MODERN GENETICS JOURNAL (MGJ)
Year:2013 | Volume:7 | Issue:4 (31)|Papers Count:15

Microorganisms are the base of life on the earth, and provide a high degree of biological diversity. This biodiversity can be used in improvement of our knowledge about new genes, metabolic pathways and their products. Identification of their genetic and biological diversity constitutes an important step of the research projects. Many microorganisms are nonculturable under in vitro conditions; therefore, it would limit our perception on physiology, genetic and ecology of microbial communities. Application of metagenomics tools (i.e. culture free methodologies for microbial diversity studies) provides good tools dominating this problem. Denaturing Gradient Gel Electrophoresis (PCR-DGGE) in metagenomics is one of the most efficient methods for differentiation of PCR fragments with the same size obtained as result of specific amplification of a determined gene through microbial community (e.g. 16S rDNA gene for prokaryotes and 18S rDNA gene for eukaryotes). In the other word, DGGE is a technique, which can separate fragments that are similar in size and different in sequence. Therefore, using DGGE methodology, diagnosis of microbial diseases and identification of microorganisms in environmental samples will be easier and faster. In this paper, we tried to report a short review on the mechanism, major applications, advantages and disadvantages of this technology.

Caspian trout (Salmo trutta caspius) is an anadromous and endemic subspecies of the Brown trout in the Caspian Sea. In recent years, there has been a tremendous decline in its population, which has exposed it to extinction. Sex determination of Salmonids, particularly from economic viewpoint, aiming to produce all-female populations which mature at older ages compared to males, has high importance in aquaculture. In this study, caudal fin clips from 10 female and 10 male specimens were analyzed with AFLP method using 96 different EcoRI/MseI primer combinations to determine sex-linked markers. Among primer combinations used in this study, 15 combinations produced different bands between males and females. However, after analyzing more specimens it was obvious that the detected bands were not sex specific and might be the result of the genetic diversity existing among individuals. The present study can be a good start in sex determination studies of Caspian trout; finally, the use of more primer combinations is suggested to find sex determination markers in Caspian trout.

Wheat has known as the most important cereal in world’s agriculture which has provided over to 30% of cereals of the world. Genetic variation is too important as the leaven of plant breeding. Like many other crops, the genetic variation is diminishing also in the wheat. Therefor, plant breeders are looking for the new gene sources they proposed the wheat native varieties its wild relatives as a potential useful valuable source of genetic variation which may applied on wheat breeding successfully. In this study, genetic variation of 30 genotypes of Agilops tauschii sp. Were investigated using SSR (Microsatellite) marker. Here, after the DNA extraction based on modified CTAB method quantitative qualitative evaluation of extracted DNA, DNA amplification (PCR) was carried out. Next, electrophoresis of amplified DNA on 3% agarose gelling agent was performed after the band appearing data analysis of genetic variation, number of 71 allels were recognized that 69 allels of them found to be polymorphic. Total mean of allel per locus was 4.6 mean value of 0.654 was calculated for polymorphism contents. The highest degree of dissimilarity was observed from 3 12 the lowest from 7 10 genotypes. The highest the lowest genetic gap of 0.85 0.265 respectively was obtained from dice of 0.92 0.42 from jacard method. Evaluation of dissimilarity between genotypes showed that northern regions of iran specially mazandaran province is the variety center the main origin of Agilops tauschii sp. this species has transferred from these regions to other places.

Morphinan group alkaloids in poppy are synthesized from two L-Tyrosine amino acids by 17 anzymatic stages through several continuous oxidative reactions. The first key enzyme on this path is L-Tyrosine decarboxylase (TYDC). Tyrosine decarboxylase is a common cyclic amino acid in plants which in different plant species, biosynthesis of a large number of primary and secondary metabolites depends on it. For over expression of this gene in opium poppy, a suitable gene construct named pBI121-TK was designed, so that Kozak Enhancer as a gene expression enhancer was added at upstream of TYDC2 gene’s start codon and was coloned in pTZ57R/T plasmid. Then, in GUS location under control of CaMV35S promoter and Nos terminator, it entered T-DNA area of pBI121 binary plasmid. Gene transfer optimization by GUS histochemical assay in agroinfiltrated plants was done by pBI121 plasmid containing GUS gene and eventually the agrobacterium containing pBI121-TK recombinant construct was transferred to six-week long plants according to the optimized condition. Amount of morphinan alkaloids was measured by HPLC device. The obtained results indicate 75.2% increase of morphine, codein and thebaine in recombinant sample relative to the control sample.

