Investigating the effect of drought stress and methanol spraying on the influential genes in the Calvin cycle and photorespiration of rapeseed (Brassica napus).

Due to global warming and changes in precipitation patterns, many regions are prone to permanent drought. Rapeseed (Brassica napus ) is one of the main sources of edible oils worldwide, and its production and yield are affected by drought. In this study, gene expression alterations under drought stress are investigated with bioinformatics studies to examine evolutionary relations of conserved motifs structure and interactions among Calvin cycle and photorespiration pathways key genes in drought-tolerant (SLM046) and drought-sensitive (Hayola308) genotypes of rapeseed. Investigating the conservation and evolutionary relationships revealed high conservation in motifs of FBPase, PRK, GlyK and NADP-ME enzymes. The analysis of protein interactions showed the correlation between FTRC, FBPase1, PRKX1, GlyKX2 and NADP-ME4 genes. Furthermore, in rapeseed, for the GlyKX2 and NADP-ME4 genes, four microRNAs of the miR172 family and four members of the miR167 family were identified as post-transcriptional regulators, respectively. The expression of ferredoxin thioredoxin reductase, fructose-1,6-bisphosphatase genes, phosphoribulokinase, glycerate kinase and malic enzyme 4 genes in the two rapeseed genotypes were evaluated by real-time qPCR method under 72h of drought stress and methanol foliar application. As a result, the highest expression levels of FTRC, PRKX1, GlyKX2, NADP-ME4 and FBPase1 were observed in methanol foliar application on the SLM046 genotype at 24h. In contrast, in methanol foliar application on the Hayola308 genotype, the highest expression levels of FTRC, PRKX1, GlyKX2, NADP-ME4 and FBPase1 were observed 8h after the treatment. Our study illustrated that methanol foliar application enhanced plant tolerance under drought stress.

Evaluation of protein's interaction and the regulatory network of some drought-responsive genes in Canola under drought and re-watering conditions.

Drought stress is one of the most important environmental stresses that severely limits the growth and yield of Canola. The re-watering can compensate for the damage caused by drought stress. Investigation of protein's interaction of genes involved in important drought-responsive pathways and their regulatory network by microRNAs (miRNAs) under drought and re-watering conditions are helpful approaches to discovering drought-stress tolerance and recovery mechanisms. In this study, the protein's interaction and functional enrichment analyses of glycolysis, pentose phosphate, glyoxylate cycle, fatty acid biosynthesis, heat shock factor main genes, and the regulatory network of key genes by miRNAs were investigated by in silico analysis. Then, the relative expression of key genes and their related miRNAs were investigated in tolerant and susceptible genotypes of Canola under drought and re-watering conditions by Real-time PCR technique. The bna-miR156b/c/g, bna-miR395d/e/f, bna-miR396a, and all the studied key genes except HSFA1E and PK showed changes in expression levels in one or both genotypes after re-watering. The PPC1 and HSFB2B expression decreased, whereas the MLS and CAC3 expression increased in both genotypes under re-watering treatment after drought stress. It could cause the regulation of oxaloacetate production, the increase of the glyoxylate cycle, lipid biosynthesis, and the reduction of the negative regulation of HSFs under re-watering conditions. It seems that PPC1, G6PD2, MLS, CAC3, and HSFB2B were involved in the recovery mechanisms after drought stress of Canola. They were regulated by drought-responsive miRNAs to respond appropriately to drought stress. Therefore, regulating these genes could be important in plant recovery mechanisms. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01345-1.

Cold-responsive transcription factors in Arabidopsis and rice: A regulatory network analysis using array data and gene co-expression network.

Plant growth and development can be influenced by cold stress. Responses of plants to cold are regulated in part by transcription factors (TFs) and microRNAs, which their determination would be necessary in comprehension of the corresponding molecular cues. Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. Common TF encoding genes were from ERF, MYB, bHLH, NFY, bZIP, GATA, HSF and WRKY families. NFY A4/C2/A10 were the significant hub TFs in both plants. Phytohormone responsive cis-elements such as ABRE, TGA, TCA and LTR were the common cis-elements in TF promoters. Arabidopsis had more responsive TFs compared to rice possibly due to its greater adaptation to ranges geographical latitudes. Rice had more relevant miRNAs probably because of its bigger genome size. The interacting partners and co-expressed genes were different for the common TFs so that of the downstream regulatory networks and the corresponding metabolic pathways. Identified cold-responsive TFs in (A + R) seemed to be more engaged in energy metabolism esp. photosynthesis, and signal transduction, respectively. At post-transcriptional level, miR5075 showed to target many identified TFs in rice. In comparison, the predictions showed that identified TFs are being targeted by diverse groups of miRNAs in Arabidopsis. Novel TFs, miRNAs and co-expressed genes were introduced as cold-responsive markers that can be harnessed in future studies and development of crop tolerant varieties.

