Agricultural Biotechnology Journal
Year:2024 | Volume:16 | Issue:2|Papers Count:12

ObjectiveMoringa oleifera L. belongs to the Moringaceae family and is known for its important medicinal chemicals, including flavonoids, coumarins, quinones, phenolic compounds, and alkaloids. This study focused on determining the best conditions for producing callus tissue from Moringa leaf explants and analyzing the biochemical compounds in the resulting calluses. Materials and methodsLeaf explants of the Moringa plant were cultured on the MS medium with various plant growth regulators (Kin or BAP at 0, 0.1, and 0.5 mg/L) either alone or in combination with 2,4-D, NAA, or IBA (each at 0, 0.5, 1, 2, and 4 mg/L). The percentage of callus production, root, and shoot formation, as well as the biochemical compounds (total flavonoid and anthocyanin contents) of the resulting calli, were recorded after 4 weeks. ResultsThis research revealed a significant difference between most hormonal treatments and the control treatment regarding the percentage of callus tissue production, roots, and shoots derived from callus tissue, as well as the fresh weight of the collected callus. The most effective hormonal treatment for callus tissue production (100%) was observed with the MS medium supplemented with 2 mg/L 2,4-D and 0.5 mg/L BAP. Also, the highest percentage of root production from callus tissue (100%) was associated with MS medium containing 2 or 4 mg/L NAA and 0.5 mg/L BAP. The MS medium supplemented with 1 mg/L NAA and 0.5 mg/L BAP exhibited the highest percentage (30.53%) of shoot production from M. oleifera callus. Furthermore, there was a significant difference among various treatments in terms of the biochemical compound contents of the resulting callus.ConclusionsBased on the findings, the use of plant hormones had a positive impact on callus tissue production, as well as root and shoot production, and the biochemical characteristics of the Moringa plant. The maximum fresh weight of the callus was attained by utilizing BAP and 2-4-D in the MS medium. Enhancing the amount of flavonoid and anthocyanin in plant callus is crucial to boost the antioxidant and anticancer properties. In this study, the highest levels of biochemical compounds, particularly total flavonoid and anthocyanin content in the in vitro culture of M. oleifera L., were associated with increased concentrations of Auxin and Cytokinin.

Objective: Basil (Ocimum basilicum) is one of the most important medicinal as well as vegetables plants that are cultivated and consumed worldwide One of the essential aspects of plant breeding programs is to study the correlation between DNA polymorphisms and phenotypic trait diversity. The purpose of this research is to investigate the genetic diversity of five basil cultivars under drought stress conditions using SCoT markers and traits, and also to analyze the relationship between traits and markers by stepwise regression.Materials and Methods: In this research, five basil genotypes were studied under drought stress in the form of a split plot based on a completely randomized design with three replications in pots and under greenhouse conditions. The main plot included drought stress in two levels (normal and drought stress) and the sub plot factor included genotype (5 levels) and their morphological and physiological traits were evaluated. Also, their genomic DNA was extracted from the leaves, and the genotypic diversity of the genotypes was investigated based on eight SCoT primers, and finally, the relationship between the traits and markers was determined by stepwise regression.Results: Correlation of traits in two conditions showed that leaf yield had a positive and significant correlation with traits of plant height and total chlorophyll. The percentage of trait changes under stress conditions showed that root length, chlorophyll a and total chlorophyll traits had the greatest decrease and cluster analysis based on them placed the genotypes in three groups and the traits in three groups. Eight primers amplified a total of 101 polymorphic bands and ScoT1 produced the most bands with 17 polymorphic bands. Cluster analysis by UPGMA and dice similarity criterion based on SCoT data were placed five basil genotypes in three groups. The results of regression analysis showed that in normal and drought stress conditions, 15 and 12 markers (alleles) had a significant relationship with the studied traits, respectively.Conclusion: Selection based on molecular markers provides a rapid method for breeding programs. The obtained genetic information of markers in this study showed their important role. Therefore, in addition to traits, it is possible to select superior genotypes and high value populations in breeding programs. The findings showed that certain markers are associated with multiple traits and emphasized the critical importance of this trait in plant breeding for simultaneous improvement of multiple traits. Insights from this study on markers have potential for application in breeding programs.

