Drought-Up-Regulated TaNAC69-1 is a Transcriptional Repressor of TaSHY2 and TaIAA7, and Enhances Root Length and Biomass in Wheat

Overexpression of NAC transcription factors from Eremopyrum triticeum promoted abiotic stress tolerance

Eremopyrum triticeum is a typical spring ephemeral species, which in China mainly distributed in the desert regions of northern Xinjiang, and play an important role in the desert ecosystems. E. triticeum has several adaptive characteristics such as short growth rhythms, high photosynthetic efficiency, high seed production, drought and salt resistance. However, the molecular regulatory mechanism of E. triticeum in responses to abiotic stress resistance is still unknown. In this study, two NAC-like transcription factor-encoding genes, EtNAC1 and EtNAC2, were isolated from E. triticeum. The predicted EtNAC1 and EtNAC2 proteins possess a typical NAC DNA-binding domain at the N-terminal region. The qRT-PCR analysis showed that EtNAC1 and EtNAC2 were highly expressed in mature roots of E. triticeum, and were significantly up-regulated under drought, high salt and abscisic acid (ABA) stresses. Subcellular localization analysis in onion epidermal cells revealed that EtNAC1 and EtNAC2 were located in the nucleus. Expression of EtNAC1 and EtNAC2 in yeast cells improved the survival rate of yeast under low temperature, H2O2, high drought and salt stresses. Overexpression of EtNAC1 and EtNAC2 in Arabidopsis thaliana conferred enhanced tolerance to drought and salt stresses, increased ABA sensitivity, and transgenic plants showed higher proline (Pro) content, but lower malondialdehyde content, lower chlorophyll leaching, lower water loss rate and stomatal aperture (width/length) than WT plants. In conclusion, EtNAC1 and EtNAC2 play important roles in abiotic stress responses of E. triticeum, which might have significant potential in crop molecular breeding for abiotic stress tolerance.

Genome-wide identification of Aux/IAA gene family members in grape and functional analysis of VaIAA3 in response to cold stress

KEY MESSAGE

Twenty-five VvIAA genes and eighteen VaIAA genes were identified from Pinot Noir and Shanputao, respectively. The overexpression of VaIAA3 in transgenic Arabidopsis increased cold tolerance by regulating auxin, ABA and ethylene signaling. Aux/IAA genes are key genes involved in regulating auxin signal transduction in plants. Although IAA genes have been characterized in various plant species, the role of IAA genes in grape cold resistance is unclear. To further explore the members of the Aux/IAA gene family in grape and their functions, in this study, using genomic data for Pinot Noir (Vitis vinifera cv. 'Pinot Noir') and Shanputao (Vitis amurensis), 25 VvIAA genes and 18 VaIAA genes were identified. The VaIAA genes presented different expression patterns at five different temperatures (28 ± 1 °C, 5 ± 1 °C, 0 ± 1 °C, -5 ± 1 °C, and -10 ± 1 °C) according to qRT‑PCR results. VaIAA3 was selected as a candidate gene for further functional analysis because of its high expression level under low-temperature stress. Subcellular localization experiments revealed that VaIAA3 was localized in the nucleus. Additionally, under 4 °C treatment for 24 h, relative expression level of VaIAA3, antioxidant enzyme activity, survival rate, and cold-responsive gene expression in three transgenic lines (OE-1, OE-2, OE-3) were greater, whereas relative electrolytic conductivity (REC), malondialdehyde (MDA) content and hydrogen peroxide (H2O2) content were lower than those of the wild type (WT). Transcriptome sequencing analysis revealed that VaIAA3 regulated cold stress resistance in Arabidopsis thaliana (Arabidopsis) through pathways involving auxin, ABA, JA, or ethylene. Importantly, heterologous overexpression of VaIAA3 increased the resistance of Arabidopsis to cold stress, which provides a theoretical basis for the further use of VaIAA3 to improve cold resistance in grape.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement

Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.

