Microbial Biotechnology
maryam sajedmarani; Soheila Talesh Sasani; Shohreh Ariaeenejad; Akram Sadeghi
Abstract
Plants with special compounds in their root exudates can strengthen a specific microbial community in the rhizosphere and prevent harmful microbial community from forming. The rhizosphere is a dynamic region around the plant root that is governed by the interaction between the plant and microorganisms. ...
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Plants with special compounds in their root exudates can strengthen a specific microbial community in the rhizosphere and prevent harmful microbial community from forming. The rhizosphere is a dynamic region around the plant root that is governed by the interaction between the plant and microorganisms. Plant root secretions can be influenced by plant species, plant growth stages and stress conditions and can be different; therefore, each microbial strain can regulate the expression of its genes at each stage of plant growth. Microbes are an unknown and huge source of secondary metabolites that play a very important role in the field of medicine and other industries. The present review focuses on factors inducing the production of new secondary metabolites from rhizosphere microbes. Each microbial strain has the potential to produce several compounds, but considering that the production of secondary metabolites is very costly for the cell, their synthesis is highly controlled by the cell. Studies have shown that changing the growth conditions of microbes, such as: temperature, salinity, co-cultivation (bacteria-bacteria, fungi-fungi, bacteria-fungi), change in oxygen concentration, aeration speed, addition of soil elements and rare metal ions, light radiation and also genetic engineering methods such as: insertion of strong inducible promoters, ribosome engineering, chromatin rearrangement, overexpression of pathway-specific regulatory genes and small molecules and chemical stimuli can help to discover new compounds. In this study, the above cases are explained in detail.
Medicinal plant Biotechnology
Faeze Aibabaei; Forough Sanjarian; Nima Ahmadi
Abstract
In the current study, the effects of three levels of methyl jasmonate concentration were studied on the hairy root cultures of Origanum vulgare. For this purpose, A. rhizogenes strain A13 was used to create stable hairy root lines from shoot explants. In this regard, two co-cultivation media (MS and ...
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In the current study, the effects of three levels of methyl jasmonate concentration were studied on the hairy root cultures of Origanum vulgare. For this purpose, A. rhizogenes strain A13 was used to create stable hairy root lines from shoot explants. In this regard, two co-cultivation media (MS and modified MS), two inoculation times (5 and 10 min) as well two concentrations of acetosyringone (0 and 100 µM) were attentively studied. Propagated hairy roots were treated with different concentrations of methyl jasmonate (0.1, 0.2, and 0.5 µM). Sampling after 24 and 96 h of methyl jasmonate application, the activities of antioxidant enzymes were evaluated. Moreover, the gene expression level of OvDXR and OvTPS2, two important genes involved in the MEP pathway, were studied using real-time PCR technique. The highest transformation rate was observed in the explants cultured modified MS which were incubated in the bacterial suspension with acetosyringone for 10 minutes. The biomass of hairy root cultures was significantly decreased by methyl jasmonate compared to control samples. In addition, the results indicated that the concentration of methyl jasmonate, harvesting time, and their interactions significantly affected the activity of catalase, peroxidase, and SOD enzymes. The expression of OvDXR significantly increased after 24 h of treatment by 0.2 µM methyl jasmonate, while in the same sample, the expression of OvTPS2 decreased noticeably. The expression of OvDXR and OvTPS2 genes was significantly increased by 0.5 µM methyl jasmonate after 96 h. The application of methyl jasmonate as an efficient elicitor in hairy root culture system of O. vulgare is suggested for the production of valuable metabolites.
Bioinformatics
Samira Mohammadi
Abstract
60 kDa heat shock proteins (HSP60s) also known as chaperonin (cpn60) play an important role in plant growth and stress response. In this study, 32 HSP60 genes were identified in the soybean genome through bioinformatics tools, which are distributed on 14 chromosomes. Most of these proteins are hydrophilic, ...
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60 kDa heat shock proteins (HSP60s) also known as chaperonin (cpn60) play an important role in plant growth and stress response. In this study, 32 HSP60 genes were identified in the soybean genome through bioinformatics tools, which are distributed on 14 chromosomes. Most of these proteins are hydrophilic, acidic, and unstable with a high aliphatic index The evolutionary tree divided HSP60 proteins of soybean, Arabidopsis, and rice into three main groups based on their cellular location. The proteins of different subgroups have highly conserved gene structure, conserved motifs, intron phase, and three-dimensional structure, which can indicate their functional similarities in different subgroups. Several cis-regulatory elements responsive to stresses, growth and hormones were found in the promoter of GmHSP60 genes, that indicate their role in plant growth and response to environmental stresses. Gene ontology (GO) analysis predicted that GmHSP60 genes were responsible for protein folding and refolding in an ATP-dependent manner in response to various stresses. Analysis of the transcriptome pattern (RNA-seq) showed that most of the GmHSP60 genes had high expression in response to salt, drought, cold, heat, submergence, and nutrient deficiency stresses, which indicates their role in improving soybean tolerance to abiotic stresses. Overall, these findings provide useful information to better understand the function of GmHSP60 genes in soybean and facilitate the way for the utilization of chaperonin family genes for achieving plant tolerance against abiotic stresses.
