مجله بیوتکنولوژی کشاورزی
سال سیزدهم شماره 3 (پیاپی 44، پاییز 1400)

Drought stress is the main restriction factor in crop production that has an adverse effect on crop quantity and quality. Canola, like many crops, is affected by stress due to water deficit. At the cellular level, plants respond to drought stress by synthesizing specific proteins. Therefore, a research with the aim of studying the response mechanism of canola to drought stress and determining proteins involved in mediating stress tolerance was carried out. 

In order to comprehend a mechanism of canola plant response to drought stress, the protein profiles of the drought-tolerant Hyola308 and drought-sensitive Sarigol leaf under different drought stress conditions based on a gel-free/label-free proteomic technique were investigated. To validate the content variation of proteins identified in the proteomic analysis, Western blot analysis was used. 

A total of 56 proteins were identified in Sarigol and Hyola308, 16 proteins were specific to Hyola308 and 16 proteins were specific to Sarigol, respectively. Of the identified proteins, 12 proteins were commonly detected between Sarigol and Hyola308. In Sarigol under different drought stress conditions, the abundance of proteins related to protein metabolism, photosynthesis and energy metabolism decreased; whereas, in Hyola308, an enhancement in proteins abundance involved in photosynthesis, energy metabolism and antioxidant defense was observed. 

It is inferred that enhancement of these protein abundance in Hyola308 leaf may be a part of tolerance mechanism of this cultivar exposed to stress and decrease in the Kelvin cycle efficiency and production of sugar and energy in Sarigol may justify growth reduction of this cultivar.

Yaghooti seedless grape is one of the early-ripens variety of grapes in Iran where its fruit marketed by mid-May. This grape has high resistance to extreme heat of the region, which made Yaghooti grape one of the unique and exclusive products of the province and country. Heavy heat-shock proteins like HSP60, HSP70 and HSP90 seems to have key role in survival and rescue the plants against the heat-stress. By considering this unique feature of the plant and key role of the HSP-70 protein in said process studied and analyzed in all three stages of cluster growth and development under influence of hormonal treatment of abscisic acid, gibberellic acid and Indole-acetic acid.

Plant materials used for total RNA extraction were sampled in three stages: cluster formation, berry formation and final size of cluster growth process. Specific primers of HSP-70 gene (1104687527) and Actin-7 gene (100232866) as housekeeping gene were designed by CLC main workbench and used for Real Time-PCR reaction. Finally, the relative expression was calculated based on the obtained Cts using Pfaffl formula. The results were analyzed using a completely randomized factorial design and Duncan test with a significance level of 0.01 using SAS 9.0 software. The co-expression network was rebuilt using Cytoscape software.

The relatively highest expression obtained for the HSP-70 at the 2nd stage of development simultaneously with the flowering and under influence of abscisic hormonal treatment. Elevation in the level of abscisic acid resulted in upregulation of ABI2 gene that subsequently supresses the internal synthesis of abscisic acid hormone and upregulation of HSP-70.

Abscisic acid in compare with Indole-acetic acid and gibberellin hormone has key role in upregulation and heat-resistance induction in Yaghooti grape. Hormone-treated clusters in comparison to the control clusters had lesser congestion and density. Gibberellin treatment cause the increase in length of cluster in addition to decrease in grapes number per cluster.

Durum wheat (Triticum turgidum) with an average annual production of 40 million tons, is the tenth most important and common crop grown worldwide. The aim of this study was to analysis the genetic diversity and population structure of durum wheat genotypes for knowledge and apply in future genomic studies using SilicoDArT markers generated by DarTseq.

The DNA of 94 durum wheat genotypes were extracted by CTAB method from fresh leaves. The quality and quantity of extracted DNA were measured using spectrophotometer and adjusted to 50 ng / μl. The DNA samples were processed at Diversity Array Technology Pty, Ltd, Australia (https://www.diversityarrays.com) for DArTseq analyses using genotyping by sequencing Platform. Genetic diversity and population structure analysis were performed on the remaining 7882 markers using: Power Markerv.3.25, DARwinver 5.0, STRUCTURE2.1., GenAlexv. 6.41 and Rv3.2.3 software.