Increasingly amplified stimulation mediated by TaNAC69-B is crucial for the leaf senescence in wheat

Leaf senescence involves massive multidimensional alterations, such as nutrient redistribution, and is closely related to crop yield and quality. No apical meristem, Arabidopsis transcription activation factor, and Cup-shaped cotyledon (NAC)-type transcription factors integrate various signals and modulate an enormous number of target genes to ensure the appropriate progression of leaf senescence. However, few leaf senescence-related NACs have been functionally characterized in wheat. Based on our previous RNA-sequencing (RNA-seq) data, we focused on a NAC family member, TaNAC69-B, which is increasingly expressed during leaf senescence in wheat. Overexpression of TaNAC69-B led to precocious leaf senescence in wheat and Arabidopsis, and affected several agricultural traits in transgenic wheat. Moreover, impaired expression of TaNAC69-B by virus-induced gene silencing retarded the leaf senescence in wheat. By RNA-seq and quantitative real-time polymerase chain reaction analysis, we confirmed that some abscisic acid (ABA) biosynthesis genes, including AAO3 and its ortholog in wheat, TraesCS2B02G270600 (TaAO3-B), were elevated by the overexpression of TaNAC69-B. Consistently, we observed more severe ABA-induced leaf senescence in TaNAC69-B-OE wheat and Arabidopsis plants. Furthermore, we determined that TaNAC69-B bound to the NAC binding site core (CGT) on the promoter regions of AAO3 and TaAO3-B. Moreover, we confirmed elevated ABA levels in TaNAC69-B-OE wheat lines. Although TaNAC69-B shares 39.83% identity (amino acid) with AtNAP, TaNAC69-B did not completely restore the delayed leaf senescence in the atnap mutant. Collectively, our results revealed a positive feedback loop, consisting of TaNAC69-B, ABA biosynthesis and leaf senescence, that is essential for the regulation of leaf senescence in wheat.

The Aux/IAA protein TaIAA15-1A confers drought tolerance in Brachypodium by regulating abscisic acid signal pathway

Overexpression of the Aux/IAA protein TaIAA15-1A from wheat improves drought tolerance by regulating the ABA signalling pathway in transgenic Brachypodium. Drought is a major abiotic stress that causes severe crop yield loss. Aux/IAA genes have been shown to be involved in drought stress responses. However, to the best of our knowledge, there has been little research on the molecular mechanism of the wheat Aux/IAA gene in the context of drought tolerance. In this study, we found that expression of the wheat Aux/IAA gene TaIAA15-1A was upregulated by PEG6000, NaCl, SA, JA, IAA and ABA. Transgenic plants overexpressing TaIAA15-1A showed higher drought tolerance than wild-type (WT) plants. The physiological analyses showed that the transgenic lines exhibited a higher survival rate, shoot length, and relative water content than the WT plants. The activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were enhanced in transgenic lines, causing a reduction in the hydrogen peroxide (H₂O₂) and superoxide anion radical (O₂^-) contents. Transcriptome analysis showed that TaIAA15-1A overexpression alters the expression of these genes involved in the auxin signalling pathway, ABA signalling pathway, phenolamides and antioxidant pathways. The results of exogenous ABA treatment suggested that TaIAA15-1A overexpression increased sensitivity to ABA at the germination and postgermination stages compared to WT plants. These results indicate that TaIAA15-1A plays a positive role in plant drought tolerance by regulating ABA-related genes and improving antioxidative stress ability and has potential application in genetically modified crops.

Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development

Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for the increased yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), essentially contributes to an improved root system in wheat. To further analyze the biological functions of QMrl-7B in root development, two sets of Triticum aestivum near-isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) named NIL^KN9204 and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411) named NIL^J411, were subjected to transcriptomic analysis. Among all the mapped genes analyzed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that mainly include N O 3 - transporters, phytohormone signaling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this study, 4308 and 2463 were specifically expressed in the NIL^KN9204 and NIL^J411, respectively. These DEGs reflect different responses of the two sets of NILs to varying N supplies, which likely involve LN-induced root growth. These results explain the better-developed root system and increased root vitality conferred by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.

