Comparative analysis of root transcriptome profiles between drought-tolerant and susceptible wheat genotypes in response to water stress

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat. In this study, the global transcriptomic and metabolomics profiles were employed to investigate the mechanisms of roots responding to water stresses using the drought-tolerant (DT) and drought-susceptible (DS) wheat genotypes. The results showed that compared with the control group, wheat roots exposed to polyethylene glycol (PEG) had 25941 differentially expressed genes (DEGs) and more upregulated genes were found in DT (8610) than DS (7141). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the drought-tolerant genotype were preferably enriched in the flavonoid biosynthetic process, anthocyanin biosynthesis and suberin biosynthesis. The integrated analysis of the transcriptome and metabolome showed that in DT, the KEGG pathways, including flavonoid biosynthesis and arginine and proline metabolism, were shared by differentially accumulated metabolites (DAMs) and DEGs at 6 h after treatment (HAT) and pathways including alanine, aspartate, glutamate metabolism and carbon metabolism were shared at 48 HAT, while in DS, the KEGG pathways shared by DAMs and DEGs only included arginine and proline metabolism at 6 HAT and the biosynthesis of amino acids at 48 HAT. Our results suggest that the drought-tolerant genotype may relieve the drought stress by producing more ROS scavengers, osmoprotectants, energy and larger roots. Interestingly, hormone signaling plays an important role in promoting the development of larger roots and a higher capability to absorb and transport water in drought-tolerant genotypes.

Growth Properties and Metabolomic Analysis Provide Insight into Drought Tolerance in Barley (Hordeum vulgare L.)

Drought stress is a major meteorological threat to crop growth and yield. Barley (Hordeum vulgare L.) is a vital cereal crop with strong drought tolerance worldwide. However, the underlying growth properties and metabolomic regulatory module of drought tolerance remains less known. Here, we investigated the plant height, spike length, effective tiller, biomass, average spikelets, 1000-grain weight, number of seeds per plant, grain weight per plant, ash content, protein content, starch content, cellulose content, and metabolomic regulation mechanisms of drought stress in barley. Our results revealed that the growth properties were different between ZDM5430 and IL-12 under drought stress at different growth stages. We found that a total of 12,235 metabolites were identified in two barley genotype root samples with drought treatment. More than 50% of these metabolites showed significant differences between the ZDM5430 and IL-12 roots. The Kyoto Encyclopedia of Genes and Genomes pathway analysis identified 368 differential metabolites mainly involved in starch and sucrose metabolism, the pentose phosphate pathway, pyrimidine metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis in ZDM5430 under drought stress, whereas the different metabolites of IL-12 under drought stress related to starch and sucrose metabolism, the pentose phosphate pathway, 2-oxocarboxylic acid metabolism, cutin, suberine and wax biosynthesis, carbon metabolism, fatty acid biosynthesis, and C5-branched dibasic acid metabolism. These metabolites have application in the tricarboxylic cycle, the urea cycle, the met salvage pathway, amino acid metabolism, unsaturated fatty acid biosynthesis, phenolic metabolism, and glycolysis. On the other hand, the expression patterns of 13 genes related to the abovementioned bioprocesses in different barley genotypes roots were proposed. These findings afford an overview for the understanding of barley roots' metabolic changes in the drought defense mechanism by revealing the differently accumulated compounds.

Aeration Alleviated the Adverse Effects of Nitrogen Topdressing Reduction on Tomato Root Vigor, Photosynthetic Performance, and Fruit Development

To explore the compensation effect of aeration on tomato vegetative and reproductive growth in arid and semi-arid areas, a two-year field experiment was conducted with four micro-nano aeration ratios (0%, 5%, 10%, and 15%) and three nitrogen topdressing levels (80, 60, and 40 kg·ha-1) during the tomato growth period in Ningxia, China. The results showed that increasing the aeration ratio in the range of 0-15% was conducive to the enhancement of tomato root vigor (the ability of triphenyltetrazolium chloride to be reduced, 3-104%) and the leaf net photosynthetic rate (14-63%), favorable to the facilitation of plant dry matter accumulation (3-59%) and plant nitrogen accumulation (2-70%), and beneficial to the improvement of tomato yield (12-44%) and fruit quality. Interestingly, since the aeration ratio exceeded 10%, the increase in the aeration ratio showed no significant effects on the single-fruit weight, tomato yield, and fruit quality. Moreover, with aerated underground drip irrigation, properly reducing the traditional nitrogen topdressing level (80 kg·ha-1) by 25% was favorable for enhancing tomato root vigor (5-31%), increasing tomato yield (0.5-9%), and improving fruit soluble solid accumulation (2-5%) and soluble sugar formation (4-9%). Importantly, increasing the aeration ratio by 5% could compensate for the adverse effects of reducing the nitrogen topdressing level by 25% by improving the leaf photosynthetic rate, promoting plant dry matter accumulation, increasing tomato yield, and enhancing the soluble solid and soluble sugar accumulation in tomato fruits. Synthetically considering the decrease in the nitrogen topdressing amount, leading to plant growth promotion, a tomato yield increase, and fruit quality improvement, a favorable nitrogen topdressing level of 60 kg·ha-1 and the corresponding proper aeration ratio of 10% were suggested for tomato underground drip irrigation in the Yinbei Irrigation District of Ningxia.

Understanding role of roots in plant response to drought: Way forward to climate-resilient crops

Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root-mediated plant responses. We have also discussed the importance of root system architecture (RSA) and the various structural and anatomical changes that it undergoes to increase survival and productivity under drought. Various genes, transcription factors, and quantitative trait loci involved in regulating root growth and development are also discussed. A summarization of various instruments and software that can be used for high-throughput phenotyping in the field is also provided in this review. More comprehensive studies are required to help build a detailed understanding of RSA and associated traits for breeding drought-resilient cultivars.