The amount of polymorphic information content (PIC) of SilicoDArT markers ranged from 0.023 to 0.499 with an average of 0.38. The mean reproducibility and call rate of sequences in all linkage groups were above 0.98 and 0.92, respectively. The number of mapped SilicoDArT markers varied from 300 markers in the linkage group (Chr1A) to 853 markers in the linkage group (Chr7B). Chromosome size covered by SilicoDArT markers ranged from 829200 kbp in the linkage group (Chr3B) to 589293.786 kbp in the linkage group (Chr1A). The results of cluster analysis by Neighbor-Joining (NJ) method, population structure and discriminant analysis of principal components were highly consistent with each other and clearly divided the studied genotypes into four distinct groups. Genetic diversity among populations was primarily within the population (76.36 vs. 23.64%).

The relatively high number of subpopulations and the presence of high genetic diversity among and within populations were the characteristics of studied durum wheat genotypes in this study. Therefore, considering the loss of 84% genetic diversity of durum wheat during the early domestication processes, these populations can be used as a valuable resource in basic and applied research in breeding projects.

Many secondary metabolites produced by plants are used in manufacturing drugs and new treatments, but are too difficult, expensive or impossible to prepared by chemical synthesis. Biotechnology progresses have provided a huge source of new chemical compounds of plant origin to various applications. Purslane (Portulaca oleracea L.) is one of the valuable medicinal plants that World Health Organization (WHO) called it Global Panacea. Hairy root induction by Agrobacterium rhizogenes is an effective method for production of secondary metabolites.

In this study, hairy roots of Purslane were produced using Agrobacterium rhizogenes strains A4 and ATCC15834. The presence of the rolB gene in the hairy roots was confirmed by PCR using rolB gene specific primers. The effect of the type of strain (A4 and ATCC15834), explant (cotyledon, hypocotyl and seedling) and also different concentrations of Iron oxide nanoparticles (0, 20, 40 and 6 mg l-1) were examined as abiotic elicitors on the hairy root induction, growth and increase of secondary metabolites of hairy roots.  

The results showed that the highest hairy root induction (80 percent) was observed in the A4 strain, seedling explants and 40 mg l-1 the iron oxide nanoparticles. The greatest hairy root length was obtained by 60 mg l-1 the iron oxide nanoparticles (4.17 cm) and also ATCC15834 strain, seedling explants and 40 mg l-1 the iron oxide nanoparticles were superior for highest phenolic and flavonoid content (4.92 and 0.48 mg g DW) and also 2,2-diphenyl-1-picrylhydrazyl (52.59%) and ferric reducing antioxidant power (60.37(Mol g-1 DW)). Hairy root lines showed significant differences in growth rate and biomass production and the largest biomass production was exhibited by G line.

Overall, the strain and explant types and iron oxide nanoparticles had considerable effects on the hairy roots induction secondary metabolites production. The results indicated significant increases in hairy root induction and medicinal compounds by A4 and ATCC15834 strains, seedling explant and 40 mg l-1 the iron oxide nanoparticles.

Indigenous animals are considered as the national treasures and strategic sources of each country. It is essential to preserve and reproduce them. Since no artificial selection has been employed in Iranian native breeds, there is considerable diversity in their genome. Therefore, having detailed information on the animals’ genome can be important for designing breeding plans in the future. The aim of this study was to identify the functional effects of single nucleotide polymorphisms and investigate the genetic diversity in the Khazak chicken ecotype using sequence information of the whole genome.

