RNA-Seq transcriptome profiling of immature grain wheat is a technique for understanding comparative modeling of baking quality.

Improving the baking quality is a primary challenge in the wheat flour production value chain, as baking quality represents a crucial factor in determining its overall value. In the present study, we conducted a comparative RNA-Seq analysis on the high baking quality mutant "O-64.1.10" genotype and its low baking quality wild type "Omid" cultivar to recognize potential genes associated with bread quality. The cDNA libraries were constructed from immature grains that were 15 days post-anthesis, with an average of 16.24 and 18.97 million paired-end short-read sequences in the mutant and wild-type, respectively. A total number of 733 transcripts with differential expression were identified, 585 genes up-regulated and 188 genes down-regulated in the "O-64.1.10" genotype compared to the "Omid". In addition, the families of HSF, bZIP, C2C2-Dof, B3-ARF, BES1, C3H, GRF, HB-HD-ZIP, PLATZ, MADS-MIKC, GARP-G2-like, NAC, OFP and TUB were appeared as the key transcription factors with specific expression in the "O-64.1.10" genotype. At the same time, pathways related to baking quality were identified through Kyoto Encyclopedia of Genes and Genomes. Collectively, we found that the endoplasmic network, metabolic pathways, secondary metabolite biosynthesis, hormone signaling pathway, B group vitamins, protein pathways, pathways associated with carbohydrate and fat metabolism, as well as the biosynthesis and metabolism of various amino acids, have a great deal of potential to play a significant role in the baking quality. Ultimately, the RNA-seq results were confirmed using quantitative Reverse Transcription PCR for some hub genes such as alpha-gliadin, low molecular weight glutenin subunit and terpene synthase (gibberellin) and as a resource for future study, 127 EST-SSR primers were generated using RNA-seq data.

RNA-seq analysis and reconstruction of gene networks involved in response to salinity stress in quinoa (cv. Titicaca).

To better understand the mechanisms involved in salinity stress, the adaptability of quinoa cv. Titicaca-a halophytic plant-was investigated at the transcriptome level under saline and non-saline conditions. RNA-sequencing analysis of leaf tissue at the four-leaf stage by Illumina paired-end method was used to compare salt stress treatment (four days after stress at 13.8 dsm-1) and control. Among the obtained 30,846,354 transcripts sequenced, 30,303 differentially expressed genes from the control and stress treatment samples were identified, with 3363 genes expressed ≥ 2 and false discovery rate (FDR) of < 0.001. Six differential expression genes were then selected and qRT-PCR was used to confirm the RNA-seq results. Some of the genes (Include; CML39, CBSX5, TRX1, GRXC9, SnRKγ1 and BAG6) and signaling pathways discussed in this paper not been previously studied in quinoa. Genes with ≥ 2 were used to design the gene interaction network using Cytoscape software, and AgriGO software and STRING database were used for gene ontology. The results led to the identification of 14 key genes involved in salt stress. The most effective hub genes involved in salt tolerance were the heat shock protein gene family. The transcription factors that showed a significant increase in expression under stress conditions mainly belonged to the WRKY, bZIP and MYB families. Ontology analysis of salt stress-responsive genes and hub genes revealed that metabolic pathways, binding, cellular processes and cellular anatomical entity are among the most effective processes involved in salt stress.

Identification of salinity responsive genes in lavender through cDNA-AFLP.

Currently, a global demand exists forlavender as a significant medicinal plant and source of essential oils. Freshwater and arable lands are two major factors that inhibit extensive farming of medicinal plants in Iran. Saline water from seas and salty soil may be new resources for agricultural use, especially for medicinal plants. We sought to extend our knowledge of the Lavandula angustifolia genome and molecular basis of its salinity tolerance by using cDNA amplified fragment length polymorphism (cDNA-AFLP) to investigate the changes in plant transcriptomes in response to NaCl. All identified transcript derived fragments (TDF) were assigned as novel L. angustifolia genes related to signal transduction, regulation of gene expression, alternative splicing, autophagy, and secondary metabolite biosynthesis. qRT-PCR analysis of the TDFs in response to different concentrations of NaCl revealed various levels of mRNA of the identified genes in this plant. Our findings provided primary insights into the molecular response of L. angustifolia to salinity.

The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley.

Considering the complex nature of salinity tolerance mechanisms, the use of isogenic lines or mutants possessing the same genetic background albeit different tolerance to salinity is a suitable method for reduction of analytical complexity to study these mechanisms. In the present study, whole transcriptome analysis was evaluated using RNA-seq method between a salt-tolerant mutant line "M4-73-30" and its wild-type "Zarjou" cultivar at seedling stage after six hours of exposure to salt stress (300 mM NaCl). Transcriptome sequencing yielded 20 million reads for each genotype. A total number of 7116 transcripts with differential expression were identified, 1586 and 1479 of which were obtained with significantly increased expression in the mutant and the wild-type, respectively. In addition, the families of WRKY, ERF, AP2/EREBP, NAC, CTR/DRE, AP2/ERF, MAD, MIKC, HSF, and bZIP were identified as the important transcription factors with specific expression in the mutant genotype. The RNA-seq results were confirmed at several time points using qRT-PCR for some important salt-responsive genes. In general, the results revealed that the mutant accumulated higher levels of sodium ion in the root and decreased its transfer to the shoot. Also, the mutant increased the amount of potassium ion leading to the maintenance a high ratio [K+]/[Na+] in the shoot compared to its wild-type via fast stomata closure and consequently transpiration reduction under the salt stress. Moreover, a reduction in photosynthesis and respiration was observed in the mutant, resulting in utilization of the stored energy and the carbon for maintaining the plant tissues, which is considered as a mechanism of salt tolerance in plants. Up-regulation of catalase, peroxidase, and ascorbate peroxidase genes has resulted in higher accumulation of H2O2 in the wild-type compared to the mutant. Therefore, the wild-type initiated rapid ROS signals which led to less oxidative scavenging in comparison with the mutant. The mutant increased expression in the ion transporters and the channels related to the salinity to maintain the ion homeostasis. In overall, the results demonstrated that the mutant responded better to the salt stress under both osmotic and ionic stress phases and lower damage was observed in the mutant compared to its wild-type under the salt stress.