Soil Water Deficit Reduced Root Hydraulic Conductivity of Common Reed (Phragmites australis)

Alterations in root hydraulics in response to varying moisture conditions remain a subject of debate. In our investigation, we subjected common reeds (Phragmites australis) to a 45-day treatment with four distinct soil moisture levels. The findings unveiled that, in response to drought stress, the total root length, surface area, volume, and average diameter exhibited varying degrees of reduction. Anatomically, drought caused a reduction in root diameter (RD), cortex thickness (CT), vessel diameter (VD), and root cross-sectional area (RCA). A decrease in soil moisture significantly reduced both whole- and single-root hydraulic conductivity (Lpwr, Lpsr). The total length, surface area, volume, and average diameter of the reed root system were significantly correlated with Lpwr, while RD, CT, and RCA were significantly correlated with Lpsr. A decrease in soil moisture content significantly influenced root morphological and anatomical characteristics, which, in turn, altered Lpr, and the transcriptome results suggest that this may be associated with the variation in the expression of abscisic acid (ABA) and aquaporins (AQPs) genes. Our initial findings address a gap in our understanding of reed hydraulics, offering fresh theoretical insights into how herbaceous plants respond to external stressors.

Sesame (Sesamum indicum L.) response to drought stress: susceptible and tolerant genotypes exhibit different physiological, biochemical, and molecular response patterns

Drought is one of the main environmental stresses affecting the quality and quantity of sesame production worldwide. The present study was conducted to investigate the effect of drought stress and subsequent re-watering on physiological, biochemical, and molecular responses of two contrasted sesame genotypes (susceptible vs. tolerant). Results showed that plant growth, photosynthetic rate, stomatal conductance, transpiration rate, and relative water content were negatively affected in both genotypes during water deficit. Both genotypes accumulated more soluble sugars, free amino acids, and proline and exhibited an increased enzyme activity for peroxidase, catalase, superoxide dismutase, and pyruvate dehydrogenase in response to drought damages including increased lipid peroxidation and membrane disruption. However, the tolerant genotype revealed a more extended root system and a more efficient photosynthetic apparatus. It also accumulated more soluble sugars (152%), free amino acids (48%), proline (75%), and antioxidant enzymes while showing lower electrolyte leakage (26%), lipid peroxidation (31%), and starch (35%) content, compared to the susceptible genotype at severe drought. Moreover, drought-related genes such as MnSOD1, MnSOD2, and PDHA-M were more expressed in the tolerant genotype, which encode manganese-dependent superoxide dismutase and the alpha subunit of pyruvate dehydrogenase, respectively. Upon re-watering, tolerant genotype recovered to almost normal levels of photosynthesis, carboxylation efficiency, lipid peroxidation, and electrolyte leakage, while susceptible genotype still suffered critical issues. Overall, these results suggest that a developed root system and an efficient photosynthetic apparatus along with the timely and effective accumulation of protective compounds enabled the tolerant sesame to withstand stress and successfully return to a normal growth state after drought relief. The findings of this study can be used as promising criteria for evaluating genotypes under drought stress in future sesame breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01372-y.

Comparative transcriptome analysis reveals the key genes and pathways involved in drought stress response of two wheat (Triticum aestivum L) varieties

Drought stress results in significant yield losses in wheat production. Although studies have reported a number of wheat drought tolerance genes, a deeper understanding of the tolerance mechanisms is required for improving wheat tolerance against drought stress. In this study, we found that "Deguo 2" exhibited higher tolerance to drought than "Truman". Transcriptomics analysis enabled identification of 6084 and 7146 differentially expressed genes (DEGs), mainly mapping flavonoid biosynthesis, plant hormone, phenolamides and antioxidant pathways and revealed altered expression levels of about 700 genes. Exogenous melatonin application enhanced wheat tolerance against drought stress. Co-expression analysis showed that bHLH and bZIP transcription factors may be involved in the regulation of various pathway genes. Take together, these results provide new insights for us on exploring the crosstalk between phytohormones and secondary metabolites, and will deepen the understanding of the complex tolerance mechanisms against drought stress in wheat.

Insights into physiological and molecular mechanisms underlying efficient utilization of boron in different boron efficient Beta vulgaris L. varieties

Boron (B) deficiency and consequent limitation of plant yield and quality, particularly of sugar beet (Beta vulgaris L.) has emerged as a maior problem,which is exacerbating due to cultivar dependent variability in B deficiency tolerance. Pertinently, the current study was designed to elucidate the physiological and molecular mechanisms of B deficiency tolerance of sugar beet varieties KWS1197 (B-efficient variety) and KWS0143 (B-inefficient variety). A hydroponic experiment was conducted employing two B levels B0.1 (0.1 μM L^-1 H₃BO₃, deficiency) and B50 (50 μM L^-1 H₃BO₃, adequacy). Boron deficiency greatly inhibited root elongation and dry matter accumulation; however, formation of lateral roots stimulated and average root diameter was increased. Results exhibited that by up-regulating the expression of NIP5-1, NIP6-1, and BOR2, and suppressing the expression of BOR4, cultivar KWS1197, in contrast to KWS0143, managed to transfer sufficient amount of B to the aboveground plant parts, facilitating its effective absorption and utilization. Accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) was also mellowed in KWS1197, as well as the oxidative damage to root cells via preservation of the antioxidant enzyme system. Additionally, the expression of essential enzymes for biosynthesis of phytohormone (PYR/PYL) and lignin (COMT, POX, and CCoAOMT) were found to be highly up-regulated in KWS1197. Deductively, through effective B absorption and transportation, balanced nutrient accumulation, and an activated antioxidant enzyme system, B-efficient cultivars may cope with B deficiency while retaining a superior cellular structure to enable root development.

Wheat Omics: Advancements and Opportunities

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.