Bioinformatics
Sara Dezhsetan; Parivash Nezami Anbaran; Mahdi Behnamian
Abstract
The MYB transcription factor superfamily has a fundamental role in plant growth and development, activation of stress-responsive genes, and in some cases biosynthesis of key metabolites. The availability of potato, Arabidopsis (dicotyledonous), maize and barley (monocotyledonous) genome sequences provided ...
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The MYB transcription factor superfamily has a fundamental role in plant growth and development, activation of stress-responsive genes, and in some cases biosynthesis of key metabolites. The availability of potato, Arabidopsis (dicotyledonous), maize and barley (monocotyledonous) genome sequences provided the opportunity to identify 121, 139, 190 and 144 non-redundant MYB genes in these linages, respectively. In the study of the evolutionary characteristics of MYB conserved domains in two monocotyledonous plants, corn and barley, they were remarkably similar to each other in terms of alignment and order of placement. This characteristic was also true in relation to two dicotyledonous plants, potato and Arabidopsis, but the difference between MYB conserved domains in monocots and dicots was significant. In other words, it seems that despite the similarity of MYB genes in monocots and dicots, this gene family in the evolution in monocots and dicots have derived from each other. The 2R-MYB members were the most common subgroup of the MYB family in monocots and dicots and only one member of the 4R-MYB subfamily was observed in maize. In all four plants, the main reason for the functional differentiation of genes in this gene family was segmental duplication that has led to positive and purifying evolutionary selection. MYB gene family was located on all chromosomes of potato, Arabidopsis, maize and barley with non-uniform distribution. The expression pattern of AT1G57560, AT2G47190, AT3G23250 and AT1G56650 genes changed in more than one test of abiotic stress and hormonal response. Also, the expression pattern of AT1G74080, AT4G12350, AT4G22680, AT2G47190, AT1G48000, AT2G39880, AT5G40330 and AT5G16600 genes changed in more than one biotic stress test. On the other hand, the expression pattern of the AT2G47190 gene showed increased expression in several biotic and abiotic stresses. The presence of diverse and numerous regulatory Cis elements in response to stresses and hormones in the promoter region of MYB genes and the investigation of the expression profiles of this gene family in biotic and abiotic stresses in Arabidopsis indicates the functional diversity of the genes of this superfamily. In silico investigation of MYB gene superfamily in monocots and dicots provides a framework for comparative, evolutionary and functional studies of the members of this important gene superfamily.
Bioinformatics
Mohammad Mohsenzadeh Golfazani; Alireza Tarang; Ramin Seighalani
Abstract
There is much information about the regulation of gene expression in response to various stresses at the transcriptional level. Nevertheless, there is limited information about this process at the post-transcriptional level. The diversity and complexity of miRNA regulation indicates their importance ...
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There is much information about the regulation of gene expression in response to various stresses at the transcriptional level. Nevertheless, there is limited information about this process at the post-transcriptional level. The diversity and complexity of miRNA regulation indicates their importance in biological processes. Many miRNA regulatory modules can form a complex miRNA-mRNA regulatory network. Therefore, research on miRNA-mRNA regulatory networks can provide valuable information for understanding complex biological processes. These data are very important to further study the stress tolerance mechanisms in plants, especially in rapeseed. In this research, the selection of miRNAs related to drought and salinity stress was made by reviewing the articles on abiotic stresses. Then the target genes were identified using the sequences of mature miRNAs and psRNATarget online software. A gene list of 225 identified target genes was prepared using the UniProt database. Their functional pathway was identified utilizing the DAVID bioinformatics database and KEGG database according to default parameters. Investigations showed that these target genes were involved in several biological pathways including ribosome, spliceosome, proteasome, purine metabolism, selenocompound metabolism, and sulfur metabolism. In addition, the STRING database was used to check co-expression genes. Our result indicated the existence of 37 co-expression genes among the identified target genes.
Molecular Plant Breeding
Mojtaba Khayam Nekouei; Mohammad Reza Ghaffari; Mohsen Mardi; Zahra Ghorbanzadeh; Rasmieh Hamid; Mehrshad Zeinalabedini
Abstract
Today, using advanced technologies such as the global positioning system (GPS), agricultural drones, satellite mapping, remote sensors, and precision agriculture machinery provides farmers with a lot of big data during production. According to the reports, this can be considered a part of the digital ...
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Today, using advanced technologies such as the global positioning system (GPS), agricultural drones, satellite mapping, remote sensors, and precision agriculture machinery provides farmers with a lot of big data during production. According to the reports, this can be considered a part of the digital economy in precision agriculture and be economically exploited. The analysis of this data cannot be processed by traditional processing systems due to its complexity. Given the size and complexity of big data, artificial intelligence can transform this data into valuable information through machine learning algorithms. This technology is being used to performance prediction algorithms, reducing agricultural inputs such as fertilizers and poisons, monitoring the growing conditions, pest management, breeding, molecular studies and finally value chain management. Developing programs using artificial intelligence technology will soon be able to manage the time of agricultural products entering the market, in addition to determining the planting time in order to increase productivity. The production of bio fertilizer from agricultural waste can be another achievement of the development of algorithms based on artificial intelligence to reduce the negative environmental effects and increase the economic productivity of the remaining waste from agricultural products. This study discusses the important applications of artificial intelligence in agriculture and its impact on Precision agriculture.
