BMC-Rice-s12864-018-5279-4.pdf

Rice

Background: Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique. Results: A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL, OsNAAT, OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29. Conclusions: The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k + , ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent.

THE PLANT CELL ONLINE, 2001

Transcript regulation in response to high salinity was investigated for salt-tolerant rice (var Pokkali) with microarrays including 1728 cDNAs from libraries of salt-stressed roots. NaCl at 150 mM reduced photosynthesis to one tenth of the prestress value within minutes. Hybridizations of RNA to microarray slides probed for changes in transcripts from 15 min to 1 week after salt shock. Beginning 15 min after the shock, Pokkali showed upregulation of transcripts. Approximately 10% of the transcripts in Pokkali were significantly upregulated or downregulated within 1 hr of salt stress. The initial differences between control and stressed plants continued for hours but became less pronounced as the plants adapted over time. The interpretation of an adaptive process was supported by the similar analysis of salinity-sensitive rice (var IR29), in which the immediate response exhibited by Pokkali was delayed and later resulted in downregulation of transcription and death. The upregulated functions observed with Pokkali at different time points during stress adaptation changed over time. Increased protein synthesis and protein turnover were observed at early time points, followed by the induction of known stress-responsive transcripts within hours, and the induction of transcripts for defenserelated functions later. After 1 week, the nature of upregulated transcripts (e.g., aquaporins) indicated recovery.

Plant Signaling & Behavior, 2012

Journal of Plant Biochemistry and Biotechnology, 2011

Soil salinity is a major constraint to rice production worldwide; hence intensive efforts are on to identify genes that make rice varieties tolerant to the salt stress. In this study, four rice varieties differing in tolerance to salinity were studied for differential gene expression through microarray analysis of RNA extracted from rice seedlings grown under control and salt stress conditions. Overall 1,696 gene probes in the tolerant and 2,220 gene probes in the sensitive varieties showed significant differential expression under salt stress as compared to control plants, but only 72 of these were common between the tolerant and susceptible variety groups. Fifty highest responsive genes in the tolerant and sensitive variety groups included some of the well known salt responsive genes, e. g. basic proline-rich protein, zinc finger protein and late embryogenesis abundant protein. We identified 6 genes that were commonly differentially expressed under salt stress in all the four varieties studied and hence could be the nodal points for transcriptional regulation under salt stress. These included genes for FACT complex subunit SSRP1-A, ORM1, abscisic stress ripening protein, photosystem II 10 kDa protein, negative transcription regulator-like protein and purple acid phosphatase. Expression patterns of the 6 genes were similar in the four genotypes except that all of these were down regulated in the salt tolerant variety CSR 27 under salt stress, while one gene was uniquely over expressed in highly salt sensitive variety VSR 156. These lists may contain the probable candidate genes for salt tolerance.

PLoS ONE, 2011

One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models responded to salinity in a similar way to crop species, and changes in the concentration of shoot Cl 2 correlated well with tolerance. Metabolic changes were partially conserved, but divergence was observed amongst the genotypes. Transcriptome analysis showed that about 60% of expressed genes were responsive to salt treatment in one or more species, but less than 1% was responsive in all. Therefore, genotype-specific transcriptional and metabolic changes overshadowed conserved responses to salinity and represent an impediment to simple translational genomics. However, 'triangulation' from multiple genotypes enabled the identification of conserved and tolerant-specific responses that may provide durable tolerance across species. Citation: Sanchez DH, Pieckenstain FL, Szymanski J, Erban A, Bromke M, et al. (2011) Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics. PLoS ONE 6(2): e17094.

Wild salt-tolerant barley (Hordeum spontaneum) is the ancestor of cultivated barley (Hordeum vulgare or H. vulgare). Although the cultivated barley genome is well studied, little is known about genome structure and function of its wild ancestor. In the present study, RNA-Seq analysis was performed on young leaves of wild barley treated with salt (500 mM NaCl) at four different time intervals. Transcriptome sequencing yielded 103 to 115 million reads for all replicates of each treatment, corresponding to over 10 billion nucleotides per sample. Of the total reads, between 74.8 and 80.3% could be mapped and 77.4 to 81.7% of the transcripts were found in the H. vulgare unigene database (unigene-mapped). The unmapped wild barley reads for all treatments and replicates were assembled de novo and the resulting contigs were used as a new reference genome. This resulted in 94.3 to 95.3% of the unmapped reads mapping to the new reference. The number of differentially expressed transcripts was 9277, 3861 of which were unigene-mapped. The annotated unigene- and de novo-mapped transcripts (5100) were utilized to generate expression clusters across time of salt stress treatment. Two-dimensional hierarchical clustering classified differential expression profiles into nine expression clusters, four of which were selected for further analysis. Differentially expressed transcripts were assigned to the main functional categories. The most important groups were ‘‘response to external stimulus’’ and ‘‘electron-carrier activity’’. Highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis, reactive oxygen species (ROS) scavenging, ethylene production, signaling network and protein refolding. The comparisons demonstrated that mRNA-Seq is an efficient method for the analysis of differentially expressed genes and biological processes under salt stress.

Journal of Plant Research, 2017

samples were then compared, leading to the discovery of 4096 DEGs. Based on the functional annotation results obtained, the enrichment factor of each functional group in DEGs was calculated in relation to the total reads obtained. It was found that the group with the highest gene modulation was involved in the secondary metabolite biosynthesis of plants, with approximately 2.5% increase in relation to the total reads obtained. This suggests an extensive transcriptional reprogramming of the secondary metabolic pathways after stress induction, which could be directly responsible for the salt tolerance capability of Bajong. Keywords mRNA-seq • Wild rice variety • Antioxidant content • Salt stress • Plant phytochemicals Abbreviations COG Clusters of orthologous groups DEGs Differentially expressed genes DPPH Di(phenyl)-(2,4,6-trinitrophenyl) iminoazanium GMO Genetically modified organism GO Gene ontology KEGG Kyoto encyclopedia of gene and genome LEA Late embryogenesis abundant ROS Reactive oxygen species RWC Relative water content SOS Salt overly sensitive TFC Total flavonoid content TPC Total phenolic content

Genes

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased ...

Plant response to salinity-induced stress, like most physiological responses, is specie specific. Despite this specificity, the response is often elicitor dependent, which tends to activate a more general response. While stress in plants may be classified as being biotic or abiotic, both types are known to be influenced by signaling pathway. One of the phenotypically well-characterized specific responses in plants is the production of secondary metabolites. However, the overall signaling pattern and its effects on corresponding genes often lead to their differential expression, which turn it specific. This implies that general and specific responses are activated for each situation. Key mediators amongst the chemical entities with specific physiological effects involved in the signaling pathways include jasmonic acid and acetyl salicylic acid, while the more general mediators include plant growth regulators such as auxins and cytokinins. The molecular mechanism of action of these molecules involves promoter activation that bear specific recognition elements, to which transcription factors can bind to enhance or repress the expression of a given gene. The application of high-throughput techniques has shown that microRNA and chromatin remodeling are involved in exposing such regions under different stress conditions. Here, we discuss the observed differences in salt stress tolerance, and sensitivity to high or low exposure to salt in plants, which correlate with varying degrees of the production of secondary metabolites. It is exposed from the perspective of gene expression under plant growth regulators to physiological response. The role of microRNA and chromatin remodeling as signal elements to control gene expression at DNA binding sites, interacting with transcription factors, which may in turn be affected by microRNAs are also discussed.

BMC Genomics, 2009

Background: Rice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley.