جستجوی مقالات مرتبط با کلیدواژه "توالی یابی" در نشریات گروه "بیوتکنولوژی و ژنتیک گیاهی"

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

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

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

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

In order to detection and differentiation of two complications of disorder and lack of podding in soybeans, while visiting 185 soybean fields in Golestan and Mazandaran provinces, only from the summer cultivation of 17 fields from five different places in Golestan province, plants with signs of disorder and the lack of acute podding were identified and 17 samples were selected from each field and sampling was done from the leaves or stems of the mentioned plants in order to extract RNA and DNA. Then, PCR was performed to detect nepovirus using the degenerate primer of nepovirus and to detect phytoplasma using a pair of general primers and a nested PCR test. The results of electrophoresis confirmed the amplification of the 1800 bp band in the general PCR, the 1250 bp fragment in the nested PCR related to phytoplasma, and also the amplification of the 640 bp band related to a nepovirus. Besides, no band of healthy plants was observed. at the same time, tissue grafting and mechanical inoculation were performed on GPX soybean benchmark plant using the mentioned samples and two types of symptoms appeared. From the sequencing of the disordered samples (production of a small number of seeds and small pods), Tomato ring spot virus strain ep31_63026 and from the sequencing of the samples with non-encapsulation (grassiness and no formation of pods and seeds), Aster yellows phytoplasma from the 16SrI-B group were identified, which confirmed the results of the reference plant. The phylogenetic analysis of sequencing results confirmed the presence of Phytoplasma and Nepovirus only in the summer culture of samples that had symptoms of disorder and lack of podding.

The high nutritional value has made potato the fourth most important food source after wheat, rice and corn worldwide. In this study, in order to identify and investigate the expression pattern of the most significant genes involved in the synthesis of flavonoids at different potato tuber developmental stages, the RNA sequencing data was obtained from three different potato tuber development stages, namely; initiation of stolon formation, stolon swallowing and initiation of tuber formation. In order to validate the expression of identified genes involved in the biosynthesis of flavonoids in potato tuber (62 genes), the expression of significant genes were evaluated by using qRT-PCR method. The results of this study showed that at the stolon swallowing stage, 10 and 11 genes had a significant increase and decrease in expression, respectively. Comparing the stolon swallowing stage with initiation of stolon formation, 7 and 20 genes showed a significant increase and decrease in expression. At the initiation of tuber formation, it was found that 14 genes had a significant decrease in expression. In total, 4 key genes CYP98A3, ACT, SAT and BEAT were identified with significant changes among developmental stages. The amount of flavonoid in the three developmental stages was also significantly increased with the transition of developmental stages. The average of flavonoid content was 1.9, 7.2 and 24.8 mg/gFW for tree developmental stages, respectively. Since CYP98A3, ACT, SAT and BEAT are key genes involved in the biosynthesis of secondary metabolites in the potato tuber, they can be considered as possible candidate genes for alteration of flavonoids content in potato.

The aim of this study was to investigate the nucleotide diversity and the phylogenetic analysis of pancreatic ribonuclease gene in two different species, Baluchi and Urial sheep. Baluchi sheep blood samples were collected from Abbas Abad Animal Breeding Center, Mashhad and Urial sheep blood samples were collected from Khorasan Razavi Environmental Department. The 4347 bp pancreatic ribonuclease gene was amplified and sequenced using seven primer pairs that were designed to overlap each other. Comparison of 4347 bp pancreatic ribonuclease gene sequences obtained from both Baluchi and Urial sheep strains showed 10 nucleotide differences with 99.78% similarity. Also results of comparison of pancreatic ribonuclease gene from the sheep reference genome (Accession number of XM_004010384) with Urial sheep and Baluchi showed differences in 18 nucleotides with 99.61% similarity and 10 nucleotides with 99.78% similarity, respectively. The results of the present study confirmed that although the pancreatic ribonuclease coding enzyme sequences of the two species, Baluchi and Urial and the reference gene sequences from the NCBI database are completely similar, but the upstream and downstream nucleotide sequences of this gene have 10 nucleotide differences with each other. There are 18 nucleotide differences with the sheep reference sequence. Results of genetic interval matrix and phylogenetic tree sequences of Baluchi sheep and Urial sheep obtained in this study with other gene sequences registered from pancreatic ribonuclease in the NCBI database, it confirmed that both Baluchi and Urial sheep species with the sheep reference sequence for pancreatic ribonuclease gene sequence were assigned to a goat species belonged to the same clade.