Bioinformatics
Mozhdeh Arab; Seyed Kamal Kazemitabar; Seyyed Hamidreza Hashemi-petroudi
Abstract
Calcineurin B-like proteins (CBLs) are a subfamily of calcium sensors that play a role in various plant cell processes and molecular functions. In sesame (Sesamum indicum), in silico analysis of the CBL gene family was performed to identify CBL proteins involved in calcium signaling. Using their orthologic ...
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Calcineurin B-like proteins (CBLs) are a subfamily of calcium sensors that play a role in various plant cell processes and molecular functions. In sesame (Sesamum indicum), in silico analysis of the CBL gene family was performed to identify CBL proteins involved in calcium signaling. Using their orthologic relationships with Arabidopsis homolog genes, the nine SiCBL genes were identified and subdivided into six groups: SiCBL1, SiCBL2, SiCBL3, SiCBL4, SiCBL8, SiCBL10. The molecular weight of SiCBL proteins ranged from 24.4 to 37.9 kDa, the Isoelectric acid pH range, the instability index ranged from 33.99 to 47.46 percent, the aliphatic index ranged from 80.29 to 10.89, and the GRAVY ranged from -0.420 to 0.061. Prediction of post-translational modifications revealed that palmitoylation motif was observed in all siCBL, however majority of them did not have myristoylaton motif. In term of gene structure, 11% of SiCBL genes had nine exons, 11% had eight exons and 77% had seven exons. The RNA-seq pattern of the SiCBL subfamily under PEG treatment revealed that, whereas members of this gene family had generally similar expression patterns in both susceptible and tolerant cultivars, due to functional Convergence, each member of this gene family had a distinct expression pattern. Future research on the expression of SiCBL and SiCIPK gene family genes under various abiotic conditions could aid in understanding the mechanism of expression control of SOS-related genes.
Molecular Plant Breeding
Somayeh Ebrahimi; Ahmad Ismaili; Seyed Sajad Sohrabi; Hasan Torabi Podeh
Abstract
Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock ...
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Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock transcription factors (HSFs) in the molecular mechanism of response to various abiotic stresses has been confirmed; therefore, this study used the analysis of RNA sequencing data to identify, classify and evaluate changes in HSF expression in lentil under water-deficit stress, and finally, the expression of some transcripts were examined using qRT-PCR. From the total assembled transcripts of lentil, 35 transcripts belonging to three HSF classes were identified. Also, according to the results, the expression of 14.28% of the identified transcripts, which often belonged to class A, is altered in lentil under water-deficit stress. The expression of 14.28% of the identified transcripts, most of which belonged to class A, is altered in lentil under water-deficit stress. In general, the results show that changes in the expression of some transcripts of one HSF gene take precedence over those of other transcripts of that gene in response to drought stress; therefore, it is of particular importance to study alternative splicing in response to this environmental factor in lentil. The HSF genes identified in this study can be used in future experiments to understand better the molecular mechanism of water-deficit stress tolerance in lentil.
Biotic and Abiotic stress
Fatemeh Bavandpouri; Ezatollah Farshadfar; Kianoosh Chegamirza; Mohsen Farshadfar; Mohammad Bihamta
Abstract
This study was aimed to investigate the reaction of wheat different genotypes to callus induction in the mature embryo stage and the relationship between the traits obtained from the tissue culture and the agronomic traits. A field experiment was conducted in the form of randomized complete block design ...
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This study was aimed to investigate the reaction of wheat different genotypes to callus induction in the mature embryo stage and the relationship between the traits obtained from the tissue culture and the agronomic traits. A field experiment was conducted in the form of randomized complete block design with three replications under rainfed and irrigated conditions in Razi University. In the callus induction stage, mature embryos of 25 bread wheat genotypes from a factorial experiment in the form of a completely randomized basic design including two factors, genotype at 25 levels and 2, 4-D hormone at 3 levels of 1, 2 and 3 mg/L and kinetin 0.2 mg/L was used in six replications. Variance analysis in tissue culture conditions showed that there is a significant difference between genotypes in terms of all investigated traits except the percentage of relative water content of callus. Cluster analysis under laboratory and field conditions showed that genotypes No. 15 (WC-47638), 6 (WC-4840), 13 (WC-5001), 18 (WC-47569) and the Pishtaz cultivar were jointly superior in both conditions and they took the highest values of callus diameter, callus fresh weight, callus growth rate, grain yield, chaff yield, xteragen length, grain weight per spike, peduncle to height ratio, harvest index, seed filling period, vegetative growth rate and seed filling rate. Based on the path analysis in irrigation conditions, the traits of 1000 seed weight, number of seeds per spike, vegetative growth rate, length of other internodes, number of spikes per square meter, grain weight per spike and days to appearance of spike have the most direct effect on tissue culture traits. Also, according to the first canonical function for tissue culture traits (V1) and agronomic traits (W1) in rainfed conditions, plants with higher values of grain yield, larger callus diameter, and with a higher weight of 1000 seeds have a higher callus growth rate and in irrigation conditions, plants with high grain yield and grain weight per spike, callus growth speed is higher. Based on the obtained results, the investigated traits are suitable criteria for selecting cultivars in in vivo and in vitro conditions.