In this study, 17 Khazak chicken samples were sequenced using Next Generation Sequencing (NGS) technique. After preprocessing short sequences using FastQC, Trimmomatic, BWA, Picard software and the GATK program, single nucleotide polymorphisms were identified in GATK program using the UnifiedGenotyper tool. Samtools software was applied to calculate short reads coverage and the percentage of read alignment with the reference genome. The filtering steps of SNPs were performed using Plink software. The genetic diversity within the target population was calculated using the VCFtools program.

The mean coverage depth for 17 chickens was 6.45. After preprocessing the short sequences, were identified 15,981,176 and 10,552,735 SNPs before and after the quality control, respectively. Functional annotation of the single nucleotide polymorphisms indicated that most of the SNPs are located in the intron and intergenic regions and only 2.8% of them belong to the exon region. The rate of Transition to transversion mutations (Ti / Tv) was 2.43 and the ratio of heterozygous to homozygous SNPs was 3.3 in the Khazak birds, on average.

The higher number of heterozygous SNPs indicates that there is a high genetic diversity in the Khazak ecotype. Like other Iranian native chickens, the ecotype has the genetic diversity that can be considered a native laying ecotype in the breeding programs.

Rice is one of the most important crops in the world, which occupies a large area of arable land. Blast disease is one of the most important and destructive rice diseases, which reduces production of this product. Due to environmental pollution caused by overuse of fungicides to control this disease and on the other hand, the pathogen resistance to these chemicals, development of better and healthier strategies to control this pathogen is necessary. Biological control of plant diseases using antagonists can be a promising alternative method.

In this study, indirect effect of Trichoderma harzianum fungus on pathogenic fungus, Magnaporthe oryzae, under greenhouse conditions was investigated by induction of systemic resistance in susceptible Tarom cultivar. For this purpose, expression of several important defense genes was investigated using real-time qPCR technique in plants symbiont with Trichoderma compared to control plants (without Trichoderma) at different times after infection with pathogenic fungi.

The results showed increasing expression level of NPR1, PR2 and PR3 genes after pathogen inoculation in plants symbiont with Trichoderma compared to the control plants that there was statistically significat difference about PR2 and PR3 genes. Nevertheles in a number of times, there was no significant difference in expression level of the evaluated genes between two treatments. Examination of various morphological traits such as root, stem and leaf dry weight, root length, stem diameter and plant height showed an increase in plants symbiont with Trichoderma compared to control plants (without Trichoderma), although this difference was not significant about these traits except for plant height. Chlorophyll a and b levels were also measured as physiological traits in both treatments. Although amount of chlorophyll a was higher in plants symbiont with Trichoderma than control plants, but no significant difference was observed. Phenotypic study of interaction of rice plant and pathogen in presence of Trichoderma showed a significant difference about disease severity in plants symbiont with Trichoderma compared to control plants.

These results could somewhat indicate the systemic protection of the rice plant against M. oryzae due to symbiosis of the plant root with Trichoderma harzianum and induction of resistance and increase in pathogenesis-related genes, but this is not enough. Therefore, it is necessary to repeat greenhouse experiment to ensure that there is a significant difference in expression of the studied genes between symbiotic and control plants.

Plant genetic variation, during the long-term domestication of the cultivated barley, especially after the modern breeding and intensive cultivation, reduced significantly, leading to genetic erosion in this crop as well. Wild relatives of cultivated barley are potential source of valuable genetic materials for barley improvement. Genetic variation of wild species belonging to primary gene pool of barley is important in employing in barley breeding program, particularly for tolerance to biotic and abiotic stresses. Being a close relative of wild species (H. spontaneum L.) and the lack of tolerance genes among the cultivated genotypes of barley makes gene introgression the appropriate avenue to transfer desired genes such as abiotic stress tolerance.

In this research a backcross populations (BC2F1) developed from interspecific hybridization between cultivated barley and its wild relative (H. spontaneum L.) was assessed for genetic diversity using molecular markers which are valuable to assist background selection for recurrent parent.