Drought is one of the most important abiotic stresses in agriculture, which limit crops production. Drought tolerance is a complicated trait that is controlled by polygenes, which is expresses the difficulty of breeding of drought tolerance. Variety of strategies has been used to improve this trait in crops, including traditional selection methods and genetic engineering. In this case, irradiation is an appropriate approach for improving the level of genetic variation in a short time. Many studies show that the expression of most genes in environmentally variable conditions is based on the combination control of several transcription factors and their binding to the elements in the promoter. Therefore sequencing of one of the genes involved in the degradation of proteins (26Sp7) using genome sequencing, sequencing of promoter using NEW PLACE and plantCARE software, And the expression pattern 26Sp7 in mutant line T-65-58-8 (semi-drought tolerant) derived from Tabasi (drought-sensitive) radiated with gamma rays in seedling stage during drought stress by QRT-PCR were studid. The expression of the 26Sp7 in Tabasi and mutant showed an increase in all stress treatments. So, in the mutant line, it has peaked in 3 hours after start of stress. On the other hand, in Tabasi, with the onset of drought stress, the expression of this gene increased, until it reached maximum in 48 hours after stress. The expression in the Tabasi showed an increase in gene expression in all stress treatments, which in turn probably indicates the destruction of proteins in drought stress treatments, which also verified the sensitivity of this variety. on the other hand, the promoter sequences of this gene indicate regulatory elements during drought stress such as dehydration responsive elements (DRE) and the binding site of MYB and MYC proteins and abcisic acid responsive elements (ABRE) and responded to light (GT) and gene transcription regulator elements such as the TATA box and the CAAT box. Thus, the increased expression of this gene during drought stress may be attributed to the binding sites of transcription factors that cause this gene expression during drought.

Cynara cardunculus L is a diploid herbaceous plant and perennial. Artichoke sugar is a fructan that has the least effect on blood sugar and is very useful for diabetics in this regard. The aim of this study was to isolate, identify, and evaluate the relative expression of the fructan 1-exhohydrolase gene (FEH1) gene in the artichoke plant. In order to identify and evaluate the molecular evolution of FEH1 gene, DNA was extracted from leaf samples of artichoke and after amplification was sequenced by PCR technique. Also in order to investigate the effects of salinity, silver nanoparticles of green synthesis and salicylic acid on the change of relative expression of FEH1 gene, an experiment was performed as a factorial in a completely randomized design in a greenhouse. The relative expression pattern of this gene was measured by Real Time PCR. The results of analysis and analysis of nucleotide sequences of the FEH1 gene showed that the highest frequency belonged to Guanin (31.56) and the lowest frequency belonged to Tymien base(12.4). The results of the Neutrality test also showed a directional choice on this gene during evolution. A phylogenetic study of the FEH-1 gene sequence and its comparison with other similar sequences in different plants proved that the similarity between the studied sequences was high(more 90%) and the plants were slightly different from each other in terms of genetic distance. The results of comparing the mean interactions of salicylic acid and salinity concentrations showed that the application of 12  ds m-1of salinity alone significantly increased the expression of FEH1 gene at the probability level of one percent. The use of salicylic acid in combination with salinity moderated the effects of salinity and also reduced FEH1 gene expression. Also, the results of comparing the average interaction of salicylic acid and nano silver concentrations showed that in the treatment of 200 and 400 mM salicylic acid with 40 mM nano silver at the probability level 1% expression of FEH1 gene in artichoke plant increased significantly. Clearly, it was found that both in terms of expression and expression intensity of FEH1 gene, there is a high potential to focus on increasing soluble sugars and ultimately increase plant tolerance to salinity stress in artichoke .