LC-MS based identification of stylosin and tschimgine from fungal endophytes associated with Ferula ovina.

OBJECTIVES: Ferula ovina is an Iranian medicinal plant. Tschimgine and stylosin are two of its major monoterpene derivatives. In this study, we proceeded to investigate some fungal endophytes from F. ovina that can produce plant secondary metabolites. MATERIALS AND METHODS: The isolated endophytic fungi were fermented in potato dextrose broth (PDB) medium and their extracts were screened for the presence of the plant compounds by liquid chromatography-tandem mass spectrometry (LC-MS). Endophytes identification was performed by morphological and molecular methods. Three markers (ITS, LSU, and TEF1) were used for accurate molecular identification. RESULTS: Forty isolates from 9 different genera of endophytic fungi were identified, of which two recently reported species of O. ferulica and Pithoascus persicus were able to produce tschimgine and stylosin. CONCLUSION: These fungi can be used as a substitute for the production of plant's medicinal compounds independent of wild populations of the source plant.

Genetic differentiation between bitter and sweet asafetida plants using ISSR markers.

Bitter (Ferula pseudalliacea) and sweet (Ferula assa-foetida) asafetida (Apiaceae family) are well-known economic and medicinal herbs owing to their gum. This study investigates genetic differentiation of F. pseudalliacea and F. assa-foetida using ISSR markers, to determine the effective primer and to assess the possibility of separating sweet and bitter plant populations from each other. Results showed that among 22 primers, eight markers reproduced obvious DNA patterns and revealed 234 scorable DNA bands. ISSR-16 and ISSR-55 primers had better performance than other primers according to the number of bands, PIC and Marker Index. Bitter population showed polymorphic loci (224), percentage of polymorphic loci (95.73%) and observed number of alleles (1.96 ± 0.2), while sweet populations showed the amount of these parameters as 218, 93.16% and 1.93 ± 0.25, respectively. Estimated Gst of sweet population was 0.09 and Gst of bitter population was 0.06. Comparing gene flow in bitter and sweet populations showed a lower level of gene flow between sweet populations (Nm = 4.93) compared to bitter ones (Nm = 7.89). Within group genetic similarity of sweet asafetida population was higher than between group variation of bitter and sweet populations. The highest similarity was observed between bitter populations (0.95). The highest genetic dissimilarity was also estimated between bitter and sweet populations (0.08). Cluster analysis grouped four studied populations into 13 clusters using Jaccard's similarity coefficient and UPGMA method. Principal coordinate analysis showed that 61.02% of total variance was explained using three components and it could completely separate populations as well as cluster analysis. These grouping correspond nearly with geographical distribution. Analysis of molecular variance showed that genetic variation within populations (87%) was more than among populations (13%). The results indicated that ISSR marker is suitable to investigate genetic diversity of asafetida populations and could separate populations of the same genera with similar germplasm.

Persian sturgeon insulin-like growth factor I: molecular cloning and expression during various nutritional conditions.

The effects of different periods of starvation (1, 2, 3, and 4 weeks) and subsequent re-feeding (over a 4 week) on the compensatory growth performance and insulin-like growth factor I (IGF-I) mRNA expression in liver and white muscle were investigated in juvenile Persian sturgeon (Acipenser persicus). First, a fragment of 617 nucleotides coding for IGF-I was cloned from liver, which included an open reading frame of 486 nucleotides, encoding a 162 amino acid preproIGF-I. This is composed of a 45 aa for signal peptide, a 117 aa for the mature peptide comprising the B, C, A, and D domains, and a 47 aa for E domain. The mature Persian sturgeon IGF-I exhibits high sequence identities with other sturgeon species and teleost, ranging between 68 and 95 %. The pattern of IGF-I mRNA expression in the liver and white muscle was measured in response to different periods of starvation and subsequent re-feeding. Nutritional status influenced IGF-I mRNA expression pattern in both liver and muscle. IGF-I mRNA expression in the liver increased during starvation, before decreasing after re-feeding. Furthermore, white muscle IGF-I mRNA expression showed better responses to nutritional status and decreased following starvation and increased by re-feeding. However, changes in the expression of IGF-I mRNA were not significantly different between any of the treatments in both tissues. These data suggest that muscle and liver IGF-I mRNA expression do not have a regulatory role for somatic growth induced by compensatory growth in Persain sturgeon.