Arliquin and POPGENE softwares were used to analyze genetic diversity and molecular variance (AMOVA) among populations, respectively. Gst and Nm parameters had an average of 0.59 and 0.34, respectively, indicating a low gene flow among nine groups of backcross families. The AMOVA results showed that majority of genetic diversity belonged to within population variation (86.48%). Nei's genetic similarity ranged from 0.41 to 0.92 which were consistent with those of genetic distance

Microsatellite markers have strong differentiation ability to discriminate the resultant genotypes from a bi-parental cross.

Mitochondria are an excellent source for explaining cytoplasmic inheritance because of their important roles in cell metabolism and because they are primarily inherited maternaly in animals. In domestic animals, various studies have reported an association between mitochondrial DNA polymorphism and production and reproduction traits. The aim of this study was to investigate the polymorphism of ATPase6 and ATPase8 genes and their effects on the rates of in vitro maturation of oocytes (IVM) and in vitro culture of embryos (IVC) in Sanjabi sheep.

Blood and ovary samples of adult Sanjabi ewes were collected from Bistoon slaughterhouse located in Kermanshah. In the laboratory, after separating the excess tissue around the ovaries and washing them, a cumulus-oocyte complex with a diameter of more than 3 mm from the follicles was aspirated. 100 samples containing more than two oocytes were transferred to dishes containing in vitro maturation (IVM) medium. After the oocytes matured, fresh Sanjabi ram sperm were used for in vitro fertilization of each sample. For in vitro culture, putative zygotes formed in the previous stage were cultured in synthesized ovarian fluid medium for 48 hours. DNA extraction was performed using the salting out method. A 895 bp fragments of DNA containing ATPase6 and ATPase8 genes were amplified by PCR and the samples were genotyped using a modified SSCP method. The Kruskal-Wallis nonparametric test was used to investigate the relationship between the observed genotype patterns and IVM and IVC rates.

The results of this study showed the existence of polymorphisms in the studied gene regions and five different band patterns A (50%), B (12%), C (9), D (21) and E (8%) were observed. Analysis of the relationship between these patterns and IVM and IVC showed no significant relationship between them (p>0.05).

Despite the observation of polymorphisms in ATPase6 and ATPase8 genes using the modified SSCP method, these polymorphisms had no effect on the rate of IVM and IVC.

The genetic improvement of carnation (Dianthus Caryophyllus), as one of the most important cut flowers in the world, is of utmost significance. For this purpose, the use of in vitro breeding techniques is very important. One of the most crucial in vitro breeding needs of carnation is accessibility to a regeneration method with maximum productivity and minimum genetic modification probability. The present study aimed to determine an optimal and fast method for the direct regeneration of carnation cultivars by employing various regulators and adenine hemi-sulfate for the first time in these cultivars.

For the determination of the optimal level of the culture medium compositions toward the direct regeneration of carnation cultivars (Skimo, Tibor, and Labret), an experiment with a completely randomized design was designed and implemented in an MS culture medium, in different concentrations of growth regulators, including four levels of TDZ (0.5, 1, 2, and 3mg/L), two levels of IAA (0.5 and 1mg/L), and four levels of adenine hemi-sulfate (0. 20, 40, and 80mg/l), were used.

The model used for this experiment was significant at the level of 1%, where R2=96% and CV=22, indicating the acceptable accuracy of the analysis. With respect to the results, it was observed that, in the leaf explants of different carnation cultivars, the utilization of the MS culture medium in light conditions with TDZ 2 mg/L+ IAA 0.5 mg/L occurred the direct regeneration of the leaf explants. It is worth mentioning that the addition of 40mg/L of adenine hemi-sulfate to the culture medium increased the regeneration mean from 66% to 94% among different cultivars. In addition, the mean shoot number per explant increased from 12 to 36 shoots.

