Journal of Plant Bioinformatics and Biotechnology

Original Article

Effects of culture medium and plant hormones in organogenesis in olive (CV. Kroneiki)

Bahman Fazeli-Nasab; Ahmad Farid Rahmani; Hamideh Khajeh

Volume 1, Issue 1 , June 2021, Pages 1-13

https://doi.org/10.22034/jpbb.2021.268638.1000

Abstract

A long time has passed since the first experience of In Vitro propagation of olive, but the presence of very strong end dominance in the neoplasm stage, which cannot be controlled by ... Read More A long time has passed since the first experience of In Vitro propagation of olive, but the presence of very strong end dominance in the neoplasm stage, which cannot be controlled by various cytokinin treatments, has limited the possibility of propagation in vitro. Therefore, the aim of the present study was to evaluate the micro-propagation feasibility inside olive glasses of olive cultivar Kroneiki. For branching and rooting of lateral buds, the experiment was carried out as a factorial experiment based on completely randomized design with three replications. Branching factors include five types of culture media (MS, MS1/2, MSM, MSM1/2 and OM), two types of hormones (BAP and Zeatin), and three types of hormone concentrations (control, 0.5 and 1 mg/L) and there were three types of time periods. Rooting factors include five types of culture media (MS, MS1/2, MSM, MSM1/2 and OM), two types of hormone combinations (IBA and NAA), four types of hormone concentrations (control, combination of 0.2 with 0.5, combination 0.5 with 1 and a combination of 0.75 with 1.5 mg/L) and three types of time intervals. Analysis of variance was performed by Statistix10 software and the comparison of mean traits was performed using the least significant difference test. The effects of culture medium, different hormones and also different concentrations of hormones used in the period, on the number of green leaves, number of yellow leaves, fresh weight and dry weight of seedlings as well as rooting were examined , which were found different (P <0.01). The highest length of branch (1.8 cm) was obtained in MSM culture medium with BAP hormone in the third week. The highest fresh weight (0.06 g), the highest dry weight (0.003 g) and the highest amount of green leaves (55.39%) were obtained from the treatment of MSM medium with 1 ppm of BAP hormone. The highest rooting rate (95.17%) was obtained from the treatment of MS1/2 medium with 1.5 ppm of BAP hormone and 0.75 ppm of NAA hormone in the third week. The most effective culture medium and hormone on branching was MSM culture medium with 1 ppm BAP hormone and on rooting, MS1 culture medium with 1.5 ppm BAP hormone and 0.75 ppm NAA hormone.

Original Article

Effects of Culture Medium and Concentration of Different Growth Regulators on Organogenesis Damask rose (Rosa damascena Mill)

Hamideh Khajeh; Farzaneh Fazeli; Ayoub Mazarie

Volume 1, Issue 1 , June 2021, Pages 14-27

https://doi.org/10.22034/jpbb.2021.276335.1004

Abstract

In vitro cultivation method is a proper way to fast propagation of commercial rose cultivars with high uniformity, and even today, it is regarded as a desirable solution for correction ... Read More

Review Article

A Review of RNA Motifs, Identification Algorithms and their Function on Plants

Davoud Naderi; Raheba Jami; Fazal UR Rehman

Volume 1, Issue 1 , June 2021, Pages 28-40

https://doi.org/10.22034/jpbb.2021.271442.1001

Abstract

Recent Genomic research has significantly developed human knowledge on structural non-coding RNAs (ncRNAs) which folds into characteristic secondary structures and performs specific-structure ... Read More Recent Genomic research has significantly developed human knowledge on structural non-coding RNAs (ncRNAs) which folds into characteristic secondary structures and performs specific-structure dependent biological functions. Hence, RNA secondary structure prediction is among the most commonly evaluated issues in computational RNA biology. The aim of the present study is to introduce the key role of RNA motifs in biological processes. Such motifs are specifically effective in regulating gene expression, maintaining structure and strength of RNA molecule, splicing the early mRNA, and providing the most appropriate recognition site for protein binding. Doing research and analyzing RNA motifs requires using several methods and algorithms which can provide the structure and properties of these building blocks in organisms. Generally, the most successful computational methods used in organizing RNA include the QRNA, RNAz, and CMfinder algorithms, which correlate nucleotides and other features of RNA structure formation and maintenance. In plants, RNA Recognition Motif (RRM), an 80- amino acid protected motif, is one of the most abundant protein motifs in eukaryotes. This motif has various important roles like participating in growth processes and responding to stresses in plants, and accelerating different metabolic processes. In addition, further analysis of ORRM family members represented presence of ORRM2, ORRM3 and ORRM4 acting as RNA editing factors in mitochondria as well as ORRM6 which is a chloroplast RNA editing factor. Among the construction motifs, the Pseudoknot motif which contributes to several biological activities such as altering expression of pathogenic genes in some viruses and formation of telomerase and self-truncating introns is of great significance, since these are important breeding factors in biotechnology. Based on the results of the study, it can be proposed that further studies on bioinformatics analysis of plant motifs are required to be implemented to open new windows on controlling pathogens in plants.

