Abiotic stresses including drought, salinity, heat, cold, flooding, and ultraviolet radiation causes crop losses worldwide. In recent times, preventing these crop losses and producing more food and feed to meet the demands of ever-increasing human populations have gained unprecedented importance. However, the proportion of agricultural lands facing multiple abiotic stresses is expected only to rise under a changing global climate fueled by anthropogenic activities. Identifying the mechanisms developed and deployed by plants to counteract abiotic stresses and maintain their growth and survival under harsh conditions thus holds great significance. Recent investigations have shown that phytohormones, including the classical auxins, cytokinins, ethylene, and gibberellins, and newer members including brassinosteroids, jasmonates, and strigolactones may prove to be important metabolic engineering targets for producing abiotic stress-tolerant crop plants. In this review, we summarize and critically assess the roles that phytohormones play in plant growth and development and abiotic stress tolerance, besides their engineering for conferring abiotic stress tolerance in transgenic crops. We also describe recent successes in identifying the roles of phytohormones under stressful conditions. We conclude by describing the recent progress and future prospects including limitations and challenges of phytohormone engineering for inducing abiotic stress tolerance in crop plants.

Phytohormones and their metabolic engineering for abiotic stress tolerance in crop plants

https://www.cell.com/trends/plant-science/pdf/S1360-1385(11)00255-X.pdf

Cytokinins: metabolism and function in plant adaptation to environmental stresses

https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00100-8.pdf

Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology

Cytokinins (CKs) are involved in response to various environmental cues, including salinity. It has been previously reported that enhancing CK contents improved salt stress tolerance in tomato. However, the underlying mechanisms of CK metabolism and signaling under salt stress conditions remain to be deciphered. Two tomato isopentenyltransferases, SlIPT3 and SlIPT4, were characterized in tomato and Arabidopsis. Both proteins displayed isopentenyltransferase (IPT) activity in vitro, while their encoding genes exhibited different spatio-temporal expression patterns during tomato plant development. SlIPT3 and SlIPT4 were affected by the endogenous CK status, tightly connected with CKs feedback regulation, as revealed by hormonal treatements. In response to salt stress, SlIPT3 and SlIPT4 were strongly repressed in tomato roots, and differently affected in young and old leaves. SlIPT3 overexpression in tomato resulted in high accumulation of different CK metabolites, following modifications of CK biosynthesis-, signaling- and degradation-gene expression. In addition, 35S::SlIPT3 tomato plants displayed improved tolerance to salinity consecutive to photosynthetic pigments and K+/Na+ ratio retention. Involvement of SlIPT3 and SlIPT4 in salt stress response was also observed in Arabidopsis ipt3 knock-out complemented plants, through maintenance of CK homeostasis. SlIPT3 and SlIPT4 are functional IPTs encoded by differently expressed genes, distinctively taking part in the salinity response. The substantial participation of SlIPT3 in CK metabolism during salt stress has been determined in 35S::SlIPT3 tomato transformants, where enhancement of CKs accumulation significantly improved plant tolerance to salinity, underlining the importance of this phytohormone in stress response.

/pdf/tomato-solanum-lycopersicum-l-slipt3-and-slipt4-37kdh7q4zx.pdf

Tomato (Solanum lycopersicum L.) SlIPT3 and SlIPT4 isopentenyltransferases mediate salt stress response in tomato

Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS), genomes and transcriptomes of virtually any species are now available for studies of adaptive evolution. We experimentally manipulated temperature conditions for two groups of crimson spotted rainbowfish (Melanotaenia duboulayi) and measured differences in RNA transcription between them. This non-migratory species is found across a latitudinal thermal gradient in eastern Australia and is predicted to be negatively impacted by ongoing environmental and climatic change. Using next generation RNA-seq technologies on an Illumina HiSeq2000 platform, we assembled a de novo transcriptome and tested for differential expression across the treatment groups. Quality of the assembly was high with a N50 length of 1856 bases. Of the 107,749 assembled contigs, we identified 4251 that were differentially expressed according to a consensus of four different mapping and significance testing approaches. Once duplicate isoforms were removed, we were able to annotate 614 up-regulated transfrags and 349 that showed reduced expression in the higher temperature group. Annotated blast matches reveal that differentially expressed genes correspond to critical metabolic pathways previously shown to be important for temperature tolerance in other fish species. Our results indicate that rainbowfish exhibit predictable plastic regulatory responses to temperature stress and the genes we identified provide excellent candidates for further investigations of population adaptation to increasing temperatures.

/pdf/rna-seq-analysis-reveals-extensive-transcriptional-2plrrus6bk.pdf

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species

Background: Bamboo occupies an important phylogenetic node in the grass family with remarkable sizes, woodiness and a striking life history. However, limited genetic research has focused on bamboo partially because of the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bamboo research. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset for the Ma bamboo (Dendrocalamus latiflorus Munro). Results: The Ma bamboo transcriptome was sequenced using the Illumina paired-end sequencing technology. We produced 15,138,726 reads and assembled them into 103,354 scaffolds. A total of 68,229 unigenes were identified, among which 46,087 were annotated in the NCBI non-redundant protein database and 28,165 were annotated in the Swiss-Prot database. Of these annotated unigenes, 11,921 and 10,147 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 45,649 unigenes onto 292 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. The annotated unigenes were compared against Moso bamboo, rice and millet. Unigenes that did not match any of those three sequence datasets are considered to be Ma bamboo unique. We predicted 105 unigenes encoding eight key enzymes involved in lignin biosynthesis. In addition, 621 simple sequence repeats (SSRs) were detected. Conclusion: Our data provide the most comprehensive transcriptomic resource currently available for D. latiflorus Munro. Candidate genes potentially involved in growth and development were identified, and those predicted to be unique to Ma bamboo are expected to give a better insight on Ma bamboo gene diversity. Numerous SSRs characterized contributed to marker development. These data constitute a new valuable resource for genomic studies on D. latiflorus Munro and, more generally, bamboo.

Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform

Soil salinity is a serious worldwide problem. To improve the salt tolerance of plants, an increasing number of genes related to abiotic stress have been recently expressed by genetic engineers. In the present study, the successful introduction into tobacco of isopentenyl transferase (IPT) from Agrobacterium tumefaciens via Agrobacterium-mediated transformation is reported. A stress-inducible genetic construct was cloned using IPT under the control of the stress-inducible promoter rd29A from Arabidopsis thaliana. A total of 40 putative transgenic plant lines were obtained from independent Kan-resistant shoots. IPT integration into the tobacco genome was confirmed by polymerase chain reaction (PCR) and Southern blot analyses. Four positive transgenic lines each with a single T-DNA insertion were obtained. Real-time PCR confirmed a marked increase in IPT expression in young tobacco plants harboring rd29A-IPT after short-term exposure to salt. Ectopic IPT overexpression IPT under the control of the stress-inducible rd29A promoter resulted in significantly enhanced tolerance to salt stress. No obvious adverse effect on growth and development was observed in transgenic plants. Two IPT transgenic lines, T10 and T25, were chosen for further physiological analyses. The leaves of transgenic tobacco plants showed significantly prolonged chlorophyll retention times under a 2-week salt-stress treatment (150 mmol L−1). In contrast, the leaves of the non-transformed plants (wild type) gradually senesced under the same condition. After re-watering for 2 weeks, chlorophyll in transgenic plants increased to a level comparable with that in the unstressed plants. On the other hand, the level in the non-transgenic control still remained low. Malondialdehyde (MDA) levels increased in both transgenic plants and the control after salt stress. However, the MDA levels only mildly increased in transgenic plants, and dramatically increased in the control. After re-watering for 7 days, MDA in transgenic plants returned to normal, whereas the level in the control remained high. Superoxide dismutase activity also similarly increased in transgenic plants during salt stress, and returned to normal after re-watering. These results indicate that enhanced reactive oxygen species scavenging capability may play a significant role in acquiring tolerance to abiotic stress.