Generally, the results of the experiments showed that the mixing of the MS base medium, leaf explants in light conditions, and the TDZ 2 mg/L+ IAA 0.5 mg/L+As 40 mg/L regulator composition significantly led to the leaf regeneration of carnation cultivars. Briefly, the results of this study proved that the use of adenine hemi-sulfate significantly impacted the upsurge of the direct regeneration rate of carnation cultivars.

Hyssopus officinalis, one of the most important medicinal plants belongs to the Lamiaceae family and it is rich in essential oils that is used for medicinal purposes, health care and food. By tissue culture method such as; callus production and plant regeneration, we able to increase the production of quality and quantity of effective secondary metabolites in this medicinal important plant. This study was performed on MS medium, aimed to determine the most appropriate concentration of auxin and cytokinin plant growth regulators to obtain the maximum efficiency in induction and production of callus and in vitro regeneration of plantlets from leaf and hypocotyl explants of Hyssopus officinalis.

Callus induction was evaluated in a factorial experiment based on completely randomized design (CRD) with three replications. In this experiment, different levels of NAA plant growth regulator (0, 0.5, 1 and 2 mg/L) and two different types of explant, leaves and hypocotyl explants were used. Traits including, relative growth rate, fresh and dry weight, diameter, color and physical structure and the percentage of callus induction was measured. Also, the direct and indirect regeneration was evaluated in a factorial experiment based on completely randomized design (CRD) with three replications. The different levels of plant growth regulator (1 and 2 mg/L NAA) and (2 and 4 mg/L BAP) were used and regeneration percentage were measured.

The highest percentage of callus induction (100 %) were obtained on MS medium with 2 mg/L NAA in hypocotyl explants. The highest percentage of direct regeneration (73 %) and indirect regeneration (80 %) were observed in MS medium with combinations of 2 mg/L NAA and 4 mg/L BAP in hypocotyl and calli derived from hypocotyl.

The results showed that the hypocotyl explant was more suitable for callus induction and regeneration in Hyssopus officinalis.

Since nutrition affects all the interactions of the body, especially the genome as well as the expression of genes, and all organisms are always feeding, and without feeding life is not possible. Therefore, the aim of this study was to review the role of nutrition in gene expression, DNA replication, prevention of DNA damage and DNA repair.

In this study, the keywords such as cancer, ribonuclease, ribonuclease inhibitor and RNA were used to search in databases including Scopus, SID, IranDoc, PubMed, Google Scholar, Web of Science and Iran Medex. In order to select the documents used, all articles published in non-English and Persian languages, duplicate articles, articles that could not be accessed to the full text, as well as articles that were presented as abstracts were removed. Finally, the selected cases were thoroughly studied and summarized in order to prepare the current review.

Regulation of gene expression is essential to life and health and is sensitive to endogenous and dietary and other environmental factors that exert their action at multiple levels and by multiple mechanisms. There are important and intimate links between diet/nutrition, metabolic status, signaling pathways, and gene regulation. Postgenomic technologies including microarray hybridization and massive next-generation sequencing (RNA-Seq) enable nowadays highthroughput analysis, at genome-wide level, of the transcriptome and its dynamics (presence and quantity of RNAs, RNA expression patterns). Further, changes induced by dietary or other factors in TF binding site occupancy, chromatin features, global patterns of transcript decay, and translational profiling can also be studied nowadays at a genome-wide level. There is overwhelming evidence that a large number of micronutrients (vitamins and minerals) are required as cofactors for enzymes or as part of the structure of proteins (metalloenzymes) involved in DNA repair, prevention of oxidative damage to DNA, as well as maintenance and methylation of DNA. The role of micronutrients in the maintenance of genome stability has been extensively reviewed. Some of micronutrients involved in various genome stability processes. There are various mechanisms by which micronutrient deficiency could cause DNA damage, accelerate senescence and chromosomal instability.

Integration of results from these varied technologies will ultimately allow a comprehensive, system-wide understanding of gene expression control and of diet-gene-health relationships in modern nutrition science.