ObjectiveIdentifying the strains carrying acquired tetracycline resistance genes is one of the important points in evaluating the safety of probiotic strains. The aim of the present study is to comprehensively evaluate tetracycline resistance in lactobacillus spp. isolated from the digestive system of Iranian backyard chickens.Materials and methodsIn the present study, the phenotypic sensitivity patterns of 36 lactobacillus isolates belonging to four species L. reuteri, L. salivarius, L. crispatus and L. johnsonii were evaluated by measuring the Minimum Inhibitory Concentration (MIC) to tetracycline. After that, four tetracycline resistance genes tet(L), tet(M), tet(W) and tet(O) were detected in isolates with phenotypic resistance to this antibiotic based on the polymerase chain reaction method.ResultsAs a result, four isolates of L. reuteri, three isolates of L.salivarius, two isolates of L. crispatus and four isolates of L. johnsonii among the studied lactobacillus spp. showed phenotypic resistance to tetracycline. After the detection of tetracycline resistance genes in isolates with phenotypic resistance, the presence of tet(W) gene was confirmed in all investigated isolates. The simultaneous presence of tet(M), tet(L) and tet(W) genes was observed in three studied L. salivarius isolates. It was also found that the phenotypic resistance observed in three isolates of L. johnsoniiABRIG7, L. johnsoniiABRIG14 and L. johnsoniiABRIG24 is caused by the simultaneous presence of tet(O) and tet(W) genes.ConclusionsThis study showed that tetracycline resistance among Lactobacilli isolated from digestive system of Iranian backyard Chickens is due to the presence of single or multiple resistance genes.. We also found that tet(W) is the most widespread tetracycline resistance gene among investigated Lactobacillus isolates. Therefore, local poultry breeders should refrain from arbitrarily using tetracycline, and when the digestive system of domestic chickens is the source for probiotic microorganism selection, the evaluation of resistance to tetracycline from the phenotypic and molecular point of view should be taken into consideration in order to select safe strains.

Aegilops species possessing the U genome are the most widely distributed species in the world. Considering the limitation in the genetic diversity in cultivated wheat, the use of wild relatives and other species of Aegilops can be provided a rich and diverse gene pool of new and ideal alleles for breeders. Therefore, the main goals of the present study were investigation of genetic diversity and population structure in Aegilops accessions collected from different regions of Iran using the CBDP markers.Materials and methodsIn this study, the genetic diversity among 77 Aegilops accessions collected from 18 provinces in Iran and belonging to five species including Ae. biuncialis (UUMM genome), Ae. columnaris (UUMM genome) Ae. Neglecta (UUMM genome), Ae. triuncialis (UUCC genome), Ae. umbellulata (UU genome) , was evaluated using 15 CBDP primers. The obtained molecular data were subjected to statistical analyses using GenAlEx ver. 6.502, DARwin ver. 6, and Structure ver. 2.3.4 softwares. ResultsA total of 189 polymorphic fragments were amplified using 15 used CBDP primers (95.27%). The PIC index ranged from 0.28 (CBDP15) to 0.42 (CBDP-2 CBDP-4) with an average of 0.35. The results of analysis of molecular variance (AMOVA) revealed that the highest proportion of genetic variance referred to within species (76%). Among all species, Ae. triuncialis showed the highest values of genetic parameters. The highest level of genetic similarity was found between Ae. biuncialis with Ae. columnaris (0.905) and Ae.biuncialis with Ae. neglecta (0.879). Although cluster analysis based on CBDP data classified all accessions into three main groups the grouping pattern was exactly in accordance with the genomic constitution of species. Moreover, the clustering pattern was confirmed by a principal coordinate’s analysis (PCoA). The population structure analysis further confirmed the results obtained from the cluster analysis and PCoA, so all studied accessions were grouped based on their genomic structure, degree of genetic similarity, and geographic similarities.ConclusionResults of the present study showed a high usefulness of CBDP markers in evaluating the genetic diversity in the Aegilops germplasm. Therefore, it seems that this marker technique can be used in programs related to the preparation of genetic maps and molecular phylogenetic studies. Also, the existence of high genetic diversity among some Iranian Aegilops species can provides a significant prospect for breeders to use them in pre-breeding programs in wheat.

