11 cM for spleen percentage. The proportion of the F2 phenotypic variation explained by the significant additive, dominance and imprinting QTL effects ranged from 2.22 to 11.11%. In the current study, QTL affecting different traits were mapped to similar chromosomal regions. These evidence are indicative of genetic correlation among traits and correlated response to selection. If these traits are really controlled by the same pleiotropic QTL or by closely linked QTL, therefore they are in linkage disequilibrium (LD). However, higher resolution analysis is required to distinguish LD from pleiotropic.
The present study identified informative QTL regions that may form a useful resource as part of our advance on developing DNA tests for carcass quality and internal organs in Japanese quail. However, it should be noted that to identify candidate genes and informative markers in linkage disequilibrium with QTL affecting carcass and internal organs traits, association studies using SNP markers may be needed for the significant QTL regions detected in this study. The results showed that the identified positions for some carcass and internal organs traits on chromosome 5 were similar to the characteristics of quantitative traits (including pleiotropic and epistasis effects) and can be effective in phenotypic differences of trait. Such results are indicative of genetic correlation among traits and correlated response to selection.

A cross F2 plan was used to identify quantitative trait loci (QTL) affecting growth on chromosome 2 of quail. In this study, a three-generation population was developed of reciprocal crosses of two strains of Japanese quail (white male layer × wild female broiler and wild male broiler × white female layer). Phenotypic records related to birds’ growth traits of F2 generation (422) were recorded. All three generations of birds for four microsatellite markers on chromosome 2 were genotyped. QTL analysis was performed with least squares interval mapping method based on regression in three various statistical models. In the first model, additive and dominance effects of QTL were fitted and body weight traits in four weeks (p

The purpose of this research was to locate quantitative trait loci (QTL) associated with skeletal traits on chromosome 5 in an F2 population of Japanese quail. The population consisted of 472 birds, phenotypic data were measured for all birds and using three microsatellite markers considered for identify QTL affecting skeletal traits. QTL analysis was performed with least squares interval mapping method fitting nine various statistical models.Genotypic and phenotypic data were analyzed for QTL mapping with interval mapping method based on regression. Significance levels were estimated at the 5 and 1% chromosome-wise. The results were detected significant QTLs for 9 traits (left leg diameter, femur bone weight, right leg length, right leg diameter, femur bone diameter, right leg weight, tibia bone weight, left leg weight and cold carcass weight). Closest marker for the major QTLs was GUJ0049 marker. More research is needed to find genes associated with these traits. Results show the non-Mendelian inheritance rule (genomic imprinting) and pleiotropic and single gene effects in several traits of bones that are important to quail breeding.

This research carried out to identify effective quantitative trait loci in growth rate and Keliber ratio on chromosome 5 of Japanese quail by microsatellite markers. A three-generation resource population was developed by using two distinct Japanese quail strains, wild and white, to map quantitative trait loci underlying growth rate and Kleiber ratio. Eight pairs of white (S) and wild (W) birds were crossed reciprocally and 34 F1 birds were produced. The F1 birds were intercrossed to generate 422 F2 offspring. All of the animals from three generations (472 birds) were genotyped for three microsatellite markers on chromosome 5. Phenotypic data including average daily again and Kleiber ratio were collected on F2 birds. QTL analysis was performed using least squares regression interval mapping method fitting five various statistical models. Significant additive QTL were identified for average daily gain from hatch to one week of age and Kleiber ratio between 3 to 4 weeks of age. Dominance and imprinting QTL effects were not significant. The F2 phenotypic variance explained by the detected additive QTL effects ranged from 1.1 to 3.6 for different traits Significant QTLs identified by doing various statically types for average daily gain and keliber ratio with various effect.

Kermani sheep is one of the most important Iranian native sheep breeds and is well-adapted to harsh environmental conditions of south-eastern part of country, where dry and hot weather is prevalent and pastures are of low quality and quantity. CIB4 protein is one member of the calcium and integrin- binding proteins family, CIB proteins which are effective in high fertility. This protein has two nucleotides’ sequence including L-CIB4 and S-CIB4. CIB4 biological functions in mammals are not well defined yet, however, a lot attentions has been received to these proteins due to their potential effects in increasing fertility. Considering the importance of this protein in fertility, we examined the expression of this gene in Kermani sheep.
In this study gene expression of CIB4 in brain, heart, lung, kidney, liver, ovary and testis (3 repeats from each tissue) in Kermani sheep (4 males and 2 females) were analyzed. Initially, the various tissues of sheep supplied and in liquid nitrogen, transported to the laboratory and then total RNA from all samples were extracted based on One Step RNA Reagent kit manual and cDNA has been made using cDNA Synthesis Kit of Fermentase Co. After amplifying CIB4 and GAPDH gene, as an internal control, results of Real Time PCR were analyzed and PCR products were separated on 2% agarose gel.
Spectrophotometry results confirmed good quality of extracted RNA and observation of two bands, 28S and 18S on gel electrophoresis of RNA showed that RNA is intact and absence of additional bands represents purity of RNA. Observation of 574 bp fragment for CIB4 gene in testis tissue and absence of this band in other tissues and observation of 150 bp fragments for GAPDH gene in all tissues indicated that this gene is only expressed in testes and in brain, heart, lung, kidney, liver and ovary is not expressed.
According to the results CIB4 gene expressed only in testis tissue of Kermani sheep and in brain, heart, lung, kidney, liver and ovary was not expressed, hence may suggest a role of the gene in ram fertility. Although we indicated that this is a testis-specific gene and express only in the testis, but the mechanisms by what CIB4 expression is regulated need to be elucidated.

