Papers by Mohammad Reza Ghaffari
Barley yield relies more on stem reserves under stress conditions at the grain filling stage. At ... more Barley yield relies more on stem reserves under stress conditions at the grain filling stage. At terminal drought stresses, the remobilization of reserved assimilates from stem to seed contributes a major role in yield. To understand the molecular mechanism of stem reserve utilization during drought stress, a comparative proteome and physiological analyses were performed on the penultimate internodes of three genotypes of barley Yousef (tolerant), Morocco (susceptible), and PBYT17 (semi-tolerant) under drought stress at 21 and 28 days after anthesis (DAA). Under water stress and well-watered conditions Yousef showed significantly higher RWC, grain yield, and stem reserve remobilization capacity than susceptible and semi-tolerant genotypes. The proteome analysis led to the identification of 1580 differentially abundant proteins (DAPs), of which 759 and 821 proteins were differentially expressed at 21 and 28 DAA, respectively. Tolerant genotype in response to drought stress increased ...
BMC plant biology, May 29, 2024
BMC Genomics
Background The mechanisms underlying rice root responses to drought during the early developmenta... more Background The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown. Results This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. T...
Suaeda salsa is a promising halophyte model to study the molecular mechanisms underlying salt tol... more Suaeda salsa is a promising halophyte model to study the molecular mechanisms underlying salt tolerance in plants. To attain a thorough knowledge of transcriptomic profiles under salt stress during seedling establishment, we accomplished whole-transcriptome sequencing on the seedlings of Suaeda salsa at 30 days after exposure to 0 mM, 200 mM, 400 mM, and 800 mM NaCl. We observed that transcripts implicated in solute transport and nutrient uptake, protein synthesis, modification, hemostasis, transcriptional regulation, and phytohormone action prominently changed at different concentrations of salinity. Likewise, significant changes in the expression level of members of gene families such as MYB, bHLH, MADS/AGL, bZIP, NAC, C2C2, B3, ERF, WRKY, HB, NF-Y, C2H2 suggest them as key players in the salt tolerance of Suaeda salsa during seedling establishment. We additionally found the superfamilies of tyrosine-like protein kinase (TLK) linked to phosphorylation and Ca2+calmodulin-dependent ...
PLOS ONE
Salinity is one of the main abiotic stresses limiting crop productivity. In the current study, th... more Salinity is one of the main abiotic stresses limiting crop productivity. In the current study, the transcriptome of wheat leaves in an Iranian salt-tolerant cultivar (Arg) was investigated in response to salinity stress to identify salinity stress-responsive genes and mechanisms. More than 114 million reads were generated from leaf tissues by the Illumina HiSeq 2500 platform. An amount of 81.9% to 85.7% of reads could be mapped to the wheat reference genome for different samples. The data analysis led to the identification of 98819 genes, including 26700 novel transcripts. A total of 4290 differentially expressed genes (DEGs) were recognized, comprising 2346 up-regulated genes and 1944 down-regulated genes. Clustering of the DEGs utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that transcripts associated with phenylpropanoid biosynthesis, transporters, transcription factors, hormone signal transduction, glycosyltransferases, exosome, and MAPK signaling might be in...
bioRxiv (Cold Spring Harbor Laboratory), May 13, 2022
Journal of Genetic Engineering and Biotechnology
Background The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato.... more Background The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato. However, little information is available about U-box genes in potato (Solanum tuberosum). In this study, 62 U-box genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, gene expression, TFBS, and synteny analysis were performed on the U-box genes. Results Based on in silico analysis, most of StU-boxs included a U-box domain; however, some of them lacked harbored domain the ARM, Pkinase_Tyr, and other domains. Based on their phylogenetic relationships, the StU-box family members were categorized into four classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of StU-box genes revealed that StU-box genes had the highest and the lowest number of TFBS in MYB and CSD, respectively. Moreover, based on in silico and gene expression data, variable frequencies of TFBS in StU-box genes could indicate that thes...
Ziel des Projektes war die Untersuchung der Metaboliten,- Enzymaktivität,- und Transkript-Signatu... more Ziel des Projektes war die Untersuchung der Metaboliten,- Enzymaktivität,- und Transkript-Signaturen, die die Entwicklung des Blattes und des Samens in Gerste bestimmen. Zwölf geographisch-verschiedene Gerste-Linien wurden unter Feld-Bedingungen angebaut und für die Untersuchungen verwendet. In der vegetativen Phase wurde eine Signatur, bestehend aus 27 Metaboliten identifiziert, während in der generativen Phase 43 (Blatt) und 60 (Samen) Metabolite eine Signatur bildeten. Die Co-Integrierung von Enzymaktivitäten und Transkripten führte zur Identifizierung von Alanin-Amino-Transferase, Phosphoglucoisomerase, cytosolische Aldolase als mögliche Biomarker zur Vorhersage von Biomasse in Blatt und Samen. Zusätzlich wurde Saccharose-Synthase, Adenin-Glucose-Pyrophosphorylase und glucose6P-Dehydrogenase als spezifische Biomarker für Samen in der generativen Phase identifiziert. Darüber hinaus führte die Netzwerk Korrelation zwischen Metaboliten und dem Samenertrag im Reifestadium zur Identi...