Identifying the genetic diversity of native goat breeds of Iran can play an important role in the management and conservation of these breeds. The purpose of the current study was genetic and phylogenetic investigation of mitochondrial genome cytochrome b region in Lori, Pakistani, Zaboli and Adeni goats.

Blood samples were collected from 16 goats of each breed 4 blood samples. After extracting DNA, fragment 684 bp of cytochrome b region genome mitochondrial amplified by primers were designed and fragment amplified after purification was sequenced. Using the DNAsp software was determined in six different haplotypes.

 The result of comparative analysis between goat breeds indicates that nucleotide diversity Pakistani and Zaboli breeds 0.35461 and 0.11199 respectively. Tajima D was obtaining 1.06945 that was significant. This confirmed the evolution by natural selection. Results from the analysis of molecular variance indicated that genetic variation was 80% of within and 20% was between populations that indicates high gene flow, migration among the studied populations or little sample size.

Based on a phylogenetic tree analysis, Lori and adni goat form a group with Capra hircus and Pakistani and Zabli goats form a separate group. This indicates the goat breeds have a common origin area.

This research was conducted to evaluate the diversity and molecular confirmation of oat gaze by DNA barcoding method. Moringa seeds were cultivated in Baluchestan province of Baluchestan province including Bennett, Kishigh, Desh, Madhadi village, Nesfaran, Condar, Tang Fanvjh entrance, mouth and seven girls. After three months, the DNA was isolated from the leaf samples and the ITS2 region was amplified and sequenced. The ClustalW sequences were combined with Mega7 software, clustering and genetic similarity and spacing. The intrinsic similarities of the Moringa Baluchistan specimens were detected in the range of 99.9%. In the present study, ITS2 did not distinguish between Balochistan's ten variants in terms of genetic variation within the group. Therefore, in order to evaluate the ability to evaluate the genetic diversity of the species, another test was performed, so that the sequences of other species of Moringa family were used in NCBI, and the Moringa sequence of the present study was compared. The Moringa-Baluchestan sample sequence with Ethiopic peregrine sequences showed homology of about 92%. The emergence in this method showed that the studied populations were divided into five groups and it was determined that the similar species were placed in the same branch. The Moringa-Baluchestan sample sequence was grouped with sequences of peregrine species in one group.Since the Moringa species in Balochistan have been introduced based on morphological keys in the Iranian flora, peregrine has been introduced. Based on the results of this study, the same was also recognized and confirmed through molecular.

This study was conducted to evaluate phylogenetic and taxonomic statue of Alburnoides parhami using COI molecular marker and morphological data. For this purpose, topotypes of 10 species of the genus Alburnoides were sampled from 6 inland water basins during 2014-2016. For morphological study, 29 morphometric and 8 meristic characters were measured and counted. For morphological comparison of this species and its closest relative based on molecular data i.e. A. holciki, Principal Component analysis and MANOVA were used. The gene of COI were analyzed using Maximum likelihood and Bayesian methods to reconstruct their phylogenetic tree. Based on the results, A. holciki and A. parhami could not differentiated based on morphological characteristics. The molecular results based on COI gene revealed a small divergence i.e. these two species were different in one nucleotide position based on nucleotide parsimony polymorphism. Therefore, it is suggested that A. parhami is junior synonym of A. parhami.