Deciphering the genetic basis of phenotypic diversity is one of the main aims of biological research. Domestic animals are useful tool for making substantial progress towards this goal. Selection signatures are the regions of the genome that are functionally important and therefore have been under either natural or artificial selection. In this paper, a whole genome scan was performed using 3000 individuals, ~50000 SNP markers from nine populations of Australian Merino sheep, with the aim of identifying divergently selected regions of the genome. Five genomic regions on 4 chromosomes were identified as putatively harboring selective sweeps. These regions were located on chromosomes 6, 7, 11 (two areas) and 26. These selected genomic regions were surveyed to find encoding putative candidate genes and 9 genes were extracted from areas Ovine Genome v3.1 Assembly.Study of the reported QTL in these regions of the sheep genome showed that they overlapped with QTL of economically important traits such as carcass yield, growth and wool traits. Further investigation of these regions in validation studies will help to identify the candidate genes for economically important traits in sheep breeds.

Determination of dispersion is one of the major challenges in the biological studies. Also, assignment test is applied to identify the origin of a specific individual, population differentiation and medical forensic cases. Therefore, the aim of this study was to determine the genetic diversity and assigning individuals to 5 populations of Camelus dromedarius in north of Kerman using 8 autosomal microsatellite markers. Eighty one blood samples were collected from Shahr-e Babak, Rafsanjan and Ravar. Total DNAs of the samples using salting out were extracted and applied for genotyping analysis. The expected heterozygosity varied from 0.77 in Sahra-e Jahad population to 0.84 in Rafsenjan 1 population. The individual’s assignment was done using 7 different methods. Among the methods base on the likelihood, the Rannala and Mountain method and among the methods base on the genetic distance, Nei DA method showed the highest accuracy. Totally, markers used in this study could assign the individuals to their source population with 29 % accuracy.

Insulin-like growth factor-1 gene (IGF1) is a biological candidate gene for investigation traits such as growth, body weight and muscles growth in different species. In this research eight pairs of white and wild quails were crossed reciprocally as a base population. A total of 34 quails were produced in first generation (F1) and 422 quails were generated by intercrossing the F1 population. Body weights at the time of hatching and different weeks were recorded in the second generation. The association between IGF1 promoter region polymorphism and body weight in different ages was investigated in F2 generation. Using PCR-SSCP assay and sequencing, a novel single nucleotide polymorphism (SNP) was identified in IGF1 promoter region in 472 birds from three Generations. Genotypic frequencies of AA, AG and GG genotypes were 0.05, 0.62 and 0.33, respectively for all generations. The frequency of A and G alleles were 0.36 and 0.64, respectively. The AA genotype was lower than AG and GG genotypes for body weights in ages of one to five weeks and slaughter time and the average of daily gain was also lower from week first to four but these differences weren’t significant. The average of daily gain was higher in females compared to males for AG genotype (P

In this research, samples were collected from three Iranian native dogs and three wolves. Whole-genome sequencing for each individual was performed using next-generation sequencing technology. All short reads were aligned to the reference genome using BWA tool. Single-nucleotide polymorphisms (SNPs) and small insertions and deletions (Indels) were detected using the genome analysis toolkit (GATK). Structural variants were predicted using the BreakDancer software. Annotating single-nucleotide polymorphisms and small insertions and deletions was done using SnpEff Software. Nucleotide diversity values in dogs and wolves samples were calculated using VCFtools. In current researche, 12459651 SNPs were detected that 7819789 and 10454994 were for dog and wolf, respectively. Of the total number of Single-nucleotide polymorphisms, 53.57%, 31.989% and 0.811% were located within intergenic, introns and exon regions. The results showed that structural diversity of wolf genome is higher than that in dog.

This study aimed to identify genes that show signatures of selection for mutations in Iranian native cattle breeds. The data consisted of genotypes for ~777962 SNP markers of 90 animals from eight Iranian native cattle breeds distributing over the country. Therefore, the aim was to identifying divergently selected regions of the genome. Study of population differentiation across the genome using Weir and Cockerham’s FST test revealed some regions showing evidence of selection. Across the 30 bovine chromosomes (BTA), seven putative selection signatures were detected. These regions were located on chromosomes 1, 2, 7, 8, 12, 13 and X. Finally, study of the reported QTL regions in the orthologous areas of the cattle genome showed that the genomic regions identified in this study overlapped with the reported QTL representing economically important traits such as milk yield, cold tolerance and reproductive traits. Result of this research provided important information on existence of genetic diversity and selection signatures in Iranian native cattle.

In the present study to investigate the effect of dietary methionine restriction on IGF-1 gene expression in breast muscle6T of 6 TJapanese quail, 200 pieces of 6Tthe birds were 6Trandomly 6Tdivided into two different dietary groups containing recommended methionine supplement and without the methionine supplement. IGF-1 gene expression levels were measured using the Real time PCR techniques in breast muscle of the Japanese quail at 24 days of age. Also in this age, the body weight and bone characteristics such as 6TFemur, Humorous and tibia were recorded. The results indicate that 6TIGF-1 gene expression significantly increased when the methionine supplement was removed from the diet (P