Glutathione S-transferase (GST) genes control vital traits for metabolism of the variety of toxin... more Glutathione S-transferase (GST) genes control vital traits for metabolism of the variety of toxins that expose insects to the environment (insecticide) or plant defense systems. Sunn pest is the most important pest of wheat and barley in the Middle East where it threats food security throughout the region. Sequencing the sunn pest's RNA provides an opportunity to identify the structure and function of the different gene families. To our knowledge, this is the first study to identify 43 GST candidate genes in sunn pest using bioinformatics tools. The identified candidate genes clustered in 5 cytosolic GST (Delta, Theta, Zeta, Omega, and Sigma) and Microsomal GST using phylogenetic analysis. The Sigma subclass was identified as the biggest subclass with 22 candidate genes, while microsomal GST found to be the smallest group with one candidate gene. Given the role of GST in the interactions among the insect, toxins, and environment, our results facilitate future investigations on i...
Suitable conditions for high-value compounds hyperaccumulation are the most challenging approach ... more Suitable conditions for high-value compounds hyperaccumulation are the most challenging approach in Arthrospira platensis. In the current study, the co-production of specialty pigments and high-value metabolites was investigated with a varying concentration of well-known and candidate metabolic stressors in Arthrospira platensis. Supplementing Arthrospira platensis with a minimum of 0.50% of Monosodium glutamate (MSG) and a maximum of 2% of aspartate (ASP) increased Phycocyanin productivity by 83.36 and 64.77 percent, respectively. However, a maximum of 1.50% of MSG and a minimum of 0.50% ASP increased carotenoid content by 188.80 and 68.97 percent, respectively. These observations, coupled with those showing supplemented ASP stimulate unsaturated fatty acid accumulation, possibly through enhanced de novo biosynthesis, and essential amino acid biosynthesis to a greater extent in Arthrospira platensis. A network correlation analysis also indicated the distinct metabolite abundance an...
Background: Salinity, as one of the main abiotic stresses, critically threatens growth and fertil... more Background: Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review.Results: A total of 3449 DEGs were detected in 46 meta-QTL positions, while 1286, 86, 1729 and 348 DEGs were observed respectively in root, shoot, seedling and leaves tissues. Moreover, functional annotation of DEGs located in meta-QTLs suggested some involved biological processes (e.g. ion transport, regulation of transcription, cell wall organization and...
Scientific Reports, 2020
Rumen microbial environment hosts a variety of microorganisms that interact with each other to ca... more Rumen microbial environment hosts a variety of microorganisms that interact with each other to carry out the feed digestion and generation of several by-products especially methane, which plays an essential role in global warming as a greenhouse gas. However, due to its multi-factorial nature, the exact cause of methane production in the rumen has not yet been fully determined. The current study is an attempt to use system modeling to analyze the relationship between interacting components of rumen microbiome and its role in methane production. Metagenomic data of sheep rumen, with equal numbers of high methane yield (HMY) and low methane yield (LMY) samples, were used. As a well-known approach for the systematic comparative study of complex traits, the co-abundance networks were constructed in both operational taxonomic unit (OTU) and gene levels. A gene-catalog of 1,444 different rumen microbial strains was developed as a reference to measure gene abundances. The results from both...
Plant and Cell Physiology, 2016
Planta, 2013
To determine the contribution of polar auxin transport (PAT) to auxin accumulation and to adventi... more To determine the contribution of polar auxin transport (PAT) to auxin accumulation and to adventitious root (AR) formation in the stem base of Petunia hybrida shoot tip cuttings, the level of indole-3-acetic acid (IAA) was monitored in non-treated cuttings and cuttings treated with the auxin transport blocker naphthylphthalamic acid (NPA) and was complemented with precise anatomical studies. The temporal course of carbohydrates, amino acids and activities of controlling enzymes was also investigated. Analysis of initial spatial IAA distribution in the cuttings revealed that approximately 40 and 10 % of the total IAA pool was present in the leaves and the stem base as rooting zone, respectively. A negative correlation existed between leaf size and IAA concentration. After excision of cuttings, IAA showed an early increase in the stem base with two peaks at 2 and 24 h post excision and, thereafter, a decline to low levels. This was mirrored by the expression pattern of the auxin-responsive GH3 gene. NPA treatment completely suppressed the 24-h peak of IAA and severely inhibited root formation. It also reduced activities of cell wall and vacuolar invertases in the early phase of AR formation and inhibited the rise of activities of glucose-6-phosphate dehydrogenase and phosphofructokinase during later stages. We propose a model in which spontaneous AR formation in Petunia cuttings is dependent on PAT and on the resulting 24-h peak of IAA in the rooting zone, where it induces early cellular events and also stimulates sink establishment. Subsequent root development stimulates glycolysis and the pentose phosphate pathway.
IRANIAN JOURNAL OF …, 2010
Frontiers in Plant Science
Every winter, temperate woody plants have to cope with freezing stress. Winter hardiness is of cr... more Every winter, temperate woody plants have to cope with freezing stress. Winter hardiness is of crucial importance for pomegranate survival and productivity. A comparative morphological and metabolic study was conducted on the stems and buds of 15 field-grown mature pomegranate genotypes in seven time-points during two developmental cycles. Seasonal changes of frost hardiness, as determined by electrolyte leakage method, and metabolite analysis by HPLC and GC revealed the variability in frost hardiness and metabolic contents result from genetic background and organ, as well as seasonal condition. Morphological adaptations, as well as metabolic remodeling, are the distinct features of the hardy genotypes. Larger buds with a greater number of compressed scales and the higher number of protective leaves, together with the higher number and content of changed metabolites, especially amino acids, seem to provide a higher frost resistance for those trees. We recorded two-times the change i...
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Papers by Mohammad Reza Ghaffari