Molecular Genetics and Genetic Engineering
Parisa Daryani; Fatemeh Farzaneh Piralger; Nasser Zare; Zahra-Sadat Shobbar; Rasool Asghari Zakaria
Abstract
WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used ...
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WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used as the templates for tBLASTN searches in datasets for finding new members. An HMM profile of WRKY domain was also used to find WRKY gene family. Multiple sequence alignment was done using clustalW software, and phylogenetic trees were drawn using MEGA10 software based on a neighbour-joining method with a 1000 repeats bootstrap index. According to the results, 165 members of the WRKY gene family were found in rice, of which 63 were new members. Sequences were divided into three main groups based on the number of WRKY domains and the structure of zinc-finger motifs. Conclusively, there were 21 proteins with two WRKY conserved domains in group I, 53 proteins with one WRKY conserved domain and Cx7Cx23HxC zinc-finger motif in group III and 82 proteins with one WRKY conserved domain and Cx4-5Cx22-23HxH zinc-finger motif in group II. The chromosomal location of OsWRKYs was detected on the rice genome. The different groups were distributed on various chromosomes. The greatest number of OsWRKY genes (32 members) were located on chromosome 1. Following complementary research and identification of promising candidate genes involved in tolerance to each stress, they can be used to increase tolerance to the desired stresses and provide food security using genetic engineering or molecular breeding approaches.
Bioinformatics
Aboozar Soorni; Parnian Karimzadeh; Samira Dehghani
Abstract
Thyme species are very important due to the production of secondary metabolites such as terpenoids. Since the identification of key genes such as genes related to terpenoids biosyntesis pathway can play an effective role in plant breeding programs, especially thyme species, the present study was aimed ...
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Thyme species are very important due to the production of secondary metabolites such as terpenoids. Since the identification of key genes such as genes related to terpenoids biosyntesis pathway can play an effective role in plant breeding programs, especially thyme species, the present study was aimed to investigate the transcriptomes of T. daenensis, T. vulgaris, T. lancifolius, T. persicus, T. pubescens to identify key genes in the biosynthesis of monoterpenoids, chloroplast genes sequence and evaluation of similarities and differences among these species. For this purpose, total RNAs extracted from vegetative growth were sent to Macrogene of Korea for sequencing with theIllumina HiSeq 2500 platform. After assembling the sequences using various tools, the best results was selected and transcripts were documented in different databases. Then, according to the documented results, key genes responsible in the synthesis of terpenoids and chloroplast gene sequence were identified, and then phylogenetic relationships among species was investigated. According to the evaluation indicators, the best assembly was a product of Binpacker tools. Based on the results, the sequence of 10 genes involved in the synthesis of terpenoids was obtained. Interestingly, among the identified TPSs, most of the contigs were classified into the TPSb and TPSa classes of terpenoids. The sequence of 73 chloroplast genes was extracted from the transcriptome data and finally the phylogenetic relationship was evaluated according to 400, 70 bp of cpDNA. The study of phylogenetic relationships showed a close genetic relationship between T. daenensi and T.vulgaris which can introduce T. daenensis as an appropriate replacement for T. vulgaris in different purpose, especially in pharmacological applications. The results show that Z. multiflora can most probably be as one of the ancestors of Thymus, which is significantly different from Thymus species in terms of its genetic structure, especially the key genes of the terpene biosynthesis pathway.
Bioinformatics
Samira Mohammadi; Ghorbanali Nematzadeh; Hamid Najafi Zarini; Seyyed Hamidreza Hashemi-petroudi
Abstract
MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target ...
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MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target NAC genes. In the present study, 68 putative NAC domain-encoding genes (NACs) were identified in Aeluropus littoralis, a halophyte plant of family Poaceae. Among the AlNAC genes identified, 4 were predicted putative targets for regulation by miR164. The high conservation of miR164 recognition sites in AlNAC genes indicates the essential role of target sites in the normal function of these genes as transcription factors. Expression profile of AlNAC1L.1 candidate gene in response to salt and drought stresses and ABA phytohormone in leaf, stem and root tissues was analyzed by RT-qPCR. The results showed that AlNAC1L.1 gene down-regulated in all tissues at 6 hours after applying stresses. Among the treatments, 600 mM NaCl treatment reduced AlNAC1L.1 expression in leaf, stem and root tissues to about -217, -26 and -9 folds, respectively. Therefore, the AlNAC1L.1 which is ortholog of known Oryza miR164-targeted NAC gene OMTN6, may play negative regulatory role in response to salt, drought and ABA treatments. These results indicated that function of some NAC proteins might be conserved among species. Collectively, these findings provided a useful resource for further analysis of the interactions between NAC genes and their intricate regulation by miR164 in response to abiotic stresses.
Proteomics
Samira Mardani Zonouz; Mahmoud Toorchi; Shaghayegh aslzad
Abstract
Drought is one of the most important factors causing abiotic stress in plants. Wheat, as a vital crop, is extensively cultivated in regions that face water scarcity at least during one period of the year. Proteomic approach is one of the ways to identify proteins involved in plant tolerance to water ...