Background and objective Ginger (Zingiber officinale Roscoe) belongs to the Zingiberaceae family and it is one of the most important spices in the world which produces spicy and fragrant flavors and it has many healing properties. This plant does not have the ability to produce seeds due to sterility. The growth of the plant through the rhizome causes the cost of cultivation and the probability of pathogen attack. Therefore, propagation using in vitro tissue culture be effective method for increasing the rate of proliferation and infection control. For obtaining the better results in tissue culture, explants should be prepared from healthy, fresh and strong maternal sources. Somatic embryogenesis usually not used for propagation due to mutation, so it is better to use the rhizome buds as explant to preserve genetic characteristics. Material and MethodsFor micropropagation, explants including shoot, leaf, collar and buds of ginger in were used and cultured on MS basal medium supplemented with 9 different hormonal combinations (BAP alone or in combination with NAA) for shoot induction. Shoots were transferred to MS medium containing 1 mg/l NAA or IBA for rooting. Plantlets were transferred to pots and gradually adapted to the greenhouse condition.ResultsThe best explant for fast and easy multiplication of ginger was the healthy rhizome. MS culture medium supplemented with 2 mg/l BAP and 1 mg/l NAA produced 7 shoots in each rhizome bud. The best treatment for rooting was MS medium containing 1 mg/l NAA which produced 7 roots per shoot. Then, the plantlets were successfully adopted in pots containing garden soil and cocopeat at greenhouse condition.ConclusionThe results of this study showed that micropropagation of ginger plant is affected by the type of growth regulators and their concentration in MS medium and the rhizome buds were the best explants for direct in vitro propagation of ginger.

ObjectivePotato Virus Y is one of the most important damaging and limiting factors of potato cultivation. Plants cope with harmful conditions by regulating the expressions of genes at different levels including transcription, post-transcription and translation, using stress tolerance or resistance mechanisms. Therefore, regulatory factors play a very important role in gene expression regulation under stress conditions. Long non-coding RNAs are one of the most important regulatory elements of genes. The present study was conducted with the aim of identifying lncRNAs and investigation of their expression changes in PVY infected potato plants.Materials and methodsIn this research CLC Genimic Workbench software was used for data analysis. After identifying lncRNAs, the genes affected by them were also analyzed. Then, Gene Ontology enrichment and KEGG pathway analysis were performed using STRING analysis and finally, the interactions between the identified lncRNAs and potato miRNAs were investigated.ResultsAccording to the obtained results, a total of 3742 sequences were identified as novel lncRNAs in PVY infected potato transcriptome, of which 769 were differentially expressed. So that 310 lncRNAs were down-regulated and 459 were up-regulated in potato in response to PVY infection. Gene Ontology analysis of co-expressed genes with identified lncRNAs show the vital role of these genes in various biological processes, biosynthesis of cellular components, protein complex formation and signal transduction. Also, genes involved in biological processes related to creating defense response against stress, hypersensitive reaction, trehalose metabolism, antiviral responses related to RNA silencing and signaling pathways to induce systemic resistance, were co-expressed with identified lncRNAs in this study. The results of co-expression network between lncRNAs and miRNAs showed interactions between 56 lncRNAs and 5 miRNAs. The most interaction was observed between lncRNAs with stumiR6024-3p.ConclusionsConsidering the interactions between examined lncRNAs and the genes involved in defense responses against stress, it is concluded that the expression changes of these lncRNAs are an important part of the response mechanism to viral disease. The obtained results can be a step towards a better understanding of lncRNAs and their function in the development of PVY tolerance and resistance cultivars.

ObjectiveNeonectria ditissima, the causal agent of fruit tree canker, is one of most destructive diseases of apple trees in producing countries with cool weather. Since it is difficult to control this disease due to the presence of the pathogenic fungus throughout the year, for better understanding of this host–pathogen interaction in order to improve management strategies, a transcriptional analysis of apple gene expression in response to N. ditissima was conducted. Materials and methodsIn the present study, we evaluated transcriptome responses to N. ditissima by selecting the partially resistant cultivar “Jonathan”. The leaf scars of apple trees were artificially inoculated with suspension of N. ditissima and water as control. Then the samples were taken for RNA extraction at three different time points, 5, 15, and 30 days after inoculation. The quality and quantity of the extracted RNA were checked and total RNA was sequenced using Illumina paired-end sequencing and Hiseq2000 sequencer. The quality of the sequence data was done by FastQC software. Then the reads were mapped to apple reference genome by TopHat2 software. Normalization and differential expression analysis of genes were performed with DESeq2. Enrichment analysis of DEGs pathways was done through KEGG software.ResultsBased on GO enrichment and KEGG pathway analyses, it was found that some of the defense response genes were differentially expressed between control and treatment groups. The data provides evidence that apple cultivars inoculated with N. ditissima exhibit significant upregulation of defense-related genes and genes involved in detoxification, peroxidase related reactions, phenylpropanoid metabolism. The highest expression level of genes related to defense was observed 30 days after inoculation. It shows that the pathogen needs time to cause infection and cannot spread quickly in the plant tissue.ConclusionIdentification of candidate genes involved in pathogenicity of N. ditissima are involved in lignification, detoxification, phosphorylation and pathogen defense. They are a valuable resource in genetic research and allow us to better understand interaction of fungus and the apple defense system, and may assists in apple canker breeding programs.

