MODERN GENETICS JOURNAL (MGJ)
Year:2019 | Volume:13 | Issue:4|Papers Count:9

Rhizobacteria that benefi t plants by stimulating growth and suppressing disease are called plant growth promoting rhizobacteria (PGPR) which includes rhizobia. In addition to nitrogen supply, rhizobia promote the growth of plant root system and improve nutritional uptake. In this research, for isolation and identification of rhizobacteria especially rhizobia in a symbiotic relation with non-cultivated legumes, 21 plant samples from 12 non-agricultural sites of Alborz province were collected. In order to isolate bacteria, serial dilutions were prepared from nodules, rhizosphere soil and roots. Bacteria were cultured and purified on YMA medium and morphological and biochemical characteristics of isolates were studied. In total, 16 purified strains were obtained. Bacterial DNA of all strains were extracted and 16S rRNA gene was amplified with specific primers using polymerase chain reaction (PCR). Strains were identified by sequences of this gene and using EzTaxon database. All isolated strains in this research belonged to 12 species. PCR reactions were also done for atpD, nodA and nifH genes by specific primers. Phylogenetic trees were constructed by maximum-likelihood statistical method and evolutionary distances were computed by using the Tamura-Nei model. Based on the obtained results from four strains of Ensifer meliloti which were isolated in this study, only Tal31 strain showed a higher growth with the increace of NaCl from one percent to two percent (w/v), therefore this strain is probably salt tolerant. This is the first time that Rhizobium laguerreae (Tal71) and Neorhizobium alkalisoli (Krj1) were isolated from root nodules of Trifolium pretense and Colutea buhsei respectively. These findings show that the host range of rhizobial strains are broader than it was estimated before.

The rumen is described as one of the most elegant and advanced cellulosic digestion systems in nature. The ruminal microbiome, by attaching and formatting microcolonies on feed particles and releasing the fiber degrading enzymes, decompose lignocellulose compounds and convert them into compounds that are usable for the host animal. The purpose of the present study was identifying and understanding the relationship between the most important bacteria that colonize rice straw during ruminal incubation and also comparing the amplicon and shotgun data generated on incubated rice straw during 24, 48, 72 and 96hrs in three fistulated animals. After bacterial isolation and DNA extraction processes, two sequencing strategies of Illumina Miseq 300PE and Hiseq4000, 100PE were used to sequence the V3-V4 region of 16S ribosomal RNA and the total metagenome. Taxonomic profiling, microbial diversity and species richness were separately prepared for each dataset and comparative analysis was performed. The results indicated that there are synergistic and/or overlapping effects among the members of the identified phyla, and with considering the frequency, it seems that the members of the Firmicutes, Fibrobacters, and Spirochaetes play a critical role in the colonisation process. Our study showed a weak correlation between the two methods, indicating that while taxonomic overlap exists in the phylum and family levels, the methods are different. The most highlighted difference between the two sequencing methods was species-level identification, which the Hiseq method appeared much more robust in terms of genomic coverage and taxonomic profiling algorithm. It was also observed that the selective software for taxonomic profiling could play a vital role and even more differentiation power than the technology utilized for whole metagenome and gene-targeted sequencing.

Olive is considered one of the most significant crops, with more than 1200 distinctive cultivars and an abundant number of wild forms. In this study, the genetic diversity in a set of Iranian and foreign olive cultivar was evaluated using ISSR primers. Using 16 ISSR primers, a total of 190 bands amplified, which out of 172 were polymorphic. The average of resolving power (Rp) and polymorphic information content (PIC ) was 10. 22 and 0. 45, respectively, hence this indicating the high efficiency of these primers to further genetic diversity assay. The results of analysis of molecular variance (AMOVA) showed 7% of the total genetic diversity refer to among groups, while 93% of the total variation was found within groups. The average percentage polymorphic loci (PPL), number of observed (Na) and effective (Ne) alleles, Shannon’ s information index (I), and gene diversity (H) are 82. 11%, 1. 73, 1. 43, 0. 39 and 0. 26, respectively, and Iranian cultivars showed higher amounts of all parameters than foreign cultivars. Genetic relationships inferred from a neighbor-joining dendrogram clustered cultivars into main three groups. This grouping pattern was matched with the groups obtained by principal coordinate analysis (PCoA). Taken together, the results obtained from this study indicate the ISSR primers used in this work will be useful for genetic diversity and phylogenetic studies in the olive cultivars. Hence, the use of these primers in other genetic studies like QTL and association mapping are recommended.