Investigation of proteins' interaction network and the expression pattern of genes involved in the ABA biogenesis and antioxidant system under methanol spray in drought-stressed rapeseed.

Drought is one of the most critical abiotic stresses, which significantly impair rapeseed (Brassica napus L.) productivity. Several factors can regulate the stress response, including changes in gene expression in biological pathways, extensive protein interaction networks, and post-translational regulatory factors like microRNAs. External factors can also affect the intensity of the stress response. Therefore, this study investigated protein-protein interactions of some essential genes involved in abscisic acid (ABA) production, antioxidant system, and Krebs cycle. The expression of phyton synthase (PSY), 9-cis-epoxycarotenoid dioxygenase (NCED3), aldehyde oxidase (AAO3), thioredoxin reductase (NTRC), and glutathione reductase (GR) genes in two rapeseed genotypes, i.e., Hyola308 (drought-sensitive) and SLM046 (drought-tolerant) were evaluated using qRT-PCR technique under 72 h of drought stress and methanol foliar application. In the SLM046 (tolerant) genotype, the expression levels of PYS, NCED, AAO3, and GR genes were increased after 8 h of foliar application. The expression level of the NTR gene was increased 8 and 24 h after stress and methanol treatment. In the Hyola308 genotype, PYS, AAO3, NTR, and GR genes' expression level was increased 8 h after methanol foliar application, and the NCED gene was increased 24 h after stress with methanol treatment. In general, methanol foliar application increased the expression levels of several genes. Particularly, the gene expression was considerably higher in the SLM046 genotype than in Hyola308. Bioinformatics prediction of microRNAs targeting PSY, NCED, GR, NTRC, and AAO3 genes was performed, and 38, 38, 13, 11, and 11 microRNAs were predicted for these genes, respectively. The study of effective microRNAs showed that sometimes more than one type of microRNA could affect the desired gene, and in some cases, a conserved family of microRNAs caused the main effect on gene expression. Overall, our results lay the foundation for functional characterization of these genes or gene-miRNA modules in regulating drought stress tolerance in rapeseed.

Analysis of Brassica napus dehydrins and their Co-Expression regulatory networks in relation to cold stress.

Dehydrins (DHNs) are plant specific cold and drought stress-responsive proteins that belong to late embryogenesis abundant (LEA) protein families. B. napus DHNs (BnDHNs) were computationally analyzed to establish gene regulatory- and protein-protein interaction networks. Promoter analyses suggested functionality of phytohormones in BnDHNs gene network. The relative expressions of some BnDHNs were analyzed using qRT-PCR in seedling leaves of both cold-tolerant (Zarfam) and -sensitive (Sari Gul) canola treated/untreated by cold. Our expression data were indicative of the importance of BnDHNs in cold tolerance in Zarfam. BnDHNs were classified into three classes according to the expression pattern. Moreover, expression of three BnDHN types, SKn (BnLEA10 and BnLEA18), YnKn (BnLEA90) and YnSKn (BnLEA104) were significantly high in the tolerant cultivar at 12 h of cold treatment. Our findings put forward the possibility of considering these genes as screening biomarker to determine cold-tolerant breeding lines; something that needs to be further corroborated. Furthermore, these genes may have some implications in developing such tolerant lines via transgenesis.

Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice.

Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.

Phytochemical attributes of endemic endangered primrose (Primula heterochroma Stapf.) accessions grown in Iran.

Primula heterochroma is indigenous to Caspian coast forests in the north of Iran. Total phenols, total flavnoids, total carotenoids and antioxidant capacity of 50 P. heterochroma accessions were investigated. The highest total phenol (1272.31 mg GA equivalent/100 g fresh weight) and total flavonoids (615 mg catechin/100 g fresh weight) were observed in G5 accession from Saravan. The highest antioxidant activity was observed in G14 accession (73.03 %) from Kacha, followed by G2 accession (69.75 %) and G5 accession (66.84 %) from Saravan. The results of HPLC analysis showed that quercetin-3-glucoside was the major phenolic compound widely found in these accessions followed by chlorogenic acid. There was a linear relationship between the antioxidant capacities and the total phenols and total flavonoid. Inversely, there was no statistically significant correlation between total carotenoid and antioxidant activity. Based on the path coefficient analysis, the maximum direct effect on antioxidant was observed in total phenols (0.908). In addition, the cluster analysis based on Euclidean distance with Unweighted pair-group method using arithmetic average (UPGMA) method separated the accessions into four main groups. Our results supported that Iranian wild primrose accessions possess valuable antioxidant properties for therapeutic and potential medicinal use.