Genome-Wide Analysis of the Peptidase M24 Superfamily in Triticum aestivum Demonstrates That TaM24-9 Is Involved in Abiotic Stress Response

The peptidase M24 (Metallopeptidase 24, M24) superfamily is essential for plant growth, stress response, and pathogen defense. At present, there are few systematic reports on the identification and classification of members of the peptidase M24 proteins superfamily in wheat. In this work, we identified 53 putative candidate TaM24 genes. According to the protein sequences characteristics, these members can be roughly divided into three subfamilies: I, II, III. Most TaM24 genes are complex with multiple exons, and the motifs are relatively conserved in each sub-group. Through chromosome mapping analysis, we found that the 53 genes were unevenly distributed on 19 wheat chromosomes (except 3A and 3D), of which 68% were in triads. Analysis of gene duplication events showed that 62% of TaM24 genes in wheat came from fragment duplication events, and there were no tandem duplication events to amplify genes. Analysis of the promoter sequences of TaM24 genes revealed that cis-acting elements were rich in response elements to drought, osmotic stress, ABA, and MeJA. We also studied the expression of TaM24 in wheat tissues at developmental stages and abiotic stress. Then we selected TaM24-9 as the target for further analysis. The results showed that TaM24-9 genes strengthened the drought and salt tolerance of plants. Overall, our analysis showed that members of the peptidase M24 genes may participate in the abiotic stress response and provided potential gene resources for improving wheat resistance.

Changes in the concentrations and transcripts for gibberellins and other hormones in a growing leaf and roots of wheat seedlings in response to water restriction

BACKGROUND

Bread wheat (Triticum aestivum) is a major source of nutrition globally, but yields can be seriously compromised by water limitation. Redistribution of growth between shoots and roots is a common response to drought, promoting plant survival, but reducing yield. Gibberellins (GAs) are necessary for shoot and root elongation, but roots maintain growth at lower GA concentrations compared with shoots, making GA a suitable hormone for mediating this growth redistribution. In this study, the effect of progressive drought on GA content was determined in the base of the 4th leaf and root tips of wheat seedlings, containing the growing regions, as well as in the remaining leaf and root tissues. In addition, the contents of other selected hormones known to be involved in stress responses were determined. Transcriptome analysis was performed on equivalent tissues and drought-associated differential expression was determined for hormone-related genes.

RESULTS

After 5 days of applying progressive drought to 10-day old seedlings, the length of leaf 4 was reduced by 31% compared with watered seedlings and this was associated with significant decreases in the concentrations of bioactive GA₁ and GA₄ in the leaf base, as well as of their catabolites and precursors. Root length was unaffected by drought, while GA concentrations were slightly, but significantly higher in the tips of droughted roots compared with watered plants. Transcripts for the GA-inactivating gene TaGA2ox4 were elevated in the droughted leaf, while those for several GA-biosynthesis genes were reduced by drought, but mainly in the non-growing region. In response to drought the concentrations of abscisic acid, cis-zeatin and its riboside increased in all tissues, indole-acetic acid was unchanged, while trans-zeatin and riboside, jasmonate and salicylic acid concentrations were reduced.

CONCLUSIONS

Reduced leaf elongation and maintained root growth in wheat seedlings subjected to progressive drought were associated with attenuated and increased GA content, respectively, in the growing regions. Despite increased TaGA2ox4 expression, lower GA levels in the leaf base of droughted plants were due to reduced biosynthesis rather than increased catabolism. In contrast to GA, the other hormones analysed responded to drought similarly in the leaf and roots, indicating organ-specific differential regulation of GA metabolism in response to drought.

Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants

In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?

Enhancing plant growth and biomass production by overexpression of GA20ox gene under control of a root preferential promoter

Overexpression of GA20 oxidase gene has been a recent trend for improving plant growth and biomass. Constitutive expression of GA20ox has successfully improved plant growth and biomass in several plant species. However, the constitutive expression of this gene causes side-effects, such as reduced leaf size and stem diameter, etc. To avoid these effects, we identified and employed different tissue-specific promoters for GA20ox overexpression. In this study, we examined the utility of At1g promoter to drive the expression of GUS (β-glucuronidase) reporter and AtGA20ox genes in tobacco and Melia azedarach. Histochemical GUS assays and quantitative real-time-PCR results in tobacco showed that At1g was a root-preferential promoter whose expression was particularly strong in root tips. The ectopic expression of AtGA20ox gene under the control of At1g promoter showed improved plant growth and biomass of both tobacco and M. azedarach transgenic plants. Stem length as well as stem and root fresh weight increased by up to 1.5-3 folds in transgenic tobacco and 2 folds in transgenic M. azedarach. Both tobacco and M. azedarach transgenic plants showed increases in root xylem width with xylem to phloem ratio over 150-200% as compared to WT plants. Importantly, no significant difference in leaf shape and size was observed between At1g::AtGA20ox transgenic and WT plants. These results demonstrate the great utility of At1g promoter, when driving AtGA20ox gene, for growth and biomass improvements in woody plants and potentially some other plant species.