Comparative transcriptome analysis of wheat in response to corn leaf aphid, Rhopalosiphum maidis F. infestation

Aphids are one of the most important insect pests of wheat crop in all wheat growing regions of the world. Amongst various aphid species, the corn leaf aphid (Rhopalosiphum maidis F.) is considered one of the most destructive insect pests of wheat in the North Western Plains region of India. Transcriptome profiling of highly susceptible wheat Triticum durum genotype, A-9-30-1 and tolerant wheat Triticum aestivum genotype, HD2967 was performed to investigate aphid-host interactions. The results obtained from differential gene expression analysis of R. maidis on the highly susceptible genotype, A-9-30-1 plants, when compared with the tolerant genotype, HD2967, showed that 212 genes were significantly upregulated and 1009 genes were significantly downregulated. Our findings demonstrated that the genes associated with defense were significantly higher in response to R. maidis on HD2967 as compared to A-9-30-1. Additionally, various genes with physiological attributes were expressed during aphid attack. Based on gene ontology classification, three classifications, such as, cellular components (CC), molecular function (MF), and biological processes (BP) of sequences were identified. KEGG enrichment analysis revealed that twenty-five pathway genes were differentially expressed during the infestation of wheat with R. maidis. Notable changes were observed in A-9-30-1 and HD2967 transcriptomic profiling after infestation. The results obtained in the present study will help to elucidate the mechanism governing host-pest interaction and may lead to the development of new methods for increasing the resistance level of wheat against R. maidis, including over-expression of defense-related genes.

Network of the transcriptome and metabolomics reveals a novel regulation of drought resistance during germination in wheat

BACKGROUND AND AIMS

The North China Plain, the highest winter-wheat-producing region of China, is seriously threatened by drought. Traditional irrigation wastes a significant amount of water during the sowing season. Therefore, it is necessary to study the drought resistance of wheat during germination to maintain agricultural ecological security. From several main cultivars in the North China Plain, we screened the drought-resistant cultivar JM47 and drought-sensitive cultivar AK58 during germination using the polyethylene glycol (PEG) drought simulation method. An integrated analysis of the transcriptome and metabolomics was performed to understand the regulatory networks related to drought resistance in wheat germination and verify key regulatory genes.

METHODS

Transcriptional and metabolic changes were investigated using statistical analyses and gene-metabolite correlation networks. Transcript and metabolite profiles were obtained through high-throughput RNA-sequencing data analysis and ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry, respectively.

KEY RESULTS

A total of 8083 and 2911 differentially expressed genes (DEGs) and 173 and 148 differential metabolites were identified in AK58 and JM47, respectively, under drought stress. According to the integrated analysis results, mammalian target of rapamycin (mTOR) signalling was prominently enriched in JM47. A decrease in α-linolenic acid content was consistent with the performance of DEGs involved in jasmonic acid biosynthesis in the two cultivars under drought stress. Abscisic acid (ABA) content decreased more in JM47 than in AK58, and linoleic acid content decreased in AK58 but increased in JM47. α-Tocotrienol was upregulated and strongly correlated with α-linolenic acid metabolism.

CONCLUSIONS

The DEGs that participated in the mTOR and α-linolenic acid metabolism pathways were considered candidate DEGs related to drought resistance and the key metabolites α-tocotrienol, linoleic acid and l-leucine, which could trigger a comprehensive and systemic effect on drought resistance during germination by activating mTOR-ABA signalling and the interaction of various hormones.

Brassinosteroids induced drought resistance of contrasting drought-responsive genotypes of maize at physiological and transcriptomic levels

The present study investigated the brassinosteroid-induced drought resistance of contrasting drought-responsive maize genotypes at physiological and transcriptomic levels. The brassinosteroid (BR) contents along with different morphology characteristics, viz., plant height (PH), shoot dry weight (SDW), root dry weight (RDW), number of leaves (NL), the specific mass of the fourth leaf, and antioxidant activities, were investigated in two maize lines that differed in their degree of drought tolerance. In response to either control, drought, or brassinosteroid treatments, the KEGG enrichment analysis showed that plant hormonal signal transduction and starch and sucrose metabolism were augmented in both lines. In contrast, the phenylpropanoid biosynthesis was augmented in lines H21L0R1 and 478. Our results demonstrate drought-responsive molecular mechanisms and provide valuable information regarding candidate gene resources for drought improvement in maize crop. The differences observed for BR content among the maize lines were correlated with their degree of drought tolerance, as the highly tolerant genotype showed higher BR content under drought stress.

Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants, show strong drought tolerance and environmental adaptability. They are ideal model plants for studying the molecular mechanisms of drought tolerance. Transcriptomic and metabolomic analyses were performed to reveal the response mechanisms of H. ammodendron and H. persicum to a drought environment at the levels of transcription and physiological metabolism. The results showed that the morphological structures of H. ammodendron and H. persicum showed adaptability to drought stress. Under drought conditions, the peroxidase activity, abscisic acid content, auxin content, and gibberellin content of H. ammodendron increased, while the contents of proline and malondialdehyde decreased. The amino acid content of H. persicum was increased, while the contents of proline, malondialdehyde, auxin, and gibberellin were decreased. Under drought conditions, 12,233 and 17,953 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum , respectively, including members of multiple transcription factor families such as FAR1, AP2/ERF, C2H2, bHLH, MYB, C2C2, and WRKY that were significantly up-regulated under drought stress. In the positive ion mode, 296 and 452 differential metabolites (DEMs) were identified in H. ammodendron and H. persicum, respectively; in the negative ion mode, 252 and 354 DEMs were identified, primarily in carbohydrate and lipid metabolism. A combined transcriptome and metabolome analysis showed that drought stress promoted the glycolysis/gluconeogenesis pathways of H. ammodendron and H. persicum and increased the expression of amino acid synthesis pathways, consistent with the physiological results. In addition, transcriptome and metabolome were jointly used to analyze the expression changes of the genes/metabolites of H. ammodendron and H. persicum that were associated with drought tolerance but were regulated differently in the two plants. This study identified drought-tolerance genes and metabolites in H. ammodendron and H. persicum and has provided new ideas for studying the drought stress response of Haloxylon.

