In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.

Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

Cytokinins are classic plant hormones that orchestrate plant growth, development, and physiology. They affect gene expression in target cells by activating a multistep phosphorelay network. Type-B response regulators, acting as transcriptional activators, mediate the final step in the signaling cascade. Previously, we have introduced a synthetic reporter, Two Component signaling Sensor (TCS)::green fluorescent protein (GFP), which reflects the transcriptional activity of type-B response regulators. TCS::GFP was instrumental in uncovering roles of cytokinin and deepening our understanding of existing functions. However, TCS-mediated expression of reporters is weak in some developmental contexts where cytokinin signaling has a documented role, such as in the shoot apical meristem or in the vasculature of Arabidopsis (Arabidopsis thaliana). We also observed that GFP expression becomes rapidly silenced in TCS::GFP transgenic plants. Here, we present an improved version of the reporter, TCS new (TCSn), which, compared with TCS, is more sensitive to phosphorelay signaling in Arabidopsis and maize (Zea mays) cellular assays while retaining its specificity. Transgenic Arabidopsis TCSn::GFP plants exhibit strong and dynamic GFP expression patterns consistent with known cytokinin functions. In addition, GFP expression has been stable over generations, allowing for crosses with different genetic backgrounds. Thus, TCSn represents a significant improvement to report the transcriptional output profile of phosphorelay signaling networks in Arabidopsis, maize, and likely other plants that display common response regulator DNA-binding specificities.

/pdf/a-robust-and-sensitive-synthetic-sensor-to-monitor-the-3nof1sukvq.pdf

A Robust and Sensitive Synthetic Sensor to Monitor the Transcriptional Output of the Cytokinin Signaling Network in Planta

https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00090-8.pdf

Ethylene Signaling in Rice and Arabidopsis: Conserved and Diverged Aspects

Root size and architecture are important crop plant traits, as they determine access to water and soil nutrients. The plant hormone cytokinin is a negative regulator of root growth and branching. Here, we generated transgenic barley (Hordeum vulgare) plants with an enlarged root system by enhancing cytokinin degradation in roots to explore the potential of cytokinin modulations in improving root functions. This was achieved through root-specific expression of a CYTOKININ OXIDASE/DEHYDROGENASE gene. Enhanced biomass allocation to roots did not penalize shoot growth or seed yield, indicating that these plants were not source limited. In leaves of transgenic lines, the concentrations of several macroelements and microelements were increased, particularly those with low soil mobility (phosphorus, manganese, and zinc). Importantly, seeds contained up to 44% more zinc, which is beneficial for human nutrition. Transgenic lines also demonstrated dampened stress responses to long-term drought conditions, indicating lower drought sensitivity. Taken together, this work demonstrates that root engineering of cereals is a promising strategy to improve nutrient efficiency, biofortification, and drought tolerance.

/pdf/root-engineering-in-barley-increasing-cytokinin-degradation-3jav857mmp.pdf

Root Engineering in Barley: Increasing Cytokinin Degradation Produces a Larger Root System, Mineral Enrichment in the Shoot and Improved Drought Tolerance

The AP2/ERF transcription factor family, one of the largest families unique to plants, performs a significant role in terms of regulation of growth and development, and responses to biotic and abiotic stresses. Moso bamboo (Phyllostachys edulis) is a fast-growing non-timber forest species with the highest ecological, economic and social values of all bamboos in Asia. The draft genome of moso bamboo and the available genomes of other plants provide great opportunities to research global information on the AP2/ERF family in moso bamboo. In total, 116 AP2/ERF transcription factors were identified in moso bamboo. The phylogeny analyses indicated that the 116 AP2/ERF genes could be divided into three subfamilies: AP2, RAV and ERF; and the ERF subfamily genes were divided into 11 groups. The gene structures, exons/introns and conserved motifs of the PeAP2/ERF genes were analyzed. Analysis of the evolutionary patterns and divergence showed the PeAP2/ERF genes underwent a large-scale event around 15 million years ago (MYA) and the division time of AP2/ERF family genes between rice and moso bamboo was 15–23 MYA. We surveyed the putative promoter regions of the PeDREBs and showed that largely stress-related cis-elements existed in these genes. Further analysis of expression patterns of PeDREBs revealed that the most were strongly induced by drought, low-temperature and/or high salinity stresses in roots and, in contrast, most PeDREB genes had negative functions in leaves under the same respective stresses. In this study there were two main interesting points: there were fewer members of the PeDREB subfamily in moso bamboo than in other plants and there were differences in DREB gene expression profiles between leaves and roots triggered in response to abiotic stress. The information produced from this study may be valuable in overcoming challenges in cultivating moso bamboo.

/pdf/genome-wide-analysis-of-the-ap2-erf-transcription-factors-4oqg4f4kf4.pdf

Genome-Wide Analysis of the AP2/ERF Transcription Factors Family and the Expression Patterns of DREB Genes in Moso Bamboo (Phyllostachys edulis).

The ethylene response factor (ERF) family are members of the APETALA2 (AP2)/ERF transcription factor superfamily; they are known to play an important role in plant adaptation to biotic and abiotic stress ERF genes have been studied in Arabidopsis, rice, grape, and maize; however, there are few reports of ERF genes in sorghum We identified 105 sorghum ERF (SbERF) genes, which were categorized into 12 groups (A-1 to A-6 and B-1 to B-6) based on their sequence similarity, and this new method of classification for ERF genes was then further characterized A comprehensive bioinformatic analysis of SbERF genes was performed using a sorghum genomic database, to analyze the phylogeny of SbERF genes, identify other conserved motifs apart from the AP2/ERF domain, map SbERF genes to the 10 sorghum chromosomes, and determine the tissue-specific expression patterns of SbERF genes Gene clustering indicates that SbERF genes were generated by tandem duplications Comparison of SbERF genes with maize ERF homologs suggests lateral gene transfer between monocot species These results can contribute to our understanting of the evolution of the ERF gene family

https://www.funpecrp.com.br/gmr/year2013/vol12-2/pdf/gmr1822.pdf

A genome-wide analysis of the ERF gene family in sorghum.

Cytokinins play many vital roles in plant development and physiology. In plants, cytokinin signals are sensed and transduced by the two-component signal system. This signaling cascade is typically composed of three proteins: a sensory histidine kinase, a histidine phosphotransfer protein, and a response regulator. Through a comprehensive genome-wide analysis of the maize (Zea mays) genome, 48 genes were identified, including 11 ZmHKs, 9 ZmHPs, and 28 ZmRRs (21 A-type ZmRRs and 7 B-type ZmRRs). Using maize genome sequence databases, we analyzed conserved protein motifs and established phylogenetic relationships based on gene structure, homology, and chromosomal location. The duplication of these two-component system genes in the maize genome corresponded to the clusters of these genes in the phylogenetic trees. Sequence analysis of the duplicate genes demonstrated that one gene may be in gene duplication, and that there was significant variation in the evolutionary history of the different gene families. We assessed the expression levels of all ZmRRs in the leaves and roots by reverse transcription PCR; they were all found to be active. Our results provide a foundation for functional and evolutionary studies on maize two-component signal system proteins.

/pdf/genome-wide-identification-classification-and-analysis-of-2uvlmsaeh4.pdf

J. Fan

Papers

A genome-wide analysis of the ERF gene family in sorghum.

Genome-wide identification, classification, and analysis of two-component signal system genes in maize