A NAC Transcription Factor TuNAC69 Contributes to ANK-NLR-WRKY NLR-Mediated Stripe Rust Resistance in the Diploid Wheat Triticum urartu

Stripe rust is one of the most devastating diseases in wheat. Nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain receptors (NLRs) recognize pathogenic effectors and trigger plant immunity. We previously identified a unique NLR protein YrU1 in the diploid wheat Triticum urartu, which contains an N-terminal ANK domain and a C-terminal WRKY domain and confers disease resistance to stripe rust fungus Puccinia striiformis f. sp. Tritici (Pst). However, how YrU1 functions in disease resistance is not clear. In this study, through the RNA-seq analysis, we found that the expression of a NAC member TuNAC69 was significantly up-regulated after inoculation with Pst in the presence of YrU1. TuNAC69 was mainly localized in the nucleus and showed transcriptional activation in yeast. Knockdown TuNAC69 in diploid wheat Triticum urartu PI428309 that contains YrU1 by virus-induced gene silencing reduced the resistance to stripe rust. In addition, overexpression of TuNAC69 in Arabidopsis enhanced the resistance to powdery mildew Golovinomyces cichoracearum. In summary, our study indicates that TuNAC69 participates in the immune response mediated by NLR protein YrU1, and likely plays an important role in disease resistance to other pathogens.

A stress-responsive transcription factor PeNAC1 regulating beta-D-glucan biosynthetic genes enhances salt tolerance in oat

A Populus euphratica NAC gene regulates (1,3; 1,4)-β-D-glucan content in oat developing seed and improves the spikelet number and grain number per spike in transgenic oat under salinity conditions Salinity is the major factor affecting the production and quality of oat, and improving oat salt tolerance to increase yield and quality is vital. (1,3;1,4)-β-D-glucan in Gramineae is the key component in response to various environmental signals, and it is the most important functional ingredient in oat grain. The NAC transcription factors are important candidate genes used in genetic engineering to improve plant abiotic stress tolerance. In this study, we introduced Populus euphratica PeNAC1, controlled by its own promoter, into hexaploid cultivated oat and produced six transgenic lines. Compared to the non-transgenic control, the expression of PeNAC1 significantly improved the seed germination rate, seedling survival rate, and leaf chlorophyll content in the transgenic plants under salt stress. These physiological changes increased the spikelet number and grain number per spike in the transgenic oat under salinity conditions and reduced the yield loss per plant. The results indicated that the heterologous expression of PeNAC1 plays an effective role in improving the salt tolerance in transgenic oat. In addition, overexpressing PeNAC1 significantly increased the (1,3;1,4)-β-D-glucan content as well as the expression level of the (1,3;1,4)-β-D-glucan biosynthetic genes AsCslF3, AsCslF6, and AsCslF9 in the transgenic lines under salt stress, which suggested that PeNAC1 regulates the synthesis of (1,3;1,4)-β-D-glucan. Our research should assist in the discovery of the diverse action modes of NAC proteins, while PeNAC1 will be useful for improving the salt tolerance and quality of oat through molecular breeding.

Expression dynamics indicate the role of Jasmonic acid biosynthesis pathway in regulating macronutrient (N, P and K+) deficiency tolerance in rice (Oryza sativa L.)