Salinity is one of the main osmotic stresses limiting plants growth and development through changes in osmatic and ionic balance. In order to mapping of the genomic regions of controlling quantitative trait locus (QTLs), related to salinity tolerance in barley and assessment of associated indices, an experiment was conducted during 2016-2017 using 100 families of barley along with their parents (badia × comino) in randomized completely design with three replications. The application of stress in four leaf stages of barley was applied as salting with a 10-day interval. Irrigation with 5 dS of water was started and in next steps, the salinity of irrigation water increased at 10, 15 and 20 dS / m2. In total 12 QTLs detected in the situation of normal and 8 QTL in the stress. condition. Total phenotypic variance explained by the QTLs varied from 9 to 14. 3 percent, which the lowest related to stem length, chlrophyll content under normal conditions and the highest related to total number of leaves under stress conditions. The highest LOD was the total leaf weight trait obtained under stress condition (3. 354). Stable QTLs in three environments as well as linked markers could be used in the marker assisted selection (MAS) to improve characteristics under salinity conditions at different trials replicated over years.

The emergence antibiotic resistant among pathogenic bacteria has become a serious threat to global public health in recent decades. With regards to the increasing prevalence of resistance to conventional antibiotics, many studies have focused on the development of antimicrobial peptides as an alternative antibacterial therapy. Defensins, are group of cysteine-rich antimicrobial peptides that are present in animals and plants. They are as components of the host defense system which acts against pathogens and pests. The purpose of this study was to identify, clone and characterize of some defensins genes from oat plant. For this purpose, the complete gene family of wheat was retrieved from GenBank and aligned against oat plant transcriptome. The resulted sequences were assembled and obtained contigs and singletons were aligned against nr database using BLASTn tools. The results were evaluated for the presence of complete ORF and sequences with complete ORF were used for primer designing. Then, the total RNA was extracted from oat pooled tissues and cDNA were synthesized. The fragments were amplified, cloned in pTZ57R/T vector and sequenced. The results of bioinformatics analysis, confirmed the presence of the nine genes encoding defensin in oat plant transcriptome. Five of these genes were cloned and sequenced. These genes contained the complete ORFs between 234-246 bp that produced peptides with length 77-81 amino acids. In addition, identified defensins comprised Knot1 functional domain from the gamma-thionin family. Identification and characterization of genes is the first step in the genetic engineering and production of organisms with favorable traits. In this study for the first time, the complete coding sequence of five defensin genes were isolated and characterized from the oat plant.

Plant organs and latex of greater celandine are rich in isoquinolin alkaloids that sanguinarine, a member of benzofenanthridine, is one of the most important metabolites, which its accumulation mainly reported in the roots. Sanguinarine biosynthesis requires seven enzymatic steps from the pre-substance s-reticulin using berberine bridge enzyme (BBE), cheilanthifoline synthase (CFS), stylopine synthase (STS), tetrahydroprotoberberine cis-N-methyltransferase (TNMT), protopine 6-hydroxylase (P6H), S-cis-N-methylstylopine 14-hydroxylase (MSH) and dihydro benzophenanthridine oxidase (DBOX). The study of biosynthetic pathways and the identification of factors affecting the production of secondary metabolites are important steps in metabolite engineering. Nanoparticles are a new category of elicitors that act as inducers for the production of secondary metabolites. For this purpose, the effect of titanium dioxide nanoparticles was investigated on the expression changes of the celandine sanguinarine biosynthetic pathway genes in a factorial experiment with three factors included titanium dioxide concentrations, spraying period and post-induction time. Analysis of variance for the expression of STS, P6H, BBE and MSH genes revealed significant differences in titanium dioxide concentrations, post-induction times, spraying period, different organs and their interactions at P≤ 0. 05, 0. 01 levels of probability. The accumulation of STS and P6H transcripts in the roots was 2-3 times higher than the leaves and stems, and also the transcripts of the BBE and MSH genes was four times higher in the root than the stem. Totally, the concentration of 500 mg/L titanium dioxide increased the expression of STS, P6H, BBE and MSH genes by 63, 66, 500 and 91%, respectively, relative to control treatment. The 24 and 48 hours post-induction time resulted in maximum expression in all four studied genes in comparison to 72 hours post-induction time, and 500 mg/L titanium dioxide showed the highest expression for STS, P6H and BBE genes, and 1000 mg/L for MSH gene. From the results it can be concluded that titanium dioxide nanoparticles are effective in increasing the production of celandine sanguinarine through the regulation of its biosynthetic pathway genes.

