Showing 6 results for Haplotype
Mohsen Gholizadeh, Ghodrat Rahimi Mianji, Ardeshir Nejati Javaremi,
Volume 5, Issue 10 (2-2015)
Abstract
Twinning trait is an important trait in sheep breeding. Reproductive traits differ greatly across sheep breeds, but also between sheep in a single flock. Identification of ewes with higher twinning rate and more raised lambs per year is an important parameter for breeding and farming success. A genome-wide haplotype association study, using 42,416 Single Nucleotide Polymorphisms (SNPs) was conducted to identify genomic regions affecting twinning rate in Baluchi sheep. We also studied LD patterns in this population. Blood samples from a total of 96 sheep from two herds and data on their twinning rate during the first four parities were collected. Animals were genotyped using the IlluminaOvineSNP50K BeadChip assay. Genetic stratification and herd effect were included as confounding effects and fitted into the statistical analyses. Haplotype based GWAS for twinning was performed with the first MDS component and herd effect as covariates. To control the Association with twinning rate was tested using the software PLINK. Suggestive associations were identified for SNP on chromosomes 1, 10 and 15. LD was evaluated by measuring r2 between all pairs of loci. For SNPs up to 10 kb apart, the average r2 was 0.33, for SNPs separated by 200–500 kb the average r2 was 0.086. The extent of LD in Baluchi sheep extends over much more limited distances than reported in dairy cattle and seems to be similar to other ovine populations. Further studying of these regions in validation studies will help the identification of candidate genes for twinning rate in sheep.
Yaser Bahador, Mohammadreza Mohammadabadi, Amin Khezri, Mahdieh Asadi, Leila Medhati,
Volume 7, Issue 13 (8-2016)
Abstract
The aim of this study was assestment of genetic diversity for honey bee populations in Kerman province using two inter simple sequence repeat (ISSR) primers. In this study, 30 samples from 6 populations (Kerman, Jiroft, Raein, Rabor, Bardsir and Flo) were collected. While using (AC)8G and (AGAC)4GC primers in PCR, DNA profiles of bees were found to possess 16 polymorphic fragments. The number of fragments produced in the DNA profiles of different bee cities varied from 2 to 8, with their sizes varying within 150-1000 bp. Means of Shanon Index based on (AC)8G marker for Jiroft, Kerman, Flo (Native bee of Jiroft) Rayen, Rabor and Bardsir honey bee population were 0.51, 0.36, 0.50, 0.61, 0.42 and 0.19 respectively and based on (AGAC)4GC marker in Jiroft, Kerman, Flo (Native bee of Jiroft) Rayen, Rabor and Bardsir honey bee population were 0.52, 0.51, 0.46, 0.39, 0.41 and 0.27 respectively. A cluster analysis was carried out using unweighed pair group method with arithmetic averages (UPGMA) and dendrogram illustrated genetic relationships among 30 individuals in six populations. Haplotypes were constructed computationally and frequencies were compared in each population. Based on all studied genetic criteria, we can conclude that honey bee populations in Kerman have moderate amount of genetic diversity. The results of this study can provide the basic molecular information for future research on native honey bees using ISSR markers.
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Volume 8, Issue 16 (11-2017)
Abstract
The Bactrian camel of Ardebil province, northwestern of Iran, is an adapted genetic resource and a great national wealth; however its population has dramatically decreased in numbers. Therefore, we aim to investigate the mitochondrial genetic diversity within this population. In 37 individuals, a 518-bp region of the mitochondrial DNA (mtDNA) that spanned a portion of the cytochrome b gene, the tRNAs praline and threonine, and the beginning of the control region were successfully amplified and aligned to the Bactrian mtDNA reference sequence. In total, we recovered 5 polymorphic sites and five distinct haplotypes. The heterozygosis estimated from the haplotype frequencies were 0.503 indicating an unexpected high genetic diversity within Iranian Bactrian camels. Our results have important implications for the conservation of genetic diversity and the management of livestock production to facilitate the retention of or potential increase in the camels’ economic value. Further studies using nuclear DNA such as Y chromosome markers and microsatellites or single nucleotide polymorphisms are encouraged to substantiate the results of this study.