Expression pattern indicates that JA biosynthesis pathway via regulating JA levels might control root system architecture to improve nutrient use efficiency (NUE) and N, P, K⁺ deficiency tolerance in rice. Deficiencies of macronutrients (N, P and K⁺) and consequent excessive use of fertilizers have dramatically reduced soil fertility. It calls for development of nutrient use efficient plants. Plants combat nutrient deficiencies by altering their root system architecture (RSA) to enhance the acquisition of nutrients from the soil. Amongst various phytohormones, Jasmonic acid (JA) is known to regulate plant root growth and modulate RSA. Therefore, to understand the role of JA in macronutrient deficiency in rice, expression pattern of JA biosynthesis genes was analyzed under N, P and K⁺ deficiencies. Several members belonging to different families of JA biosynthesis genes (PLA1, LOX, AOS, AOC, OPR, ACX and JAR1) showed differential expression exclusively in one nutrient deficiency or in multiple nutrient deficiencies. Expression analysis during developmental stages showed that several genes expressed significantly in vegetative tissues, particularly in root. In addition, JA biosynthesis genes were found to have significant expression under the treatment of different phytohormones, including Auxin, cytokinin, gibberellic acid (GA), abscisic acid (ABA), JA and abiotic stresses, such as drought, salinity and cold. Analysis of promoters of these genes revealed various cis-regulatory elements associated with hormone response, plant development and abiotic stresses. These findings suggest that JA biosynthesis pathway by regulating the level of JA might control the RSA thus, it may help rice plant in combating macronutrient deficiency.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

SUPER STARCHY1/ONAC025 participates in rice grain filling

NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.

Root transcriptome profiling of contrasting wheat genotypes provides an insight to their adaptive strategies to water deficit

Water deficit limits plant growth and productivity in wheat. The effect of water deficit varies considerably in the contrasting genotypes. This study attempted comparative transcriptome profiling of the tolerant (Abura) and susceptible (AUS12671) genotypes under PEG-simulated water stress via genome-wide RNA-seq technology to understand the dynamics of tolerance mechanism. Morphological and physiological analyses indicated that the tolerant genotype Abura had a higher root growth and net photosynthesis, which accounted for its higher root biomass than AUS12671 under stress. Transcriptomic analysis revealed a total of 924 differentially expressed genes (DEGs) that were unique in the contrasting genotypes under stress across time points. The susceptible genotype AUS12671 had slightly more abundant DEGs (505) than the tolerant genotype Abura (419). Gene ontology enrichment and pathway analyses of these DEGs suggested that the two genotypes differed significantly in terms of adaptive mechanism. Predominant upregulation of genes involved in various metabolic pathways was the key adaptive feature of the susceptive genotype AUS12671 indicating its energy-consuming approach in adaptation to water deficit. In contrast, downregulation the expression of genes of key pathways, such as global and overview maps, carbohydrate metabolism, and genetic information processing was the main strategy for the tolerant genotype Abura. Besides, significantly higher number of genes encoding transcription factors (TF) families like MYB and NAC, which were reported to be associated with stress defense, were differentially expressed in the tolerant genotype Abura. Gene encoding transcription factors TIFY were only differentially expressed between stressed and non-stressed conditions in the sensitive genotype. The identified DEGs and the suggested differential adaptive strategies of the contrasting genotypes provided an insight for improving water deficit tolerance in wheat.

Biotechnological strategies for improved photosynthesis in a future of elevated atmospheric CO2

The improvement of photosynthesis using biotechnological approaches has been the focus of much research. It is now vital that these strategies be assessed under future atmospheric conditions. The demand for crop products is expanding at an alarming rate due to population growth, enhanced affluence, increased per capita calorie consumption, and an escalating need for plant-based bioproducts. While solving this issue will undoubtedly involve a multifaceted approach, improving crop productivity will almost certainly provide one piece of the puzzle. The improvement of photosynthetic efficiency has been a long-standing goal of plant biotechnologists as possibly one of the last remaining means of achieving higher yielding crops. However, the vast majority of these studies have not taken into consideration possible outcomes when these plants are grown long-term under the elevated CO₂ concentrations (e[CO₂]) that will be evident in the not too distant future. Due to the considerable effect that CO₂ levels have on the photosynthetic process, these assessments should become commonplace as a means of ensuring that research in this field focuses on the most effective approaches for our future climate scenarios. In this review, we discuss the main biotechnological research strategies that are currently underway with the aim of improving photosynthetic efficiency and biomass production/yields in the context of a future of e[CO₂], as well as alternative approaches that may provide further photosynthetic benefits under these conditions.