Comparative physiological and root transcriptome analysis of two annual ryegrass cultivars under drought stress

Annual ryegrass is a widely cultivated forage grass with rapid growth and high productivity. However, drought is one of the abiotic stresses affecting ryegrass growth and quality. In this study, we compared the physiological and transcriptome responses of Chuansi No.1 (drought-tolerant, DT) and Double Barrel (drought-sensitive, DS) under drought stress simulated by PEG-6000 for 7 days. The results showed that Chuansi No. 1 had stronger physiological and biochemical parameters such as root properties, water content, osmotic adjustment ability and antioxidant ability. In addition, RNA-seq was used to elucidate the molecular mechanism of root drought resistance. We identified 8588 differentially expressed genes related to drought tolerance in root, which were mainly enriched in oxidation-reduction process, carbohydrate metabolic process, apoplast, arginine and proline metabolism, and phenylpropanoid biosynthesis pathways. The expression levels of DEGs were consistent with physiological changes of ryegrass under drought stress. We found that genes related to sucrose and starch synthesis, root development, osmotic adjustment, ABA signal regulation and specifically up-regulated transcription factors such as WRKY41, WRKY51, ERF7, ERF109, ERF110, NAC43, NAC68, bHLH162 and bHLH148 in Chuansi No. 1 may be the reason for its higher drought tolerance. This study revealed the underlying physiological and molecular mechanisms of root response to drought stress in ryegrass and provided some new candidate genes for breeding rye drought tolerant varieties.

Crop Root Responses to Drought Stress: Molecular Mechanisms, Nutrient Regulations, and Interactions with Microorganisms in the Rhizosphere

Roots play important roles in determining crop development under drought. Under such conditions, the molecular mechanisms underlying key responses and interactions with the rhizosphere in crop roots remain limited compared with model species such as Arabidopsis. This article reviews the molecular mechanisms of the morphological, physiological, and metabolic responses to drought stress in typical crop roots, along with the regulation of soil nutrients and microorganisms to these responses. Firstly, we summarize how root growth and architecture are regulated by essential genes and metabolic processes under water-deficit conditions. Secondly, the functions of the fundamental plant hormone, abscisic acid, on regulating crop root growth under drought are highlighted. Moreover, we discuss how the responses of crop roots to altered water status are impacted by nutrients, and vice versa. Finally, this article explores current knowledge of the feedback between plant and soil microbial responses to drought and the manipulation of rhizosphere microbes for improving the resilience of crop production to water stress. Through these insights, we conclude that to gain a more comprehensive understanding of drought adaption mechanisms in crop roots, future studies should have a network view, linking key responses of roots with environmental factors.

Effects of Different Chemicals on Sexual Regulation in Persimmon (Diospyros kaki Thunb.) Flowers

Research on crop sexuality is important for establishing systems for germplasm innovation and cultivating improved varieties. In this study, androecious persimmon trees were treated with various concentrations of ethrel (100, 500, and 1,000 mg/L) and zeatin (1, 5, and 10 mg/L) to investigate the morphological, physiological, and molecular characteristics of persimmon. Ethrel at 1,000 mg/L and zeatin at 10 mg/L both significantly reduced the stamen length and pollen grain diameter in androecious trees. Ethrel treatment also led to reduced stamen development with degenerated cellular contents; zeatin treatment promoted the development of arrested pistils via maintaining relatively normal mitochondrial morphology. Both treatments altered carbohydrate, amino acid, and endogenous phytohormone contents, as well as genes associated with hormone production and floral organ development. Thereafter, we explored the combined effects of four chemicals, including ethrel and zeatin, as well as zebularine and 5-azacytidine, both of which are DNA methylation inhibitors, on androecious persimmon flower development. Morphological comparisons showed that stamen length, pollen viability, and pollen grain diameter were significantly inhibited after combined treatment. Large numbers of genes involving in carbohydrate metabolic, mitogen-activated protein kinase (MAPK) signaling, and ribosome pathways, and metabolites including uridine monophosphate (UMP) and cyclamic acid were identified in response to the treatment, indicating complex regulatory mechanisms. An association analysis of transcriptomic and metabolomic data indicated that ribosomal genes have distinct effects on UMP and cyclamic acid metabolites, explaining how male floral buds of androecious persimmon trees respond to these exogenous chemicals. These findings extend the knowledge concerning sexual differentiation in persimmon; they also provide a theoretical basis for molecular breeding, high-yield cultivation, and quality improvement in persimmon.

Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes

Drought is a big challenge for agricultural production. Root attributes are the important target traits for breeding high-yielding sustainable wheat varieties against ever changing climatic conditions. However, the transcriptomic of wheat concerning root architecture remained obscure. Here, we explored RNA-Seq based transcriptome to dissect putative genes involved in root system variations in naturally occurring six genotypes (drought-tolerant and sensitive) of wheat. Global RNA-Seq based root transcriptome analysis revealed single nucleotide polymorphisms (SNPs) variations and differentially expressed genes. Putative 56 SNPs were identified related to 15 genes involved in root architecture. Enrichment of these genes using GO terms demonstrated that differentially expressed genes (DEGs) are divided into sub-categories implicated in molecular functions, cellular components and biological processes. The KEGG analysis of DEGs in each comparison of genotype include metabolic, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and biosynthesis of antibiotics. A deeper insight into DEGs unveiled various pathways involved in drought response and positive gravitropism. These genes belong to various transcription factor families such as DOF, C3H, MYB, and NAC involved in root developmental and stress-related pathways. Local White and UZ-11-CWA-8, which are drought-tolerant genotypes, harbor over-representation of most of DEGs or transcription factors. Notably, a microtubule-associated protein MAPRE1 belonging to RP/EB family recruited in positive gravitropism was enriched. Real-time PCR analysis revealed expression of MAPRE1 and PAL genes is consistent with RNA-seq data. The presented data and genetic resources seem valuable for providing genes involved in the root system architecture of drought-tolerant and susceptible genotypes.