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Drought is one of the most important factors causing abiotic stress in plants. Wheat, as a vital crop, is extensively cultivated in regions that face water scarcity at least during one period of the year. Proteomic approach is one of the ways to identify proteins involved in plant tolerance to water stress. In order to investigate the effect of water deficit stress on the root proteome pattern of desert-tolerant wheat, an experiment was conducted in the form of a completely randomized design with seven replications. Root proteins were extracted by TCA/acetone method and the protein expression pattern was analyzed using two-dimensional electrophoresis. Potential proteins involved in the response to water deficiency were identified by comparing the protein expression patterns under water deficit stress with the expression pattern in control conditions. The results revealed significant differences in root weight and root length at a 5% probability level, indicating the detrimental effects of water stress on plant roots. The proteomic analysis identified 98 reproducible protein spots, of which 10 exhibited statistically significant changes, with eight spots showing increased expression and one showing decreased expression. These protein spots were identified based on their molecular weight (MW) and isoelectric point (pI) through database searches. The identified proteins were classified into various functional categories related to stress response, including protein synthesis and accumulation, oxidative stress, response and defense against stress and metabolic pathways.
Genomics
Rezvan Mousivand; Mohammad Majdi; ّFoad Fatehi; Hamed ghobari
Abstract
One of the most harmful pests of Zagros forests is the Tortrix viridana (Lep. Tortricidae). Genetic diversity of Tortrix viridana host plant populations in the oak forests of northwestern Iran and the northern Zagros region was investigated using 28s gene sequence. The samples were collected from the ...
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One of the most harmful pests of Zagros forests is the Tortrix viridana (Lep. Tortricidae). Genetic diversity of Tortrix viridana host plant populations in the oak forests of northwestern Iran and the northern Zagros region was investigated using 28s gene sequence. The samples were collected from the forest areas of west Azarbaijan, Lorestan, Kurdistan and Kermanshah provinces. They were in the larval stage, were kept in laboratory conditions until they turned into pupa and then into a complete insect. DNA extraction was done by CTAB method. Also, in order to amplify the 28s region, the 28s gene sequence of Tortrix genus was used from NCBI for primer design. The desired region was amplified using the PCR method and the PCR products were sequenced. 21 samples were selected to investigate genetic diversity using the 28s gene, and 18 sequences DNAs were of suitable quality for further investigations. The DNA sequences were edited using Bioedit software and aligned using MegaX software, and the phylogenetic tree was drawn by UPGMA method with 1000 sampling repetitions. The evaluation of the genetic structure of populations showed that the diversity between populations is greater than within populations. The results of the phylogenetic tree also showed that different samples of the Tortrix viridana have genetic diversity based on geographical distance. Therefore, the time of appearance of the pest, their behavior and their type of control and management are also different.
Molecular Plant Breeding
Sina Ghanbari; Kianoosh Cheghamirza; leila zarei; Roghayeh Naseri; Elisabetta Mazzucotelli
Abstract
Among cereals, durum wheat (Triticum turgidum L. var. durum) is one of the most important protein and energy sources after bread wheat. It has a significant role in human nutrition in most countries. In this study, to identify and localization of QTLs controlling traits related to starch and Neutral ...
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Among cereals, durum wheat (Triticum turgidum L. var. durum) is one of the most important protein and energy sources after bread wheat. It has a significant role in human nutrition in most countries. In this study, to identify and localization of QTLs controlling traits related to starch and Neutral detergent fiber, 118 durum wheat recombinant inbred lines obtained from the cross between the local genotype of Iran-249 originated from the west of Iran and the local cultivar of Zardak from Kermanshah were evaluated in two environments (2014 and 2015) under rainfall conditions using randomized complete block design along with parents in three replications. QTL analysis for each trait was performed using the inclusive composite interval mapping method to identify genomic regions that significantly affected the studied traits. A total of six QTLs were identified for the two traits measured, grain starch content and neutral detergent fiber. Three QTLs were identified on chromosome 7A and one QTL on chromosome 4B for the grain starch content trait. For the neutral detergent fiber trait, one QTL was localization on chromosome 6B and one QTL on chromosome 7A. Identifying and localization QTLs controlling traits related to seed quality characteristics can provide an opportunity to improve these traits through marker-assisted selection. Also, these results can create a basis for identifying candidate genes and map-based cloning and confirming QTL function.
Molecular Plant Breeding
Sahar Ghahramani; Reza Darvishzadeh
Abstract
Maize is the third most important cereal after wheat and rice in the world and is a major seed source for many people in Africa, Latin America and Asia. Knowledge on function and extent of genes effect is one of the necessities to achieve high yielding cultivars. In this regard, molecular marker technology ...
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Maize is the third most important cereal after wheat and rice in the world and is a major seed source for many people in Africa, Latin America and Asia. Knowledge on function and extent of genes effect is one of the necessities to achieve high yielding cultivars. In this regard, molecular marker technology has eliminated the need to know the pedigree of genotypes for estimating the kinship matrix to evaluate genotypes breeding values. In this research, 97 genotypes of maize were evaluated in a randomized complete block design (RCBD) with 6 replications for agronomical traits. In the molecular experiment, the molecular profiles of the genotypes were prepared with 28 pairs of Inter-retro transposon amplified polymorphism (IRAP) and Retro transposon-microsatellite amplified polymorphism )REMAP( primers. Estimation the breeding valueofstudied traits in maize genotypes was done through the best linear unbiased prediction (BLUP) in the mixed linear model framewo rk by integrating molecular data based calculated kinship matrix. Considering the sum of estimated breeding values ranks for the studied traits, genotypes P3L11, P10L9, P9L6, P19L5 Kahia and (Paternal) OH43 / 1042 had the highest ranks. Positive breeding value shows that these genotypes have the greatest potential in transmitting the value of traits to the next generation. Genotype P14L2 with positive and high breeding value for leaf length, leaf area, cob weight and leaf area index and P16L6 Kahia with positive and high breeding value for plant height to cob height, cob length and grain weight in the plant, can be introduced as desirable parents to improve these traits in maize breeding programs.