A wheat NAC interacts with an orphan protein and enhances resistance to Fusarium head blight disease

Taxonomically-restricted orphan genes play an important role in environmental adaptation, as recently demonstrated by the fact that the Pooideae-specific orphan TaFROG (Triticum aestivum Fusarium Resistance Orphan Gene) enhanced wheat resistance to the economically devastating Fusarium head blight (FHB) disease. Like most orphan genes, little is known about the cellular function of the encoded protein TaFROG, other than it interacts with the central stress regulator TaSnRK1α. Here, we functionally characterized a wheat (T. aestivum) NAC-like transcription factor TaNACL-D1 that interacts with TaFROG and investigated its' role in FHB using studies to assess motif analyses, yeast transactivation, protein-protein interaction, gene expression and the disease response of wheat lines overexpressing TaNACL-D1. TaNACL-D1 is a Poaceae-divergent NAC transcription factor that encodes a Triticeae-specific protein C-terminal region with transcriptional activity and a nuclear localisation signal. The TaNACL-D1/TaFROG interaction was detected in yeast and confirmed in planta, within the nucleus. Analysis of multi-protein interactions indicated that TaFROG could form simultaneously distinct protein complexes with TaNACL-D1 and TaSnRK1α in planta. TaNACL-D1 and TaFROG are co-expressed as an early response to both the causal fungal agent of FHB, Fusarium graminearum and its virulence factor deoxynivalenol (DON). Wheat lines overexpressing TaNACL-D1 were more resistant to FHB disease than wild type plants. Thus, we conclude that the orphan protein TaFROG interacts with TaNACL-D1, a NAC transcription factor that forms part of the disease response evolved within the Triticeae.

A novel QTL QTrl.saw-2D.2 associated with the total root length identified by linkage and association analyses in wheat (Triticum aestivum L.)

In wheat, a QTL QTrl.saw-2D.2 associated with the total root length was identified, presumably containing genes closely related to root development. A mapping population of 184 recombinant inbred lines derived from the cross SY95-71 × CH7034 was used to map QTL for seedling root characteristics in hydroponic culture (HC) and in soil-filled pot (SP) methods. Four traits, including maximum root length (MRL), root number (RN), total length (TRL), and root diameter (RD) were measured and used in QTL analyses. A total of 33 QTL for the four root traits were detected, 17 QTLs for TRL, six for RN, seven for MRL, and three for RD. Seven QTL were detected in both HC and SP methods, which explained 7-18% phenotypic variation. One QTL QTrl.saw-2D.2 detected in both HC and SP methods was also validated in another population comprised of 215 diverse lines. This QTL is a novel QTL that explained the highest phenotypic variation 18% in all QTL identified in the present study. Based on candidate gene and comparative genomics analyses, the QTL QTrl.saw-2D.2 may contain genes closely related to root development in wheat (Triticum aestivum L.). The two candidate genes were proposed to explore in future studies.

Overexpression of TaCML20, a calmodulin-like gene, enhances water soluble carbohydrate accumulation and yield in wheat

Calcium (Ca²⁺ ) is a universal messenger that mediates intracellular responses to extracellular stimuli in living organisms. Calmodulin (CaM) and calmodulin-like (CML) proteins are the important Ca²⁺ sensors in plants that decode Ca²⁺ -signatures to execute downstream intracellular level responses. Several studies indicate the interlinking of Ca²⁺ and sugar signaling in plants; however, no genes have been functionally characterized to provide molecular evidence. Our study found that expression of TaCML20 was significantly correlated with water soluble carbohydrate (WSC) concentrations in recombinant inbred lines in wheat. TaCML20 has four EF-hand motifs that may facilitate the binding of Ca²⁺ . To explore the role of CML20, we generated TaCML20 overexpressing transgenic lines in wheat. These lines accumulated higher WSC concentrations in the shoots, and we also found a significantly increased transcript level of sucrose:sucrose-1-fructosyltransferase (1-SST) in the internodes compared with the control plants. In addition, TaCML20 overexpressing plants showed significantly increased tillers per plant and also increased about 19% of grain weight per plant compared with control plants. The results also suggested a role for TaCML20 in drought stress, as its transcripts significantly increased in the shoots of wild-type plants under water deficit. These results uncovered the role of CML20 in determining multiple traits in wheat.

Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.)

The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat.