Objective: This study was conducted for investigating the effect of drought different levels on morphological and physiological traits of Canola and investigating relative expression of antioxidant genes to identify the antioxidant response of tolerant genotype at drought different levels.Materials and methods: The factorial experiment based on unbalanced completely random design was conducted at the end of the 5-leaf stage of Canola in 3 replications in the greenhouse of Agricultural Sciences Faculty of Gilan University on the year 2022. The effect of different drought levels, including non-stress (100%), low (75%), medium (50%), severe (25%) and very severe stress (20%FC) on morphological and physiological traits in SLM046 and Licord Canola genotypes, as well as the relative expression of important antioxidant genes of Ferredoxin-NADP+oxidoreductase (FNR) and NADPH-thioredoxin reductase (NTR) in the tolerant genotype were investigated using Real-time PCR based on Livak method. Results: The interaction effect of stress on genotype for root length, shoot and root dry weight, allometric coefficient, root water weight, chlorophyll a and b, total chlorophyll, carotenoid and anthocyanin was significant at 1% probability level. The allometric coefficient at 20%FC, and root dry weight at all levels were higher in SLM046 than Licord under drought stress. Drought stress caused a decrease in RWC at 75% FC in both genotypes. Also, the drough treatment at the level of 20% FC caused a decrease in the leaf area and the treatment of all stress levels caused a decrease in the amount of anthocyanin in both genotypes. The stress treatment at 20%FC increased the amount of chlorophyll b and total chlorophyll in SLM046 genotype. The treatment at all stress levels decreased the chlorophyll a and b, total chlorophyll and carotenoid in Licord genotype. The results showed that the expression of FNR and NTR genes increased in SLM046 genotype at higher stress levels.Conclusions: It seems that the SLM046 is tolerant under severe and very severe drought. The increase in FNR expression, which leads to the production of NADPH, is regulated by the NTR expression, and by regulating the expression of genes involved in oxidative stress, it can cause drought tolerance and plant survival in tolerant genotype.

ObjectiveMastitis, a significant infectious ailment affecting dairy cows during both dry and lactation periods, has substantial impacts on animal health, economic profitability, and the dairy industry each year. This study seeks to utilize bioinformatics analysis not only to identify hub genes and biological pathways linked to mastitis in dairy cows but also to gain a deeper understanding of its implications.Materials and methods21 microarray data samples were obtained from the GEO database (accession number GSE24217), comprising 9 healthy cow tissue samples and 12 E. coli infected tissue samples. These samples were assessed using GEO2R. Differentially expressed genes were identified based on two criteria: adjP-value > 0.05 and |LogFC| ≥ 1. Hub genes were identified using the CytoHubba plugin in Cytoscape software and topological analysis methods (DMNC, MCC, MNC, DEGREE). Signaling pathways were identified using the STRING tool based on an FDR > 0.05 index.ResultsOut of 631 differentially expressed genes, 136 had low expression, and 495 had high expression in infected breast tissue compared to healthy ones. Among these, 205 genes were co-expressed in the network. 12 hub genes, including CCL19, ALB, GAPDH, PTPRC, ICAM1, IL6, IL1B, IL18, CXCL8, CCL20, CXCL16, and CCL3, were identified. The analysis of biological pathways revealed that the studied genes are involved in 66 biological pathways, with NOD-like receptor signaling pathway, TNF signaling pathway, and IL-17 signaling pathway playing important functional roles in dairy cow mastitis disease.ConclusionsThe discovered genes and pathways have the potential to enhance our knowledge of the complex molecular mechanisms involved in mastitis development. These discoveries could shape a thorough reform initiative focused on preventing, diagnosing, and treating mastitis. These insights are expected to pave the way for the creation of precise and dependable biomarkers for early detection and prevention of bovine E. coli mastitis, ultimately facilitating personalized treatment approaches.