Molecular Plant Breeding
Alireza Nabipour; Reza Darvishzadeh; Ahmad Sarrafi
Abstract
Oilseeds are undoubtedly one of the most strategic agricultural products; their production is of basic needs for food security in any society. Sunflower with the scientific name of Helianthus annuus L. is an annual, monoecy, dicotyledonous plant that belongs to composite family. This genus consists diploid, ...
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Oilseeds are undoubtedly one of the most strategic agricultural products; their production is of basic needs for food security in any society. Sunflower with the scientific name of Helianthus annuus L. is an annual, monoecy, dicotyledonous plant that belongs to composite family. This genus consists diploid, tetraploid and hexaploid species, and common sunflower is a diploid species with a base chromosome number of x=17. Sunflower is grown mainly for its edible oil. Environmental stresses such as drought, salinity, unusual temperatures, heavy metal and UV radiation are serious threats to plant growth, metabolism and productivity. In recent years, astonishing advances in biotechnology, genetic engineering, and computer science have made breeding programs much faster, more accurate, and more efficient than ever before. New techniques, if properly incorporated into breeding programs, can dramatically increase the speed and accuracy of these programs and can reduce costs by an extraordinary amount. In this article, while briefly referring to conventional breeding methods, new methods and their application in sunflower breeding are discussed. In the last 10 years, the science of genomic has expanded the genetic information of quantitative traits, and marker assisted selection has become a practical tool.
Molecular Genetics and Genetic Engineering
Sepideh Charkhandaz; Karim Sorkheh
Abstract
The yield and acceptable quality of the oil of canola make this plant as one of the most important plants for providing edible oil. Due to the hot and dry climate in Iran and water necessary for seed germination, discovery of the solution to improve germination and seedling establishment is required. ...
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The yield and acceptable quality of the oil of canola make this plant as one of the most important plants for providing edible oil. Due to the hot and dry climate in Iran and water necessary for seed germination, discovery of the solution to improve germination and seedling establishment is required. Seed priming and treatment of seedlings with the extract of the seaweed Ascophyllum nodosum is one of the solutions for uniform germination and establishment of seedlings. The currently study have been explore the effect of application of Ascophyllum nodosum seaweed extract on seed germination and changes in the relative expression pattern of some important key genes related to gibberellic acid and brassinosteroids biosynthesis pathway using qRT-PCR. For this purpose, germination indexes were measured by the application of treatment 1% v/v treatment of Ascophyllum nodosum extract in four levels of treatment (0, 10, 15 and 30 days) until flowering stage. The leaf of sampling in each treatment was performed in three biological replications. The results of this study showed the effectiveness of seaweed extract treatment on increasing germination and seed vigor percentage, so that 100% germination of treated seeds obtained on the 3-day. The relative expression of algae extract showed an increase in the expression of EXP, ATI, ENTKO, AEC and BINSP genes, which are all important and as the key genes in the germination process compared to the control treatment. The use of seaweed extract treatment showed the highest expression in ATI (4.39) and ENTKO (5.70) genes in 30-day treatment, respectively. The lowest expressions for GIB and EXP genes in all three treatments (10, 15 and 30 days) were obtained. Also, there was the highest positive correlation between EEN and GIB (1), ENTKO and BINSP (0.98), AEC and BINSP (0.96) genes at the 5% significantly level. The correlation of these genes due to the use of algae extract ultimately led to a positive effect on the germination process of rapeseed seeds. Also, the results of heat map showed the genes of EXP and AEC (-0.57), GIB and ATI (-0.50) genes and XEN and ATI (-0.49) have a negative correlation at an error level of 5% and the increase of one led to the decrease of the other. This indicates that’s the activity of the final product of each of these genes is able to affect the germination process and promoting plant growth and development.
Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi; Esmaeil Bakhshandeh; Markus Kuhlmann
Abstract
From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. ...
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From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. Based on the unique structure of the PP2C domain, 34 AlPP2C genes were discovered and classified into ten evolutionary branches based on homology with Arabidopsis thaliana. According to exon-intron structural analyses, they possessed a wide range of exon counts. AlPP2Cs shared similar motif organization in the same evolutionary branches based on motif distribution. The motifs ABRE, MBS, DRE, STRE, and LTR, which are related with stress, were discovered in the promoter region of the AlPP2C. AlPP2Cs displayed varied expression patterns in leaf and root tissues in response to salt stress and recovery conditions, according to transcriptome analyses. The AlPP2C4 gene is only expressed in the root tissues. These results expand our understanding of the PP2C gene family and provide valuable information for future research on PP2Cs molecular function and biological processes studies.