GhSTOP1, a C2H2 type zinc finger transcription factor is essential for aluminum and proton stress tolerance and lateral root initiation in cotton

Aluminum (Al) and proton (H⁺ ) ions are major acid soil stress factors deleteriously affecting plant root growth and crop yield. In our preliminary studies, cotton (Gossypium hirsutum L.) seedlings displayed very sensitive phenotypes to Al and H⁺ rhizotoxicities. Based on previous Arabidopsis results, we aimed to characterise the Al stress responsive Sensitive to Proton rhizotoxicity 1 (GhSTOP1) transcription system in cotton using RNAi-mediated down-regulation. With the help of seed embryo apex explants, we developed transgenic cotton plants overexpressing a GhSTOP1-RNAi cassette with NPTII selection. Kanamycin-tolerant T1 seedlings were further considered for Al and H⁺ stress tolerance studies. Down-regulation of the GhSTOP1 increased sensitivity to Al and proton rhizotoxicities, and root growth was significantly reduced in RNAi lines. The expression profile of GhALMT1 (Aluminum-activated Malate Transporter 1), GhMATE (Multidrug and Toxic Compound Extrusion), GhALS3 (Aluminium Sensitive 3) and key genes involved in the GABA shunt were down-regulated in the transgenic RNAi lines. Additionally, the lateral root initiation process was delayed and expression of GhNAC1, which is involved in lateral roots, was also suppressed in transgenic lines. Besides, overexpression of GhSTOP1 in Arabidopsis accelerated root growth and AtMATE and AtALMT1 expression under Al stress conditions. These analyses indicate that GhSTOP1 is essential for the expression of several genes which are necessary for acid soil tolerance mechanisms and lateral root initiation.

Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments

Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.

May the Fittest Protein Evolve: Favoring the Plant-Specific Origin and Expansion of NAC Transcription Factors

Plant-specific NAC transcription factors (TFs) evolve during the transition from aquatic to terrestrial plant life and are amplified to become one of the biggest TF families. This is because they regulate genes involved in water conductance and cell support. They also control flower and fruit formation. The review presented here focuses on various properties, regulatory intricacies, and developmental roles of NAC family members. Processes controlled by NACs depend majorly on their transcriptional properties. NACs can function as both activators and/or repressors. Additionally, their homo/hetero dimerization abilities can also affect DNA binding and activation properties. The active protein levels are dependent on the regulatory cascades. Because NACs regulate both development and stress responses in plants, in-depth knowledge about them has the potential to help guide future crop improvement studies.

Overexpression of a predominantly root-expressed NAC transcription factor in wheat roots enhances root length, biomass and drought tolerance

TaRNAC1 is a constitutively and predominantly root-expressed NAC transcription factor. TaRNAC1 overexpression in wheat roots confers increased root length, biomass and drought tolerance and improved grain yield under water limitation. A large and deep root system is an important trait for yield sustainability of dryland cereal crops in drought-prone environments. This study investigated the role of a predominantly root-expressed NAC transcription factor from wheat (TaRNAC1) in the root growth. Expression analysis showed that TaRNAC1 was a constitutively expressed gene with high level expression in the roots and was not drought-upregulated. Overexpression of TaRNAC1 in wheat using a predominantly root-expressed promoter resulted in increased root length and biomass observed at the early growth stage and a marked increase in the maturity root biomass with dry root weight of > 70% higher than that of the wild type plants. Analysis of some root growth-related genes revealed that the expression level of GA3-ox2, which encodes GIBBERELLIN 3-OXIDASE catalysing the conversion of inactive gibberellin (GA) to active GA, was elevated in the roots of transgenic wheat. TaRNAC1 overexpressing transgenic wheat showed more dehydration tolerance under polyethylene glycol (PEG) treatment and produced more aboveground biomass and grain under water-limited conditions than the wild type plants. These data suggest that TaRNAC1 may play a role in root growth and be used as a molecular tool for potential enlargement of root system in wheat.

Heat shock factor C2a serves as a proactive mechanism for heat protection in developing grains in wheat via an ABA-mediated regulatory pathway