Casein is the most important part of the milk protein. Casein genes and their expression regulation have been the subject of extensive research due to their economic importance. Finding important regulatory elements and specific polymorphic alleles in the casein promoter region of the casein gene provides a good basis for marker assistant selection. The objective of this study was sequencing, bioinformatics analysis and motifs evaluating of partial beta-casein promoter in Dromedary and Bactrian camels in Iran. The other goal of this study was to investigate single nucleotide differences (SNPs) in Dromedary camel and Bactrian camels of Iran.
Ten blood samples of male and female Dromedary camels from the slaughterhouse of Mashhad and 5 blood samples of Bactrian camels from the Natural Resources of Animal Research Station of Ardebil province were collected. After the DNA extraction, PCR reaction performed by gene specific primers and samples were sent to Bioneer Company for sequencing. Consensus sequence were obtained for Dromedary and Bactrian camels and motifs, phylogeny analysis and haplotypes were studied.
Based on the comparison of the sequences obtained with the sequences recorded in the NCBI database (part of the whole sequence), it was found that the studied region does not have SNPs, despite different haplotypes. The study revealed eight type of haplotypes in Dromedary camels and five haplotypes in Bactrian camels.

Diploid genome contains 8 genomes designated as A, B, C, D, E, F, G and K which have been identified in the genus Gossypium. The genome of A is limited only in two species as G. herbaceum and G.arboreum, and it is transferred from G. herbaceum to other species. The chloroplast genome (CP) of G. herbaceum has 160,140 bp lengths with protected quadripartite structure. Single copy regions of chloroplast genome are separated by two inverted repeat regions with a large copy region with 88,709 bp also the single copy region and each small inverted repeat regions have 20,221 and 25,605bp. The plastidic' s genome has 113 single copy genes and 19 duplicated copy genes. Single copy genes are encoding of 79 genes for protein production, four ribosomal RNA genes and 31 transfer RNA genes. Result showed that among all plastid genes only 18 genes appeared to have 1-2 intron/s and when compared with chloroplast genome of two allotetraploid species. Ycf15 gene as the only duplicated gene, rpl22 was in G. herbaceum and in the two species has studied G. herbaceum, G. barbadense. But ycf15 gene in G. barbadense and both ycf15 and rpl22 genes were lost in G. barbadense and G. hirsutum. Though the high level of SSR protection in the chloroplast genome. SSRs are useful for genetic variation analysis since they have high efficiency against genomic SSRs.

Khalkhali goat is an Iranian indigenous goat that the number of population has been decreasing nowadays. Study about the practical genetic structure is necessary for biodiversity conservation of native breeds. The aim of this study was the sequencing of Cytochrome b gene of 100 Khalkhali goat and comparison with other goat species using bioinformatics data (26 samples). we used the sequences of NCBI data to compare between goat species. The results of sequencing led to the identification of 5 mutations with 6 Haplotypes in Iranian Khalkhali goat samples. The haplotype diversity, nucleotide diversity and the average of a different nucleotide were 0.644, 0.002 and 1.822 respectively. Tajima D was obtaining 0.124 that was not significant. The result of comparison analysis between goat species indicates that nucleotide diversity in Capra hircus, Capra ibex, and Capra aegagrus were 0.047, 0.022 and 0.001 respectively. The highest genetic distance observed between Ibex and aegagrus, while the lowest was between Khalkhli goat and Capra hircus. In compare with aegagrus goat, the ibex goat was closer to Capra hircus.

Sequencing and analysis of the data obtained are best and most common methods in studies of genetic diversity. PIT-1gene is known as growth hormone IGF-1 gene. this gene is a member of family of transcription factors in the poultry is located on chromosome 1, with a length of approximately 14 kb. This gene has seven exons and five introns in poultry. The purpose of this study was analysis region of intron 5 sequence of PIT-1 gene in broiler chickens Arian lines and determining its phylogenetic relationship with other chicken breeds. For this study, blood samples were collected of seven broiler chickens of both sex Arian lines. After extracting DNA from them, target gene was amplified with specific primers and after purification was sequenced. Five different haplotypes were determined based on six single nucleotide polymorphism sequence and the final sequences of each haplotype with length approximate 260 bp which includes 21/92 % adenine, 18/8 % guanine, 32/69 % cytosine and 27/31 % thymine. After ensuring the accuracy of sequencing, submitted to gene bank database (NCBI) with accession number of JQ946630- JQ946636.The phylogenic tree was drawn with consensus sequence of PIT-1 gene of Arian line chicken and other similar sequences of different chicken breeds obtained from gene bank. Results the phylogeny indicated that Arian line chicken and American Chickens are on a lineages

One of the important perennial herb in Apiaceae family is Black caraway (Bunium persicum) which is growing naturally in some regions of Iran and a few neighboring countries. In order to evaluate genetic diversity of Iranian germplasm، nine ecotypes of the species were collected and their ITS2 and ITS1-5. 8s rRNA- ITS2 regions were amplified by PCR and sequenced. Sequences were aligned in the ClustalW method by using MegAlign program. Phylogenic dendrogram، identity and divergence matrices were designed. Low genetic diversity was found among the ecotypes in comparison with previous studies via morphological and biochemical markers. Comparison of the sequences of ITS1-5. 8s rRNA- ITS2 regions of two ecotypes (Mashhad University and Kalat Naderi) with ref-seq genomic database at NCBI، showed the highest similarity with Sorghum bicolor، Oryza sativa، Arabidopsis thaliana and Vitis vinifera sequences. Considering low similarity between the results of two distinct studies of the authors، results of morphological and biochemical markers are more reliable than molecular markers (ITS2). It could be concluded that the ITS2 molecular marker does not seem to be compatible for intra-species studies. Other convenient molecular markers for assessment of genetic diversity of black caraway are suggested.

to investigate the phylogenetic relationship of Schizothorax zarudnyi, Schizocypris altidorsalis, Barbus sharpeyi B. subquinciatus, B.xanthopterus and B.esocinus, the native barbinae species South of Iran, 10, 10, 5, 3 and 4 samples were collected from Chahnemeh’s reservoirs and Karoon River and transferred to laboratory. Genomic DNA was extracted from fin tissue by phenolchlorophorm method. PCR was performed using pair specific primers to amplification 980 bp mitochondrial cytochrome b (Cyt b) region. After checking the PCR products by electrophoresis, then they purified using purification kit and directly sequenced. Results showed that Schizothorax zarudnyi and Schizocypris altidorsalis form a monophyletic group that is sister group with Barbus sharpeyi than other species. Based on comparison Cyt b sequences of all barbus species suggested that Iranian barbinae were paraphylitic than other species. In fact, this position reflected that variation and diversion in Iranian barbinae take place in long time and independently than other barbinae in the world. The reported results could be of interest for management and conservation programs of this valuable native species.

Insulin-like growth factor I, IGF-I, plays important roles in different biological activities in fish. The present study was aimed at isolating cDNA encoding IGF-I and measuring relative gene expression levels in different tissues in the beluga, Huso huso one of the most important Iranian sturgeon. A fragment of 1229 nucleotides coding for IGF-I was cloned (AB512770.1) from liver using RACE-PCR. It included 483 nucleotides encoding sequences for deduced IGF-I protein (BAH85795.1). Deduced IGF-I involved 160 amino acids and included both the signal peptide and the proIGF-I. The proIGF-I consisted of B, C, A, D and E domains. Comparison of IGF-I in beluga and some animal species from different phyla showed high similarity especially with birds. Expression levels of IGF-I were analyzed in stomach, gill, liver, spleen, kidney, muscle, skin, intestine, heart and brain using real-time PCR. The results showed that although IGF-I expressed in all analyzed tissues, the highest IGF-I transcript levels were in the liver and intestine tissues. The lowest transcript level was measured in the muscle. The results of the present study can help scientists evaluate different aspects of molecular physiology in the beluga