Fine-tuning of SUMOylation modulates drought tolerance of apple

SUMOylation is involved in various aspects of plant biology, including drought stress. However, the relationship between SUMOylation and drought stress tolerance is complex; whether SUMOylation has a crosstalk with ubiquitination in response to drought stress remains largely unclear. In this study, we found that both increased and decreased SUMOylation led to increased survival of apple (Malus × domestica) under drought stress: both transgenic MdSUMO2A overexpressing (OE) plants and MdSUMO2 RNAi plants exhibited enhanced drought tolerance. We further confirmed that MdDREB2A is one of the MdSUMO2 targets. Both transgenic MdDREB2A OE and MdDREB2A^K192R OE plants (which lacked the key site of SUMOylation by MdSUMO2A) were more drought tolerant than wild-type plants. However, MdDREB2A^K192R OE plants had a much higher survival rate than MdDREB2A OE plants. We further showed SUMOylated MdDREB2A was conjugated with ubiquitin by MdRNF4 under drought stress, thereby triggering its protein degradation. In addition, MdRNF4 RNAi plants were more tolerant to drought stress. These results revealed the molecular mechanisms that underlie the relationship of SUMOylation with drought tolerance and provided evidence for the tight control of MdDREB2A accumulation under drought stress mediated by SUMOylation and ubiquitination.

Expression profiling of TaARGOS homoeologous drought responsive genes in bread wheat

Drought tolerant germplasm is needed to increase crop production, since water scarcity is a critical bottleneck in crop productivity worldwide. Auxin Regulated Gene involved in Organ Size (ARGOS) is a large protein family of transcription factors that plays a vital role in organ size, plant growth, development, and abiotic stress responses in plants. Although, the ARGOS gene family has been discovered and functionalized in a variety of crop plants, but a comprehensive and systematic investigation of ARGOS genes in locally used commercial wheat cultivars is still yet to be reported. The relative expression of three highly conserved TaARGOS homoeologous genes (TaARGOS-A, TaARGOS-B, TaARGOS-D) was studied in three drought-tolerant (Pakistan-2013, NARC-2009 and NR-499) and three sensitive (Borlaug-2016, NR-514 and NR-516) wheat genotypes under osmotic stress, induced by PEG-6000 at 0 (exogenous control), 2, 4, 6, and 12 h. The normalization of target genes was done using β-actin as endogenous control, whereas DREB3, as a marker gene was also transcribed, reinforcing the prevalence of dehydration in all stress treatments. Real-time quantitative PCR revealed that osmotic stress induced expression of the three TaARGOS transcripts in different wheat seedlings at distinct timepoints. Overall, all genes exhibited significantly higher expression in the drought-tolerant genotypes as compared to the sensitive ones. For instance, the expression profile of TaARGOS-A and TaARGOS-D showed more than threefold increase at 2 h and six to sevenfold increase after 4 h of osmotic stress. However, after 6 h of osmotic stress these genes started to downregulate, and the lowest gene expression was noticed after 12 h of osmotic stress. Among all the homoeologous genes, TaARGOS-D, in particular, had a more significant influence on controlling plant growth and drought tolerance as it showed the highest expression. Altogether, TaARGOSs are involved in seedling establishment and overall plant growth. In addition, the tolerant group of genotypes had a much greater relative fold expression than the sensitive genotypes. Ultimately, Pakistan-2013 showed the highest relative expression of the studied genes than other genotypes which shows its proficiency to mitigate osmotic stress. Therefore, it could be cultivated in arid and semi-arid regions under moisture-deficient regimes. These findings advocated the molecular mechanism and regulatory roles of TaARGOS genes in plant growth and osmotic stress tolerance in contrasting groups of wheat genotypes, accompanied by the genetic nature of identified genotypes in terms of their potential for drought tolerance.

Differences in Water Consumption of Wheat Varieties Are Affected by Root Morphology Characteristics and Post-anthesis Root Senescence

Selecting high-yielding wheat varieties for cultivation can effectively increase water use efficiency (WUE) in the Huang-Huai-Hai Plain, where is threatened by increasing water shortages. To further identify the difference in water use and its relationship with root morphology and senescence characteristics, wheat varieties with different yield potentials-Yannong 1212 (YN), Jimai 22 (JM), and Liangxing 99 (LX)-were studied in a high-yielding wheat field. The water consumption percentage (CP) in YN decreased from planting to anthesis; however, crop evapotranspiration and CP increased from anthesis to maturity compared with JM and LX. In YN, a higher soil water consumption from anthesis to maturity in the 0-100 cm soil layer was partly attributed to the greater root weight density in the 20-60 cm soil layer. In topsoil (0-40 cm), root length density, root surface area density, and root diameter at 20 days after anthesis, root superoxide dismutase activity, and root triphenyl tetrazolium chloride reduction activity during mid grain filling stage were higher in YN than in JM and LX. YN had the highest grain yields of 9,840 and 11,462 kg ha^-1 and increased grain yield and WUE by 12.0 and 8.4%, respectively, as compared with JM, and by 30.3 and 21.3%, respectively, as compared with LX. Ensuring more soil water extraction post-anthesis by increasing roots in the 20-60 cm soil profile, improving root morphology traits, and alleviating root senescence in the topsoil during mid-grain filling stage will assist in selecting wheat varieties with high yield and WUE.

Comparative transcriptome analysis of coleorhiza development in japonica and Indica rice

BACKGROUND

Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established.

RESULTS

In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism.

CONCLUSIONS

Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.