An Isopentyl Transferase Gene Driven by the Stress-Inducible rd29A Promoter Improves Salinity Stress Tolerance in Transgenic Tobacco

Soil salinization can lead to environmental and ecological problems worldwide. Abiotic stressors, including salinity, are suspected to regulate microRNA (miRNA) expression. Plants exposed to such abiotic stressors express specific miRNAs, which are genes encoding small non-coding RNAs of 20-24 nucleotides. miRNAs are known to exist widely in plant genomes, and are endogenous. A previous study used miRNA microarray technology and poly(A) polymerase-mediated qRT-PCR technology to analyze the expression profile of miRNAs in two types of plants, Populus cathayana L. (salt-sensitive plants) and Salix matsudana Koidz (highly salinity-tolerant plants), both belonging to the Salicaceae family. miRNA microarray hybridization revealed changes in expression of 161 miRNAs P. cathayana and 32 miRNAs in S. matsudana under salt stress. Differences in expression indicate that the same miRNA has different expression patterns in salt-sensitive plants and salt-tolerant plants under salt stress. These indicate that changes in expression of miRNAs might function as a response to varying salt concentrations. To examine this, we used qRT-PCR to select five miRNA family target genes involved in plant responses to salt stress. Upon saline treatment, the expressions of both ptc-miR474c and ptc-miR398b in P. cathayana were down-regulated, but were up-regulated in S. matsudana. Expression of the miR396 family in both types of plants was suppressed. Furthermore, we have analyzed the different expression patterns between P. cathayana and S. matsudana. Findings of this study can be utilized in future investigations of post-transcriptional gene regulation in P. cathayana and S. matsudana under saline stress.

Expression profile of miRNAs in Populus cathayana L. and Salix matsudana Koidz under salt stress

Overexpression of cysteine protease gene from Salix matsudana enhances salt tolerance in transgenic Arabidopsis

The halotolerant fungus Aspergillus glaucus CCHA was isolated from the surface of wild vegetation around a saltern with the salinity range being 0–31%. Here, a full-length cDNA library of A. glaucus under salt stress was constructed to identify genes related to salt tolerance, and one hundred clones were randomly selected for sequencing and bioinformatics analysis. Among these, 82 putative sequences were functionally annotated as being involved in signal transduction, osmolyte synthesis and transport, or regulation of transcription. Subsequently, the cDNA library was transformed into E. coli cells to screen for putative salt stress-related clones. Five putative positive clones were obtained from E. coli cells grown on LB agar containing 1 M NaCl, on which they showed rapid growth compared to the empty vector control line. Analysis of transgenic Arabidopsis thaliana lines overexpressing CCHA-2142 demonstrated that the gene conferred increased salt tolerance to plants as well by protecting the cellular membranes, suppressing the inhibition of chlorophyll biosynthesis. These results highlight the utility of this A. glaucus cDNA library as a tool for isolating and characterizing genes related to salt tolerance. Furthermore, the identified genes can be used for the study of the underlying biology of halotolerance.

/pdf/isolation-of-salt-stress-related-genes-from-aspergillus-1d67dv5sn1.pdf

Lihua Xie

Papers

Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform

An Isopentyl Transferase Gene Driven by the Stress-Inducible rd29A Promoter Improves Salinity Stress Tolerance in Transgenic Tobacco

Expression profile of miRNAs in Populus cathayana L. and Salix matsudana Koidz under salt stress

Overexpression of cysteine protease gene from Salix matsudana enhances salt tolerance in transgenic Arabidopsis

Isolation of Salt Stress-Related Genes from Aspergillus glaucus CCHA by Random Overexpression in Escherichia coli