In this study RAPDs was used to study the genetic diversity between and within populations of F. imperialis. First 160 individuals were collected from 8 wild populations of F. imperialis from zagros regions. Of the primers tested, 6 (out of 35) RAPD primers were selected for their reproducibility and high polymorphism. A total of 71 polymorphic RAPD bands were detected out of 81 bands. Cluster analysis based on Jaccards similarity coefficient using UPGMA displayed a significant component of among-populations variance. Analysis of molecular variance (AMOVA) without grouping indicated that 45% and 55% of the genetic diversity were partitioned between populations and within populations, respectively. The total gene diversity (Ht) was 0.234 and the within populations gene diversity (HS) was 0.138. The gene diversity among populations (Gst) was 0.408. This study showed that low levels of genetic diversity within population and high levels of genetic differentiation between populations of F. imperialis have been revealed. The geological distances among populations would explain the limited gene flow and high genetic structuring among the detected populations of F. imperialis from Zagros range of Iran.

Root hairs play a role in the uptake of water and nutrients from the rhizosphere and serve as a site of interaction with soil microorganisms. The process of root hair formation is well characterized in Arabidopsis (Arabidopsis thaliana). The events of cell elongation and maturation occurring in the root have been suggested to be controlled by the extensibility of the cell wall and the turgor pressure inside the cell. Expansins are mainly considered as a primary agent for cell wall loosening and extension. These proteins are encoded by a superfamily of genes that are organized into four families on a phylogenetic tree α-expansin (EXPA), b-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB). It has been demonstrated the expression of a root-specific Arabidopsis expansin gene (AtEXP18) is tightly linked to root hair initiation. In this study, Full length AtEXPA18 was amplified using High fidelity and primers having SacI and BamHI overhangs. Then it was cloned into pGEMT vector. To make the final construct, both recombinant pGEMT carrying AtEXPA18 and pBI121 were digested with restriction enzymes and finally the AtEXPA18 fragment was inserted into the binary plant expression vector pBI121 under the control of a constitutive promoter, Cauliflower mosaic virus 35S (CaMV35S) and a terminator, NOS (nopaline synthase gene). This construct was then transferred into Agrobacterium tumefaciens strain LBA4404 and subsequently transformed into Arabidopsis thaliana via Floral dip method. Transformed Arabidopsis plants were selected on selective medium containing Kanamycin, and were confirmed with RT-PCR using Neomycin Phosphotransferase (nptII) and AtEXPA18 primers.

Yield of wheat (Triticum aestivum L.), as the most important crop always has been affected by environmental stresses and nowadays achiving favorabale and stable yield is desired for researchers. Protein variation is the basic part of plant response to environmental stresses and also adaptation to environmental conditions, so the present study was carried out in order to analyze the changes in content and profile of soluble protein in two organs (root and shoot) of seedlings in two sensitive (Ghods) and resistant (Alvand) cultivars. Results showed that effect of cultivars, stresses, organs and also interactions of stress×cultivare and stress×organe were significantly effective on protein content. In root apart from salinity levels, other stresses showed significant difference toward control treatment. Also in shoot apart from the first level of salinity and drought, the other treatments increased significantly. IN Alvand cultivar except of low temperature and the second level of salinity, and also in Ghods cultivar apart from the second level of drought, other stresses levels did not show significant difference toward control treatment. So soluble protein content wich is affected by different stresses, showd varied process of changes, depend on kind of cultivare and involed organ. Polymorphism in protein electrophoretic paterns on SDS-PAGE gels was observed in organs of cultivars under diffrent stresses.

Genetic diversity assessment and core collection establishment is useful for facilitation of germplasm management and better evaluation of genetic resources in breeding programs. In spite of high level of morphological diversity in alfalfa germplasm, it has not been intended enough in breeding programs. Hence, a field investigation based on a completely randomized block design with three replications was conducted to study the genetic diversity of 110 alfalfa (Medicago sativa L.) genotypes, belonging to 11 populations, using 13 morphological traits. The analysis of variance showed significant differences (P<0.01) among studied populations for all studied traits. Genetic and phenotypic coefficients of variation were high for most of the evaluated traits, indicating high amounts of both phenotypic and genotypic variation in the studied traits amongst populations assessed. Analysis of correlation coefficients among traits showed that increased stem weight is correlated with greater leaf weight. Principal component analysis (PCA) revealed that the first three components account for 88.1% of the total variation observed. The first component was positively related to total wet weight, total dry weight, leaf wet weight, stem wet weight and stem dry weight. The second component was affected by the ratio of leaf dry weight to stem dry weight as well as number of leaves. Chlorophyll content and plant height had positive correlation with the third component. Cluster analysis using Ward’s method grouped the studied populations in two main groups; each one fall into two subgroups. Assessment of available phonotypic variation could provide useful information in germplasm management and identification of suitable populations for different breeding purposes in alfalfa.

Maize dwarf mosaic virus (Maize dwarf mosaic virus) is one of the most important and widespread maize potyviruses in the world. In order to determine the taxonomic position of the isolates of the virus in Golestan province among cereal potyviruses and other strains of MDMV and its relationship with strains of other countries, corn and johnsongrass plants with mosaic symptom and dwarfing were collected from fields of Golestan province. Samples were verified using an antiserum against MDMV by indirect ELISA. The viral RNA was isolated from an infected sample and the 3’-region of the genome of virus was amplified using potyviral degenerate and specific primers by RT-PCR. The obtained consensus sequence for CP-UTR region was 1126 nucleotides. Comparison was made between these isolates and a number of other cereal potyviruses available in GenBank and phylogenetic tree was constructed by neighbor-joining majority- rule method. In phylogenetic analysis 46 sequences were grouped into 6 viruses: SCMV, PenMV, IJMV, SrMV, ZeMV and MDMV. In this tree, isolate of Golestan were grouped with isolate of Bulgaria. Based on this analysis the Iranian isolate of MDMV has been probably originated from Europe or more probable from Mediterranean basin.

In the hybrid rice production Technology, selecting the favorite lines based on allogamy characters and increase of A lines seed is necessary. Anther lenght, panicle exesrtion, pollen sterility, stamen filaments length, stigma length, glum length and floret number is important traits of the male sterile lines. Therefore the study of seven cytoplasmic male sterility lines (release from IRRI) their maintenance and 33 male sterility lines derived of backcross (release from Iran) using was randomized complete block design. Anther lenght, panicle exesrtion, pollen sterility, stamen filaments length, stigma length, glum length, floret length, floret width, pollen fertility, panicle length, panicle exsertion rate, percentage of allogamy, Days to flowering were evaluated. The results of pollens sterility indicated that the 4 CMS lines, Neda A, Nemat A, Shastak Mohammadi A and Gerde A were completely sterile. Induction of sterile cytoplasm has led to partial exsertion of panicles. Mean comparison of traits showed that male sterile line of Hasani AR has the longest length of stigma (2.93 mm) and shortest length of anther (1.87 mm), respectively. But out crossing percentage of this was very low. Also, IR69224A showed complete sterility, with out-crossing percentage of x-=%37.79. Pollen sterility, number of florets per panicle, legume and stamen length traits has been high genotypic coefficient of variation, inheritance, genetic progress. These traits can be as selection criteria of cytoplasmic male sterility lines with out crossing rate high. Dasht A (dasht×IR68899A), Khazar A, Hasani A, Gerde A, Sang tarom A, Shastak mohammadi A with their maintainer lines were categorized in different groups. Results of this research can be suitable for parental selection and hybrid rice production program.

Genome studies of different plant until 1998 revealed that about 50% of the newly identified genes, show sequence homology and conserved genomic order in compare with those have been known in the past. This became the concept for emergence of comparative genomics. Using micro-synteny and molecular colinearity among barley un-sequenced and some sequenced genomes belonging to tribe Poaceae (Gramineae) including rice, maize and Brachypodium, the chromosomal location of the gene dense spike (dsp.ar) was investigated. The gene dsp.ar is one of the developmentally genes in barley associated with spike morphology and grain yield, which is economically very important. A 3:1 segregation ratio was observed for the dense spike phenotype among F2 plants obtained from the cross Bowman x BW265, indicating that a single gene is responsible for the phenotype. Saturation of centromeric region of barley chromosome 7H was accomplished by developing STS, EST and SNP markers and converting those to PCR-based markers by either CAPS or Pyrosequencing. Among 1993 progenies of this population, 39 lines showed recombination for polymorphic markers. The link flanking markers CAPSK06413 and SC57808 for dsp.ar gene with less than 1cM distance can be utilized for marker assisted breeding (MAS) and map-based cloning of this gene in further studies. The methods used here can be generalized to define strategies for other plant genes and genomes and utilized in plant molecular breeding projects as well. Here describe in details will be discussed.

In the present study the polymorphism of promoter region of Insulin-like growth factor 1 gene (IGF1) of west Azerbaijan native chickens was investigated. A number of 100 chickens were randomly selected from west Azebaijan native chickens breeding station and blood samples were collected. DNA was extracted from blood samples in order to amplify a fragment of 813 bp in size from IGF1 gene. The amplified fragments were subjected to restriction digestion with HinfI endonuclease and the resultant digested products were run on 2% agarose gel. The results revealed the existence of two alleles A and C for the examined locus with frequencies of 24.5% and 75.5%, respectively. Three different genotypic variants including AA, AC and CC were identified with genotypic frequencies of 5%, 39% and 56%, respectively. Chi square test based on observed and expected frequencies of different genotypic variants of IGF1 gene showed that deviation from Hardy-Weinberg equilibrium was not significant for West Azerbaijan native chickens. On the basis of obtained results it was revealed that the IGF1 gene had high degree of polymorphism and the relationship between these polymorphisms of IGF1 gene and native chickens economic traits could be assessed in chickens breeding programs.