Transcriptional profiling and physiological responses reveal new insights into drought tolerance in a semiarid adapted species, Anacardium occidentale

Water stress affects plant performance at various organisational levels, from morphological to molecular, with a drastic drop in crop yield. Integrative studies involving transcriptomics and physiological data in recognized tolerant species are appropriate strategies to identify and understand molecular and functional processes related to water deficit tolerance. The cashew tree (Anacardium occidentale) is a species naturally adapted to environments with low water availability associated with adverse conditions such as heat, high radiation and salinity. We used an integrative strategy, combining classical physiological measurements with high throughput RNA-seq to understand the main adaptive mechanisms of cashew to water deficit followed by recovery. Physiological analyses indicate that young cashew plants display typical isohydric behaviour. They first exhibit rapid stomatal closure, followed by CO₂ assimilation, thus preserving the relative water content, membrane integrity and photosystem II activity. Differential expression was observed in 1733 genes from plant leaves exposed to water deficit stress for 26 days. Among them, 705 were upregulated and 1028 were downregulated. After rewatering, 1330 (76.7%) genes returned to their basal expression level. Transcriptional, combined with physiological data, reveal that cashew plants display high phenotypic plasticity and resilience to acute water deficit, and do not activate senescence pathways. A series of genes/pathways and processes involved with drought tolerance in cashew are evidenced, particularly in carbon metabolism, photosynthesis and chloroplast homeostasis.

Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects

Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.

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.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes

Drought response is coordinated through expression changes in a large suite of genes. Interspecific variation in this response is common and associated with drought-tolerant and -sensitive genotypes. The extent to which different genetic networks orchestrate the adjustments to water deficit in tolerant and sensitive genotypes has not been fully elucidated, particularly in non-model or woody plants. Differential expression analysis via RNA-seq was evaluated in root tissue exposed to simulated drought conditions in two loblolly pine (Pinus taeda L.) clones with contrasting tolerance to drought. Loblolly pine is the prevalent conifer in southeastern U.S. and a major commercial forestry species worldwide. Significant changes in gene expression levels were found in more than 4,000 transcripts [drought-related transcripts (DRTs)]. Genotype by environment (GxE) interactions were prevalent, suggesting that different cohorts of genes are influenced by drought conditions in the tolerant vs. sensitive genotypes. Functional annotation categories and metabolic pathways associated with DRTs showed higher levels of overlap between clones, with the notable exception of GO categories in upregulated DRTs. Conversely, both differentially expressed transcription factors (TFs) and TF families were largely different between clones. Our results indicate that the response of a drought-tolerant loblolly pine genotype vs. a sensitive genotype to water limitation is remarkably different on a gene-by-gene level, although it involves similar genetic networks. Upregulated transcripts under drought conditions represent the most diverging component between genotypes, which might depend on the activation and repression of substantially different groups of TFs.

Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress

Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.

Transcriptome Analysis of Needle and Root of Pinus Massoniana in Response to Continuous Drought Stress

Pinus massoniana Lamb. is an important coniferous tree species in ecological environment construction and sustainable forestry development. The function of gene gradual change and coexpression modules of needle and root parts of P. massoniana under continuous drought stress is unclear. The physiological and transcriptional expression profiles of P. massoniana seedlings from 1a half-sibling progeny during drought stress were measured and analyzed. As a result, under continuous drought conditions, needle peroxidase (POD) activity and proline content continued to increase. The malondialdehyde (MDA) content in roots continuously increased, and the root activity continuously decreased. The needles of P. massoniana seedlings may respond to drought mainly through regulating abscisic acid (ABA) and jasmonic acid (JA) hormone-related pathways. Roots may provide plant growth through fatty acid β-oxidative decomposition, and peroxisomes may contribute to the production of ROS, resulting in the upregulation of the antioxidant defense system. P. massoniana roots and needles may implement the same antioxidant mechanism through the glutathione metabolic pathway. This study provides basic data for identifying the drought response mechanisms of the needles and roots of P. massoniana.

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes

Brachiaria (Trin.) Griseb. (syn. Urochloa P. Beauv.) is a C4 grass genus belonging to the Panicoideae. Native to Africa, these grasses are now widely grown as forages in tropical areas worldwide and are the subject of intensive breeding, particularly in South America. Tolerance to abiotic stresses such as aluminum and drought are major breeding objectives. In this study, we present the transcriptomic profiling of leaves and roots of three Brachiaria interspecific hybrid genotypes with the onset of water stress, Br12/3659-17 (gt-17), Br12/2360-9 (gt-9), and Br12/3868-18 (gt-18), previously characterized as having good, intermediate and poor tolerance to drought, respectively, in germplasm evaluation programs. RNA was extracted from leaf and root tissue of plants at estimated growing medium water contents (EWC) of 35, 15, and 5%. Differentially expressed genes (DEGs) were compared between different EWCs, 35/15, 15/5, and 35/5 using DESeq2. Overall, the proportions of DEGs enriched in all three genotypes varied in a genotype-dependent manner in relation to EWC comparison, with intermediate and sensitive gt-9 and gt-18 being more similar to each other than to drought tolerant gt-17. More specifically, GO terms relating to carbohydrate and cell wall metabolism in the leaves were enriched by up-regulated DEGs in gt-9 and gt-18, but by down-regulated DEGs in gt-17. Across all genotypes, analysis of DEG enzyme activities indicated an excess of down-regulated putative apoplastic peroxidases in the roots as water stress increased. This suggests that changes in root cell-wall architecture may be an important component of the response to water stress in Brachiaria.

Genetics and genomics of root system variation in adaptation to drought stress in cereal crops

Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.