Molecular Plant Breeding
Nasrin Akbari; Reza Darvishzadeh
Abstract
With expensing the amount of data, speed and accuracy in breeding evaluations are very important. The multivariate statistical methods, such as GGE Biplot that reduce the data volume and computational complexity, help in this direction. The use of GGE is useful for introducing genotypes with high stability ...
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With expensing the amount of data, speed and accuracy in breeding evaluations are very important. The multivariate statistical methods, such as GGE Biplot that reduce the data volume and computational complexity, help in this direction. The use of GGE is useful for introducing genotypes with high stability and performance. Therefore, in order to introduce a stable genotype with high adaptation to drought stress, 100 oilseed sunflower genotypes were evaluated in a 10×10 simple lattice design under normal and limited irrigation conditions during two successive years (2013-2014). The results of composite variance analysis revealed a significant difference among genotypes in terms of the evaluated agromorphological traits. Based on graphical evaluation of genotype × environment interaction using GGE Biplot in metan program under R, genotypes 57 (SDR19), 41 (F1250/03), 8 (254-ENSAT), 24 (8ASB2) and 26 (H049+FSB) were introduced as the best genotypes in terms of stability and performance. The genotype 8 (254-ENSAT) had the highest performance among all genotypes in all environments. Meanwhile, genotypes 26 (H049+FSB) had the highest performance in Y1D (First year-limited irrigation) and Y1N (First year-normal irrigation) environments, and genotypes 57 (SDR19), 41 (F1250/03) and 24 (8ASB2) had the highest performance in Y2D (Second year -limited irrigation) and Y2N (Second year -normal irrigation) environments. Based on the results, genotype with code number of 8 with high and stable performance can be used in all environments as a parent in the development of high-yielding and stress-tolerant hybrids. The results show that GGE Biplot is a useful statistical method to achieve practical and accurate results.
Medicinal plant Biotechnology
Hamideh Khalaj; nassim zarinpanjeh; Mojtaba Askarizadeh; Hadi Kalantari Khalilabad; Javad Shahghaghi
Abstract
To investigate the effect of salt stress on the growth and phytochemical characteristics in the in vitro cultivation of Nitraria schoberi, an experiment was conducted in the form of a factorial design with a completely random basis. The treatments included different concentrations of sodium chloride ...
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To investigate the effect of salt stress on the growth and phytochemical characteristics in the in vitro cultivation of Nitraria schoberi, an experiment was conducted in the form of a factorial design with a completely random basis. The treatments included different concentrations of sodium chloride (0, 50 and 100 mM) and sodium sulfate (0, 10 and 20 mM). First, the seeds were germinated in vitro and then the cotyledon leaves with the hypocotyl of germinated seeds were placed as explants in MS cultivation environment with 2 mg/L BAP, 0.5 mg/L IBA, and the mentioned treatments. The explants were placed in the growth room under the conditions of 16 hours of light and 8 hours of darkness at a temperature of 25±2. After 4 weeks, stem length, number of leaves, and total phenol and flavonoids were measured. The results of variance analysis showed that different levels of salt have a significant effect (at the 99% level) on the growth indices of seedlings such as the length of the stem and the number of leaves, as well as on the total amount of phenol and flavonoid in the tissue of leaves. Based on comparisons, the maximum length of the stem (4.3 cm) and the number of leaves (5.5) related to the cultivation environment without salt and the highest amount of total phenol (35.37 mg/g) and flavonoid (24.6 mg/g) g/g) related to the cultivation environment containing 50 mM sodium chloride with 10 mM sodium sulfate.
Molecular Plant Breeding
Nasrin Akbari; Reza Darvishzadeh
Abstract
Knowledge on genes effect and action (additive/dominance) is one of the necessities to achieve cultivars with high performance and quality. Estimating the breeding value (additive effect) can be done thanks to molecular markers through best linear unbiased prediction (BLUP). In the present study, 100 ...
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Knowledge on genes effect and action (additive/dominance) is one of the necessities to achieve cultivars with high performance and quality. Estimating the breeding value (additive effect) can be done thanks to molecular markers through best linear unbiased prediction (BLUP). In the present study, 100 oilseed sunflower genotypes were evaluated based on the 10×10 lattice design during two crop years of 1392-1393 under normal and drought stress (irrigation limitation) conditions. The breeding value of 13 traits in 78 genotypes out of 100 was estimated due to having genotyping data with SSR and Retrotransposon based markers in each one of normal and drought stress (irrigation limitation) conditions through BLUP. For this purpose, the kinship matrix was calculated by SSR and Retrotransposon based markers data. According to total ranks of breeding values of all studied traits estimated by molecular data of both markers, in normal conditions, genotypes 47, 11, 8 and 35 and under drought stress (irrigation limitation) conditions, genotypes 8, 11 and 35 showed the highest breeding value. Based on SSR markers data in normal conditions; genotypes 76, 36, 34 and 41 and based on Retrotransposon based markers data; genotypes 61, 78, 72 and 52, and in drought stress (irrigation limitation) conditions based on SSR markers data; genotypes 76, 38, 34, 29 and 70 and based on Retrotransposon based markers data; genotypes 16, 71, 78 and 61 showed the lowest breeding value. Considering both studied conditions and all studied traits and both molecular markers information, genotypes 8, 11 and 35 with high breeding value are introduced as desirable parents for breeding programs.