High temperature at grain filling can severely reduce wheat yield. Heat shock factors (Hsfs) are central regulators in heat acclimation. This study investigated the role of TaHsfC2a, a member of the monocot-specific HsfC2 subclass, in the regulation of heat protection genes in Triticum aestivum. Three TaHsfC2a homoeologous genes were highly expressed in wheat grains during grain filling and showed only transient up-regulation in the leaves by heat stress but were markedly up-regulated by drought and abscisic acid (ABA) treatment. Overexpression of TaHsfC2a-B in transgenic wheat resulted in up-regulation of a suite of heat protection genes (e.g. TaHSP70d and TaGalSyn). Most TaHsfC2a-B target genes were heat, drought and ABA inducible. Transactivation analysis of two representative targets (TaHSP70d and TaGalSyn) showed that TaHsfC2a-B activated expression of reporters driven by these target promoters. Promoter mutagenesis analyses revealed that heat shock element is responsible for transactivation by TaHsfC2a-B and heat/drought induction. TaHsfC2a-B-overexpressing wheat showed improved thermotolerance but not dehydration tolerance. Most TaHsfC2a-B target genes were co-up-regulated in developing grains with TaHsfC2a genes. These data suggest that TaHsfC2a-B is a transcriptional activator of heat protection genes and serves as a proactive mechanism for heat protection in developing wheat grains via the ABA-mediated regulatory pathway.

Rapid and Quantitative CELD Assay to Measure the Specificity of Transcription Factor-DNA-Binding Interactions and Identify cis-Elements

Specific interaction between transcription factor (TF) and cis-regulatory elements in the context of chromatin is the key to determining gene expression. Thus, it is important to measure DNA-binding specificity and identify cis-elements of TFs of your interest. In this chapter, we described a microwell-based assay to determine DNA-binding specificity by using translational fusion of a TF with a highly active cellulase (CELD), which hydrolyzes 4-methylumbelliferyl β-D-cellobioside to a fluorescent 4-methylumbelliferone product. The hydrolysis activity arrows us to quantify the binding strength between TF-CELD fusion protein and biotinylated DNA sequences in a 96-well microplate. The high-throughput and quantitative nature of CELD assay enable researchers to test a large number of putative DNA-binding sites of TFs, which subsequently leads to the identification of its direct target genes.

GsCHX19.3, a member of cation/H+ exchanger superfamily from wild soybean contributes to high salinity and carbonate alkaline tolerance

Cation/H+ exchangers (CHX) are characterized to be involved in plant growth, development and stress responses. Although soybean genome sequencing has been completed, the CHX family hasn't yet been systematically analyzed, especially in wild soybean. Here, through Hidden Markov Model search against Glycine soja proteome, 34 GsCHXs were identified and phylogenetically clustered into five groups. Members within each group showed high conservation in motif architecture. Interestingly, according to our previous RNA-seq data, only Group IVa members exhibited highly induced expression under carbonate alkaline stress. Among them, GsCHX19.3 displayed the greatest up-regulation in response to carbonate alkaline stress, which was further confirmed by quantitative real-time PCR analysis. We also observed the ubiquitous expression of GsCHX19.3 in different tissues and its localization on plasma membrane. Moreover, we found that GsCHX19.3 expression in AXT4K, a yeast mutant lacking four ion transporters conferred resistance to low K+ at alkali pH, as well as carbonate stress. Consistently, in Arabidopsis, GsCHX19.3 overexpression increased plant tolerance both to high salt and carbonate alkaline stresses. Furthermore, we also confirmed that GsCHX19.3 transgenic lines showed lower Na+ concentration but higher K+/Na+ values under salt-alkaline stress. Taken together, our findings indicated that GsCHX19.3 contributed to high salinity and carbonate alkaline tolerance.

Plants under Stress: Involvement of Auxin and Cytokinin

Plant growth and development are critically influenced by unpredictable abiotic factors. To survive fluctuating changes in their environments, plants have had to develop robust adaptive mechanisms. The dynamic and complementary actions of the auxin and cytokinin pathways regulate a plethora of developmental processes, and their ability to crosstalk makes them ideal candidates for mediating stress-adaptation responses. Other crucial signaling molecules responsible for the tremendous plasticity observed in plant morphology and in response to abiotic stress are reactive oxygen species (ROS). Proper temporal and spatial distribution of ROS and hormone gradients is crucial for plant survival in response to unfavorable environments. In this regard, the convergence of ROS with phytohormone pathways acts as an integrator of external and developmental signals into systemic responses organized to adapt plants to their environments. Auxin and cytokinin signaling pathways have been studied extensively. Nevertheless, we do not yet understand the impact on plant stress tolerance of the sophisticated crosstalk between the two hormones. Here, we review current knowledge on the function of auxin and cytokinin in redirecting growth induced by abiotic stress in order to deduce their potential points of crosstalk.