Root system architecture, physiological analysis and dynamic transcriptomics unravel the drought-responsive traits in rice genotypes

Drought is the major abiotic factors that limit crop productivity worldwide. To withstand stress conditions, plants alter numerous mechanisms for adaption and tolerance. Therefore, in the present study, 106 rice varieties were screened for drought tolerance phenotype via exposing different concentrations of polyethylene glycol 6000 (PEG) in the hydroponic nutrient medium at the time interval of 1, 3, and 7 days to evaluate the changes in their root system architecture. Further, based on root phenotype obtained after PEG-induced drought, two contrasting varieties drought-tolerant Heena and -sensitive Kiran were selected to study transcriptional and physiological alterations at the same stress durations. Physiological parameters (photosynthesis rate, stomatal conductance, transpiration), and non-enzymatic antioxidants (carotenoids, anthocyanins, total phenol content) production indicated better performance of Heena than Kiran. Comparatively higher accumulation of carotenoid and anthocyanin content and the increased photosynthetic rate was also observed in Heena. Root morphology (length, numbers of root hairs, seminal roots and adventitious roots) and anatomical data (lignin deposition, xylem area) enable tolerant variety Heena to better maintain membrane integrity and relative water content, which also contribute to comparatively higher biomass accumulation in Heena under drought. In transcriptome profiling, significant drought stress-associated differentially expressed genes (DEGs) were identified in both the varieties. A total of 1033 and 936 uniquely upregulated DEGs were found in Heena and Kiran respectively. The significant modulation of DEGs that were mainly associated with phytohormone signaling, stress-responsive genes (LEA, DREB), transcription factors (TFs) (AP2/ERF, MYB, WRKY, bHLH), and genes involved in photosynthesis and antioxidative mechanisms indicate better adaptive nature of Heena in stress tolerance. Additionally, the QTL-mapping analysis showed a very high number of DEGs associated with drought stress at AQHP069 QTL in Heena in comparison to Kiran which further distinguishes the drought-responsive traits at the chromosomal level in both the contrasting varieties. Overall, results support the higher capability of Heena over Kiran variety to induce numerous genes along with the development of better root architecture to endure drought stress.

Phenological, morpho-physiological and proteomic responses of Triticum boeoticum to drought stress

Drought is the most important abiotic stress limiting wheat production worldwide. Triticum boeoticum, as wild wheat, is a rich gene pool for breeding for drought stress tolerance. In this study, to identify the most drought-tolerant and susceptible genotypes, ten T. boeoticum accessions were evaluated under non-stress and drought-stress conditions for two years. Among the studied traits, water-use efficiency (WUE) was suggested as the most important trait to identify drought-tolerant genotypes. According to the desirable and undesirable areas of the bi-plot, Tb5 and Tb6 genotypes were less and more affected by drought stress, respectively. Therefore, their flag-leaves proteins were used for two-dimensional gel electrophoresis. While, Tb5 contained a high amount of yield, yield components, and WUE, Tb6 had higher levels of water use, phenological related traits, and root related characters. Of the 235 spots found in the studied accessions, 14 spots (11 and 3 spots of Tb5 and Tb6, respectively) were selected for sequencing. Of these 14 spots, 9 and 5 spots were upregulated and downregulated, respectively. The identified proteins were grouped into six functional protein clusters, which were mainly involved in photosynthesis (36%), carbohydrate metabolism (29%), chaperone (7%), oxidation and reduction (7%), lipid metabolism and biological properties of the membrane (7%) and unknown function (14%). We report for the first time that MICP, in the group of lipid metabolism proteins, was significantly changed into wild wheat in response to drought stress. Maybe, the present-identified proteins could play an important role to understand the molecular pathways of wheat drought tolerance. We believe comparing and evaluating the similarity-identified proteins of T. boeoticum with the previously identified proteins of Aegilops tauschii, can provide a new direction to improve wheat tolerance to drought stress.

Identifying key regulatory genes of maize root growth and development by RNA sequencing

Root system architecture (RSA), the spatio-temporal configuration of roots, plays vital roles in maize (Zea mays L.) development and productivity. We sequenced the maize root transcriptome of four key growth and development stages: the 6th leaf stage, the 12th leaf stage, the tasseling stage and the milk-ripe stage. Differentially expressed genes (DEGs) were detected. 81 DEGs involved in plant hormone signal transduction pathway and 26 transcription factor (TF) genes were screened. These DEGs and TFs were predicted to be potential candidate genes during maize root growth and development. Several of these genes are homologous to well-known genes regulating root architecture or development in Arabidopsis or rice, such as, Zm00001d005892 (AtERF109), Zm00001d027925 (AtERF73/HRE1), Zm00001d047017 (AtMYC2, OsMYC2), Zm00001d039245 (AtWRKY6). Identification of these key genes will provide a further understanding of the molecular mechanisms responsible for maize root growth and development, it will be beneficial to increase maize production and improve stress resistance by altering RSA traits in modern breeding.

NaCl improves reproduction by enhancing starch accumulation in the ovules of the euhalophyte Suaeda salsa

BACKGROUND

Halophytes show optimal reproduction under high-salinity conditions. However, the role of NaCl in reproduction and its possible mechanisms in the euhalophyte Suaeda salsa remain to be elucidated.

RESULTS

We performed transcript profiling of S. salsa flowers and measured starch accumulation in ovules, sugar contents in flowers, and photosynthetic parameters in the leaves of plants supplied with 0 and 200 mM NaCl. Starch accumulation in ovules, sugar contents in flowers and ovules, and net photosynthetic rate and photochemical efficiency in leaves were significantly higher in NaCl-treated plants vs. the control. We identified 14,348 differentially expressed genes in flowers of NaCl-treated vs. control plants. Many of these genes were predicted to be associated with photosynthesis, carbon utilization, and sugar and starch metabolism. These genes are crucial for maintaining photosystem structure, regulating electron transport, and improving photosynthetic efficiency in NaCl-treated plants. In addition, genes encoding fructokinase and sucrose phosphate synthase were upregulated in flowers of NaCl-treated plants.

CONCLUSIONS

The higher starch and sugar contents in the ovules and flowers of S. salsa in response to NaCl treatment are likely due to the upregulation of genes involved in photosynthesis and carbohydrate metabolism, which increase photosynthetic efficiency and accumulation of photosynthetic products under these conditions.