Wheat is the most important crop that is the main source of food for 40 percent of the world's population. This crop has a high adaptability and cultivated in a wide area of the world. The importance of wheat is due to the special properties in water absorption and elasticity of its dough. It is due to the presence of gluten protein in seeds endosperm. The variation of glutenins in wheat and its seven close relatives were investigated using four specific primers of glutenins. Sequences of replicated DNA were compared with the NCBI database data, and sequences which were more than 90% similar to a LMW-Gs or HMW-Gs of wheat were used to investigate. The results showed a high similarity between glutenins genes in wheat and other related species. However, it was observed that in many cases, similar fragments were differed in different species and there is a variation for the sequence of nucleotides among these species. Investigation of phylogenetic relationships among species showed that T. aestivum, and T. boeoticum species, which are similar in genome A, as well as Ae. tauschii, the parent of the wheat genome D, is very similar in terms of the structure of gluten genes and they located in similar clusters in phylogenetic trees. Although Ae. juvenalis and Ae. vavilovi do not show more similarity to each other, they both have a great similarity to their parent species Ae. crassa, and usually grouped together in the same cluster. The wide diversity for these proteins, among the wheat relatives, as well as the close phylogenetic relationships and the convergence of these species with wheat, makes it possible to use this great genetic diversity in wheat breeding programs

The plant family Lamiaceae contains several species with potential therapeutic activity due to their essential oils. In this study, the chloroplast genes of two species of the Lamiaceae family, Thymus syriacus and Salvia nemorosa, were sequenced to make the identification of these two species quickly and accurately. The genes matK and rbcL were used for sequencing Thymus syriacus and matK, trnL-F for Salvia nemorosa. At first, genomic DNA was extracted from the leaves of these two species, then the sequences of the desired chloroplast genes were amplified and eventually sequenced. The sequence of the obtained chloroplast genes can be used in other phylogenetic and evolutionary studies to compare the species and could therefore provide more accurate results within a shorter time especially in large-scale studies. The results shows that chloroplast regions as matK, rbcL and trnL-F can be used as DNA barcodes for identification of Salvia nemorosa and Thymus syriacus species.

Hypericum perforatum has many medicinal properties such as anti-inflammatory, anti-bacterial, anti-viral and anti-tumor; but has been reported its greatest effect on the treatment of depression which is attributed to Hyperforin and Hypericin conjugates. The aim of this study was to evaluate the effect of chitosan (0, 50, 100 and 200 ppm) and silver nanoparticles (0, 30, 60 and 90 ppm) on expression of Hyp-1 gene. For this purpose, a real-time PCR experiment was carried out in a completely randomized design with three replications in two time period such as 48 and 72 hour. The results of analysis of variance were showed that interaction of silver nanoparticles, chitosan and time period was significant on the expression of Hypericin gene (P <0. 01), so that the highest expression of Hyp-1 gene was obtained from 50 ppm chitosan with no silver nanoparticles in the period time of 48 hours. Overall, the results of this study showed that silver nano particles had a negative effect on Hyp-1 gene expression, and with increasing concentration of silver nanoparticles, the expression of Hyp-1 gene decreased. However, chitosan had a positive effect on Hyp-1 gene expression, but by increasing the concentration to 200 ppm, the amount of gene expression decreased.