Research Paper
Molecular Plant Breeding
Marjan Jannatdoust; Reza Darvishzadeh; Sattar Tahmasebi Enferadi; Maryam Monazzah
Abstract
Salinity is a major abiotic stress that limits the growth and productivity of plants in many parts of the world due to increased use of poor-quality water for irrigation and soil salinity. Plant adaptation or tolerance to salinity stress involves alteration in physiological processes and metabolic pathways ...
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Salinity is a major abiotic stress that limits the growth and productivity of plants in many parts of the world due to increased use of poor-quality water for irrigation and soil salinity. Plant adaptation or tolerance to salinity stress involves alteration in physiological processes and metabolic pathways and activating molecular or gene networks. In this study, 2DE technique was used to identify proteins responsive to salinity stress in maize. Two maize lines with different responses to salinity stress; R10 (tolerant) and S46 (sensitive) were selected. In the eight-leaf stage, salinity stress treatment of 8 dS/m was applied to plants for 20 days and then leaf proteins were extracted. Spots with more than a 1.5-fold increase or decrease in their expression were isolated and sequenced by mass spectrometry. Functional classification of protein spots per line after MS/MS revealed that the differentlly expressed proteins have different metabolic activities. In the tolerant line (R10), 5 spots including Pyruvate orthophosphate dikinase proteins, ATP synthase subunit beta, Germin-like protein, Chlorophyll a-b binding protein, Triosephosphate isomerase, and 40S ribosomal protein, respectively showed an increased expression level. Moreover, in the sensitive line (S46), one spot showed an increased expression level that related to Proteasome subunit beta proteins, and two spots including Chlorophyll a-b binding protein and Ribulose bisphosphate carboxylase small chain protein showed a decreased expression level. The proteins identified in this study and the possible related biochemical pathways provide new information on the response of maize lines (R10 and S46) to salinity stress.
Research Paper
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.
Research Paper
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.
Research Paper
Mojgan shahivand; Reza Mir drikvand; masod gomarian; Kamran Samiei
Abstract
The Real-time PCR is a very powerful technique for the analysis of gene expression in various organisms. However, normalizing gene expression data and obtaining reliable results largely depends on the selection of stable reference genes. In this study, the expression stability of six general reference ...
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The Real-time PCR is a very powerful technique for the analysis of gene expression in various organisms. However, normalizing gene expression data and obtaining reliable results largely depends on the selection of stable reference genes. In this study, the expression stability of six general reference genes (EF-1α, 18S rRNA, ACTIN, β-Tubulin, HSP and GAPDH) was investigated in green and red cultivars of sweet basil under five abiotic stresses (cold, drought, heat, salt and light). The stability of these reference genes was analyzed using BestKeeper and NormFinder softwares. Results showed that all reference genes had different expression levels in both green and red cultivars of sweet basil. There was no significant difference in expression between green and red cultivars. The highest and lowest expression levels were calculated for β-Tubulin and 18S rRNA reference genes, respectively. The results of BestKeeper software identified HSP and ACTIN genes as stable reference genes, respectively. The NormFinder software identified β-Tubulin genes as stable reference gene. Final ranking of the results of BestKeeper and NormFinder softwares identified ACTIN gene as the most stable reference gene for the gene expression studies in green and red cultivars of sweet basil using real-time PCR.
Research Paper
Bioinformatics
Hadis Boroun; Amir Siahpoosh; Seyyed Mohsen Sohrabi; Mohammad Reza Nikbakht; Javad Ghasemian Yadegari; Mohsen Mohammadi; Seyed Sajad Sohrabi
Abstract
Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin ...
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Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin gene family members were identified and characterized from onion (Allium cepa L.) using bioinformatics and experimental methods. All snakin protein sequences were retrieved from NCBI database. The snakin consensus sequence was obtained from alignment of retrieved sequences. Then, the consensus sequence was aligned against the onion transcriptome using tBLASTn tool. The resulting sequences were analyzed to determine the full-ORF, and to prediction of functional domains, signal peptides, subcellular localization, physicochemical properties, amino acid frequency and anti-microbial activity. The complete coding sequence of snakin genes were amplified by PCR. Finally, the presence of seven snakin genes, with an average ORF length of 332 bp, were confirmed in onion. The high similarity of the onion snakin genes with homologous snakin genes belonging to other plant species in terms of nucleotide and protein sequences as well as structural was revealed by bioinformatics analysis. The results also showed that all identified onion snakins had the potential antimicrobial activity. Due to the potential antimicrobial activity of identified peptides, by producing these peptides in different expression systems, they can be used as new antimicrobial agents against human, animal and plant pathogens.
Research Paper
Bioinformatics
Mozhdeh Arab; Hamid Najafi Zarrini; Ghorbanali Nematzadeh; Seyyed Hamidreza Hashemi-petroudi
Abstract
The calcineurin B-like protein (CBL) is an essential calcium sensor that plays a crucial role in plant growth, development and stress responses. The identification of a cis-acting element in the promoter region of the CBL gene family in three plants, including Oryza sativa (OsCBL), Arabidopsis thaliana ...
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The calcineurin B-like protein (CBL) is an essential calcium sensor that plays a crucial role in plant growth, development and stress responses. The identification of a cis-acting element in the promoter region of the CBL gene family in three plants, including Oryza sativa (OsCBL), Arabidopsis thaliana (AtCBL), and Arabidopsis littoralis (AtCBL), was investigated because of their importance and involvement in signal transduction under abiotic and biological stresses. Sub-cellular localization of 10 AtCBL, 10 OsCBL and six AlCBL genes showed that AtCBL4, AtCBL10, AlCBL4.2, AlCBL4.3 and AlCBL10 proteins were located in the plasma membrane. 26 CBLs were identified and grouped into two major groups based on their orthologous relatedness in the phylogenetic tree. According to a comparative analysis of the gene structure of the CBLs gene family, about 66 percent of AlCBL genes, 60 percent of AtCBL genes, and 80 percent of OsCBL genes had eight exons and seven introns. Cis-regulatory elements were identified and grouped into eight distinct classes. The ABRE, ARE, GC motif, MBS, DRE, STRE, and LTR motifs were essential stress-related elements. Different regulatory mechanisms in the promoter region of AtCBLs are responsible for their distinct expression patterns, which are regulated by numerous tissue-specific and stress-specific cis-elements. The functional analysis of AlCBL4.2 (which contains six as-1 motifs) will provide useful information about this gene's regulatory processes due to its tissue-specific and enhancer feature of as-1 motif.