ObjectiveData generation in biology and biotechnology has greatly increased in recent years due to the very rapid development of high-performance technologies. These data are obtained by studying biological molecules, such as metabolites, proteins, RNA, and DNA, to understand the role of these molecules in determining the structure, function, and dynamics of living systems. Functional genomics is a field of research that aims to characterize the function and interaction of all the major components (DNA, RNA, proteins, and metabolites, along with their modifications) that contribute to the set of observable characteristics of a cell or individual (i.e., phenotype). Furthermore, in a breeding program, genetic improvement can be maximized through accurate identification of superior animals that are selected as parents of the next generation, thereby achieving breeding goals. Artificial neural networks have been proposed to alleviate this limitation of traditional regression methods and can be used to handle nonlinear and complex data, even when the data is imprecise and noisy. Omics data can be too large and complex to handle through visual analysis or statistical correlations. This has encouraged the use of machine intelligence or artificial intelligence. The objectives of this study was to review the main applications of artificial intelligence methods in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics and metabolomics, discuss important aspects of data management, such as data integration, , cleaning, noise removal, balancing and ratio of missing data, functional genomics-system modeling, artificial intelligence and systems biology, addressing legal, ethical and economic issues related to the application of artificial intelligence methods in the field of genomics and presenting a view of possible scenarios in the future. Materials and methodsIn this review, all the researches conducted in the field of artificial intelligence application in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics and metabolomics, were tried, focusing on the applications of recent years after Increase production of big data to be studied and used.Results The studies showed that the application of artificial intelligence in all fields, including functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e., epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics, is increasing rapidly and has many benefits.

ObjectivesThis study examined the number of cases of Cryptosporidium spp. infection in domestic birds in Diwaniyah Governorate, as well as the consequences of this illness and the methods used to diagnose it. Materials and MethodsIn the study, 205 samples from different bird species were analyzed without gender being taken into account. Some of the methods used for diagnosis were the Acid Fast Stain method and the DNA nested Polymerization Technique (PCR). Nested - PCR proved out to be better than AFS because it could find Cryptosporidium faster, with highest accuracy, and sensitivity. ResultsThe results showed that 90 of the samples had Cryptosporidium infections. Among the bird species that were studied, falseco eleonorae had the lowest incidence of cryptosporidiosis at 16%, while gallus gallus domesticus had the highest incidence at 53.3%. Out of the 60 samples taken for each species, 48.3% of Meleagris gallopova and 41.6% of Anas platyrhynchos were infected. The microscope examination showed a 43.9% infection rate (90 out of 205 samples) when compared to the other method. To use nested-PCR for molecular identification, DNA had to be taken from positive infected samples using Proteinase K method. This produced positive bands that were usually amplified at around 587 bp. The nested-PCR test showed that 47.5% of the samples (19 out of 40) were infected. ConclusionsFinally, this study highlights the critical need for efficient diagnostic tools and intervention plans by demonstrating the very high incidence of Cryptosporidium infection in domestic birds in Diwaniyah Governorate. In order to prevent the spread of Cryptosporidiosis in birds, the results stress the use of nested polymerase chain reaction (PCR) methods for infection diagnosis.

Objectives Fasciolosis is a parasitic disease caused by the liver flukes Fasciola hepatica and Fasciola gigantica. These parasites primarily affect ruminants such as cattle and sheep but can also infect humans, making it a notable zoonosis. The disease is typically transmitted through the ingestion of water or vegetation contaminated with the larval stages of the parasite. Fasciolosis poses substantial economic and health challenges, particularly in regions where livestock farming is prevalent. Materials and methods In a recent study conducted in Nasiriyah, Iraq, 30 samples of Fasciola gigantica were isolated from infected cows and buffaloes at the central abattoir. The primary aim was to identify and characterize the common strains of F. gigantica present in these animals using Polymerase Chain Reaction (PCR) technology. By focusing on gene sequences, particularly the Cytochrome C Oxidase Subunit 1 gene (COX1), researchers sought to compare these strains with those registered in the NCBI-BLAST database through phylogenetic tree analysis.     Results The PCR technique successfully amplified DNA extracted from F. gigantica samples, enabling further genetic analysis. The study's results highlighted the genetic relationships between the Iraqi isolates and those from other regions. For instance, one isolate, identified as F. gigantica number 1 with the sequence number OQ152484, showed a 100% match with an Iranian isolate (OP903335) registered in the NCBI-BLAST GenBank. Another isolate, numbered OQ152485, was identical to a Turkish strain. Additionally, isolates 3 and 4 (OQ152486 and OQ152487) were closely related to Iranian isolates OQ070200 and OP903336, showing a similarity of 99.41% and 99.71%. Lastly, isolate number 5 (OQ152488) was found to be 99.41% identical to an Indian isolate (KU363230) recorded in the database. Conclusions These findings underscore the genetic diversity and potential geographic distribution of F. gigantica strains, emphasizing the importance of continued surveillance and genetic characterization to better understand the epidemiology of fasciolosis and inform control strategies.