Seyied Makan Mosavi Kashani, Ghodrat Rahimi Mianji, Hossein Moradi Shahrbabak,
Volume 9, Issue 20 (10-2018)
Abstract
The aim of this study was to find the footprint of selection in native Sarabi and Taleshi cattle breeds 296 cattle from two breeds were sampled and genotyped. by 40 k microarray of illumine company. 43 animals were removed because their ACR was below 0.09. Markers were filtered with minor allele frequency (MAF) equal 0.01 and Hardy-Weinberg equilibrium test (10-6). After filtering, 28782 markers remained. To study the genetic structure of population and sub-population principal component analysis (PCA) was used. To identify selective signals for Sarabi and Taleshi pure population theta parameter was calculated. To reduce error theta values was averaged with near marker and Manhattans graph were obtained by haploview software. Chromosomes 2, 5, 6, 7, 10, 22, 25 and 27 had selection signatures. To searching for selection signatures in both population, extended haplotype homozygosity statistics (EHH) was calculated using R software. In addition, for each chromosome LD erosion rate for ancestral and mutant alleles were calculated. To study of positions that showed signature selection, bioinformatics web site were searched. EIF4G3 gene was identified on chromosome 2. This gene have fundamental role in transfering RNA from nucleus to the cytoplasm and gene expression. ANK2 gene was identified on chromosome 6 which encodes polypeptide ankirin B expressed in all tissues. On chromosome 7 the gene ARHGAP26 was found which is a tumor suppressor genes. On chromosome 10, a gene identified that encodes protein SYNJ2BP that suppress activing protein. On chromosome 22, FAM3D protein coding gene detected that plays a role in cyto sckeleton actin biochemical pathway. This gene is expressed in the placenta and plays a role in biological functions such as migration and function of leukocyte, temperature regulation, cell survival and hematopoiesis differentiation.
Maryam Shariat, Gholam Reza Dashab, Mehdi Vafaye Valleh,
Volume 10, Issue 23 (5-2019)
Abstract
Maintaining genomic diversity in goat populations in different parts of Iran is essential for breeding programs, increasing production, survival, resistance to diseases, and various environmental changing conditions. The aim of the present study was to determine the sequence of HVR1 from the mitochondrial genome of Iranian native goats including Sistani, Pakistani, Black and Lorry ecotypes (each of 4 heads), examine the probable variation in these populations, and plotting their phylogen relationship in comparison with some animal species. Total DNA extraction was performed using phenol-chloroform method. The extracted DNA was used as template for proliferation of HVR1 region of mitochondrial genome was used and the obtained bands were sequenced by Sanger method. The nucleotide sequences with 30 sequences from the same region of the mitochondrial genome related to other animal species derived from the National Center for Biotechnology Information (NCBI) were used for genetic analysis and phylogenetic tree mapping. The average of haplotype diversity and nucleotide diversity among species were 0.994 and 0.12891, and, in the ecotypes were 1 and 0.09299, respectively. The numerical value of the replacement rate of dn/ds for the studied ecotypes and other species was calculated at 1.17 and 1.12, respectively, which indicates a positive selection in the process of evolution of this gene. The results of phylogenic tree of nucleotide sequence of HVR1 region were estimated from two major branches and 7 subspaces. Among the studied species, goat ecotypes were similar to sheep species. The genetic and phylogenic analysis of the studied species indicates the distinction and evolutionary path of each species and the HVR1 region can lead to the proper grouping of the species and sub-species that are split from them.
Marzieh Rohipoor, Mahmood Nazari, Mohamad Tagi Beigi Nassiri,
Volume 10, Issue 26 (12-2019)
Abstract
Identification of genetic characteristics is an important factor for preservation of species life. The aim of this study was to identify the genetic characteristics of the Adani goat populations based on the cytochrome b (Cyt b) gene and to detec its phylogenetic relationships with the domestic and wild goat species using NCBI database. Blood samples were taken from 12 Adani goat and subsequently DNA was extracted using Sinaclon kit. The target area (892 base pair) was proliferated by specific primers using polymerase chain reaction (PCR) method and then sequenced. By analyzing the sequences, 5 haplotypes were identified based on 12 polymorphic sites. All mutation sites were transition and nonsense. The haplotype and nucleotide diversity and the average of a different nucleotide based on Cyt b region were estimated 0.57, 0.002 and 2.273, respectively. These results indicated high genetic variation in Adani goat. Using the NJ phylogenetic test results indicated that the Adani goat was located in the C. hircus branch and C. Aegagrus was in closer to them in compare with C. ibex. The placement of Capra hircus's goats and Adani goats in a similar branch is rational because of the dispersion of various races of this species throughout the world.