Original Article

Cholinesterase and Aliesterase as a Natural Enzymatic Defense against Chlorpyrifos in Field Populations of Spodoptera Littoralis (Boisdüval, 1833)(Lepidoptera, Noctüidae)

Seham Mansour Ismail

Volume 1, Issue 1 , June 2021, Pages 41-50

https://doi.org/10.22034/jpbb.2021.288332.1007

Abstract

In insecticide resistance research on cotton leafworm multiple resistance mechanisms, including behavioral resistance, some types of physiological resistance (e.g. increasing activities ... Read More

Original Article

In vitro Production of PPV-free Sweet cherry (Prunus avium cv. Siahe-Mashhad) by Meristem culture and micro-grafting

Mohammad Esmaeil Naddaf; Gholamreza Rabiei; Ebrahim Ganji Moghadam; Abdorahman Mohammadkhani

Volume 1, Issue 1 , June 2021, Pages 51-59

https://doi.org/10.22034/jpbb.2021.282382.1005

Abstract

Plum Pox Virus (PPV) is one of the most common viral agents in sweet cherry. This study was carried out to investigate the effect of culturing method and explant type for production ... Read More

Original Article

In Silico Genome-Wide Identification and Characterization of Glutathione Peroxidase Gene Family in Wild Cherries (Prunus avium L)

Zahra Shirazi; Fatemeh Khakdan

Volume 1, Issue 1 , June 2021, Pages 60-72

https://doi.org/10.22034/jpbb.2021.289018.1008

Abstract

Biotic and abiotic stresses are the main problems affecting the quantity and quality losses of antioxidants in wild cherry (Prunus avium L), which provide health benefits to humans, ... Read More Biotic and abiotic stresses are the main problems affecting the quantity and quality losses of antioxidants in wild cherry (Prunus avium L), which provide health benefits to humans, such as anti-allergic, anti-inflammatory, antimicrobial, and anti-cancer benefits. Glutathione peroxidase (GPX) isoenzymes act a major role in responding to oxidative stresses through the multiple metabolic pathways. Protein sequences of GPXs family form Arabidopsis thaliana and Oryza sativa were used to identify homologous proteins by the BlastP in the sweet cherry’s genome. After the alignment, the existence of the specific domain, phylogenetic relationships, subcellular localization analysis, as well as exon-intron structures and conserved motives were evaluated in this study. MicroRNA target site and codon usage bias were also investigated. Furthermore, the existence of cis-regulatory element and SSR markers were identified. The three-dimensional structure of the GPXs protein prediction and the accuracy of the predicted model was also investigated. Regarding molecular docking, the best pose for considering the accuracy of binding site was evaluated. Finally, by analyzing biological process and molecular function, gene ontology of the predicted protein was considered. We identified the five GPX genes in P. avium that classified into 3 separate groups based on their phylogenetic relationships. The predicted subcellular localization showed the GPX proteins that localized both chloroplast and mitochondria. Also, results showed ENC values were ranked 45.92 to 59.21 in PavGPX3 and PavGPX2. The results of cis‐regulatory elements showed PavGPX8 contained ten cis‐regulatory elements which was the lowest number among PavGPXs. The best pose and protein interaction in the verified 3D model were the first pose with the -28.5 minimization energy in docking process. It was concluded that the precise information on putative roles of P. avium GPXs genes could be helpful in determining their functional characterizations. The presence of several developmental process, stresses, light and hormones- responsive elements in the upstream of these genes, and GPXs‐targeted miRNAs suggested that GPX family members may play various roles in different biological responses. Finally, the GPXs gene was proposed as a good candidate for genetic engineering and breeding programs in order to introduce an abiotic stress- tolerant cultivar.

Journal of Plant Bioinformatics and Biotechnology

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Volume 2 (2022)

Volume 1 (2021)

Volume & Issue: Volume 1, Issue 1, June 2021, Pages 1-72

Effects of culture medium and plant hormones in organogenesis in olive (CV. Kroneiki)

Abstract

Effects of Culture Medium and Concentration of Different Growth Regulators on Organogenesis Damask rose (Rosa damascena Mill)

Abstract

A Review of RNA Motifs, Identification Algorithms and their Function on Plants

Abstract

Cholinesterase and Aliesterase as a Natural Enzymatic Defense against Chlorpyrifos in Field Populations of Spodoptera Littoralis (Boisdüval, 1833)(Lepidoptera, Noctüidae)

Abstract

In vitro Production of PPV-free Sweet cherry (Prunus avium cv. Siahe-Mashhad) by Meristem culture and micro-grafting

Abstract

In Silico Genome-Wide Identification and Characterization of Glutathione Peroxidase Gene Family in Wild Cherries (Prunus avium L)

Abstract