Molecular Plant Breeding
Amir Forghani Saravani; Babak Rabiei; AliAkbar Ebadi
Abstract
Rice grain quality is a complex characteristic that can be divided into milling quality, appearance quality, cooking quality, and nutritional quality. Most studies on rice grain quality show the importance of chromosomes number one and six in the genetic control of various traits in rice. In the present ...
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Rice grain quality is a complex characteristic that can be divided into milling quality, appearance quality, cooking quality, and nutritional quality. Most studies on rice grain quality show the importance of chromosomes number one and six in the genetic control of various traits in rice. In the present study, the validation of 35 microsatellite markers linked to grain quality characteristics which all located on two chromosomes one and six, was performed in 144 recombinant inbred lines of F10 population resulted from the cross between Sepidrood (an Iranian improved cultivar with inferior quality) and Gharib (an Iranian local cultivar with good quality). The results of regression analysis showed that 25 markers were linked to different quantitative and qualitative traits, and explained from 16 to 39% of the variance of different traits, but the markers RM253, RM246, RM190, RM104, RM314, RM3827 and RM7434 had stronger linkage. Construction of the linkage map of 35 microsatellite markers in the studied population showed that the map length was 236.5 cM and the average distance between adjacent markers was 6.95 cM. QTL analysis by the composite interval mapping method showed that 40 QTLs controlled the measured traits in the studied population and the phenotypic variance controlled by the identified QTLs ranged from 7.57 to 37.41% for milling quality and head rice percentage, respectively. Based on this analysis, 23 markers were closer to the QTLs controlling the studied traits in this research. Of these, some markers were linked to several different traits. In total, the results of regression analysis and QTL analysis showed that the markers RM253, RM246, RM340, RM243, RM4128, RM314, RM3827, RM7434, RM104 and RM190 were the informative markers linked to grain quality characteristics, which can be used in marker-assisted selection programs in the future.
Biotic and Abiotic stress
Maryam Faramarzi Jafar Beiglou; Farhad Nazarian-Firouzabadi; Seyed Sajad Sohrabi; Ali Moghadam
Abstract
Plant diseases, particularly diseases caused by fungi and oomycetes pose significant challenges in modern agriculture worldwide. Pathogen associated molecular pattern (PAMP) like chitin found in the cell walls of fungi and oomycetes, trigger defence signalling, leading to expression of R-genes and the ...
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Plant diseases, particularly diseases caused by fungi and oomycetes pose significant challenges in modern agriculture worldwide. Pathogen associated molecular pattern (PAMP) like chitin found in the cell walls of fungi and oomycetes, trigger defence signalling, leading to expression of R-genes and the production of reactive oxygen species (ROS), and accumulation of a wide range of metabolites. Chitin elicitors prompt the expression of defence-related genes such as chitinases, ultimately the resulting in the breakdown of chitin in the pathogen's cell wall. To assess the expression level of certain chitinases in potatoes and the activity of antioxidant enzymes, leaves of a tolerant potato genotype (jelly) was challenged with chitin oligomers in vitro. Result of this study revealed that 48 hours post chitin induction, the expression of different classes of chitinase genes were significantly increased. Class I chitinase (Soltu.DM.10G017450) and class III chitinase (Soltu.DM.11G026160) genes, had respectively the highest (5.5-fold relative to control) and the lowest (1.1-fold relative to control) expression level after 48 hours post chitin inoculation. However, the activities of antioxidant enzymes catalase and ascorbate peroxidase did not change significantly compared to the control. These findings suggest that the application of chitin does not activate the signaling pathways involved in the biosynthesis of antioxidant enzymes 48 hours after chitin treatment. In addition, results of this study may imply that chitinase genes can be cloned by genetic engineering approaches to generate transgenic plants resistant to pathogens.
Bioinformatics
Samira Karimi; Mahin Pouresmaeil
Abstract
Bioinformatics is an interdisciplinary science that utilizes information technologies to organize and analyze biological data. This science enables researchers to perform comprehensive and documented investigations on various biological problems without the need for expensive and time-consuming laboratory ...
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Bioinformatics is an interdisciplinary science that utilizes information technologies to organize and analyze biological data. This science enables researchers to perform comprehensive and documented investigations on various biological problems without the need for expensive and time-consuming laboratory experiments .In this study, we acquired the reverse transcriptase (RT) sequence of eight virus strains from NCBI with the following accession numbers: NC_001497.2, NC_001648.1, NC_001839.2, NC_003977.2, AF053008.1, EF428979.1, NC_001802.1. We investigated the structural and functional characteristics, domains, and motifs. The analysis revealed that the proteins from the eight virus strains, belonging to different families, exhibited distinct properties that set them apart from one another. The analysis also showed that these proteins are found in the membrane, cytoplasm, and periplasm, and all of them contain at least one specific domain of the reverse transcriptase enzyme. Based on all the analyses performed, Cauliflower mosaic virus, Cassava vein mosaic virus, and Soybean chlorotic mottle virus, all belonging to the Caulimoviridae family, were suitable for producing RT enzymes. The ability of these viruses to adapt to different plant hosts could potentially lead to the development of more efficient and cost-effective methods for producing RT enzymes. This adaptability could also open up new possibilities for genetic engineering and biotechnology, enabling the development of more effective enzymes.