Transcriptome analysis of genes and pathways associated with salt tolerance in alfalfa under non-uniform salt stress

Soil salinity of fields is often non-uniform. To obtain a better understanding of molecular response to non-uniform salt stress, we conducted transcriptomic analysis on the leaves and roots of alfalfa grown under 0/0, 200/200, and 0/200 mM NaCl treatments. A total of 233,742 unigenes were obtained from the assembled cDNA libraries. There were 98 and 710 unigenes identified as significantly differentially expressed genes (DEGs) in the leaves of non-uniform and uniform salt treatment, respectively. Furthermore, there were 5178 DEGs in the roots under uniform salt stress, 273 DEGs in the non-saline side and 4616 in the high-saline side roots under non-uniform salt stress. Alfalfa treated with non-uniform salinity had greater dry weight and less salt damage compared to treatment with uniform salinity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs in roots revealed that both sides of the non-uniform salinity were enriched in pathways related to "phenylpropanoid biosynthesis" and "linoleic acid metabolism"; and "MAPK signaling pathway-plant" was also indicated as a key pathway in the high-saline roots. We also combined a set of important salt-response genes and found that roots from the non-saline side developed more roots with increased water uptake by altering the expression of aquaporins and genes related to growth regulation. Moreover, the hormone signal transduction and the antioxidant pathway probably play important roles in inducing more salt-related genes and increasing resistance to non-uniform salt stress on both sides of the roots.

Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

BACKGROUND

Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet.

METHODS

We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively.

RESULTS

In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress.

CONCLUSION

We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.

Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding

BACKGROUND

Orchardgrass (Dactylis glomerata L.) is a popular cool-season perennial grass with a high production value, and orchardgrass seed is the fourth top-selling forage grass seed in the world. However, its yield and quality are often affected by flooding. To date, the molecular responses of orchardgrass to flooding were poorly understood.

RESULTS

Here, we performed mRNA-seq to explore the transcriptomic responses of orchardgrass to a short term flooding (8 h and 24 h). There were 1454 and 565 differentially expressed genes identified in the 8 h and 24 h of flooding, respectively, compared to well control. GO functional enrichment analysis showed that oxidoreductase activity and oxidation-reduction process were highly present, suggesting that flooding induced the response to oxygen stress. Pathways enrichment analysis highlights the importance of glutathione metabolism, peroxidase, glycolysis and plant hormone signal transduction in response to flooding acclimation. Besides, the ROS clearance system is activated by significantly expressed glutathione S-transferase and genes encoding SOD and CAT (CAT1 and CDS2). The significant positive correlation between RNA sequencing data and a qPCR analysis indicated that the identified genes were credible.

CONCLUSION

In the process of orchardgrass response to flooding stress, multiple differential genes and biological processes have participated in its acclimation to flooding, especially the biological processes involved in the removal of ROS. These results provide a basis for further research on the adaptation mechanism of orchardgrass to flood tolerance.

Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat

Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.

Root Physiological Traits and Transcriptome Analyses Reveal that Root Zone Water Retention Confers Drought Tolerance to Opisthopappus taihangensis

Opisthopappus taihangensis (Ling) Shih, as a relative of chrysanthemum, mainly survives on the cracks of steep slopes and cliffs. Due to the harsh environment in which O. taihangensis lives, it has evolved strong adaptive traits to drought stress. The root system first perceives soil water deficiency, triggering a multi-pronged response mechanism to maintain water potential; however, the drought tolerance mechanism of O. taihangensis roots remains unclear. Therefore, roots were selected as materials to explore the physiological and molecular responsive mechanisms. We found that the roots had a stronger water retention capacity than the leaves. This result was attributed to ABA accumulation, which promoted an increased accumulation of proline and trehalose to maintain cell osmotic pressure, activated SOD and POD to scavenge ROS to protect root cell membrane structure and induced suberin depositions to minimize water backflow to dry soil. Transcriptome sequencing analyses further confirmed that O. taihangensis strongly activated genes involved in the ABA signalling pathway, osmolyte metabolism, antioxidant enzyme activity and biosynthesis of suberin monomer. Overall, these results not only will provide new insights into the drought response mechanisms of O. taihangensis but also will be helpful for future drought breeding programmes of chrysanthemum.

TiO2 nanoparticles and multi-walled carbon nanotubes monitoring and bioremediation potential using ciliates Pseudocohnilembus persalinus

In recent years, the release of nanomaterials pollutants to water bodies, to a great extent, attributed to anthropogenic activities. Their impacts on aquatic organisms as well as nanomaterial monitoring and bioremediation using organism have drawn much attentions. However, studies on relationship of nano-contaminants and aquatic organisms are very scarce. Our results showed that titanium dioxide nanoparticles (TiO₂-NPs) and Multi-walled carbon nanotubes (MWCNTs) caused an obvious cell decreases on the whole, but a significant increase at 48 h TiO₂-NPs exposure, indicating a resistant mechanism in ciliates for nano-toxic. Besides, MWCNTs was more toxic to Pseudocohnilembus persalinus than that of TiO₂-NPs in terms of EC₅₀ value. It is firstly found that P. persalinus ingested and released TiO₂-NPs through cytostome and cytoproct, which might be the reason that TiO₂-NPs less toxic than MWCNTs. The significantly increased superoxide dismutase (SOD) and glutathione S-transferase (GST) enzyme activities and expression levels were evaluated by reactive oxygen species ROS generation, which demonstrated that P. persalinus antioxidant defense enzyme played roles on nano-toxic resistant in ciliates. Moreover, the integrated biomarker response (IBR) was also determined, which demonstrated that MWCNTs had comparatively higher values than those of TiO₂-NPs after higher concentration exposure to ciliates. In addition, it was confirmed by the present work that sod, gst and cat played different roles on immunity, and the sensitivity of cat gene expression to these two nanomaterials exposure was dissimilar. Damages of shrunk as well as losses of cilia on the cell surface caused by TiO₂-NPs and MWCNTs exposure in P. persalinus using SEM revealed possible physical hazards of aggregated nanomaterials. Our findings will be helpful to understand the effect mechanisms of NPs on ciliates, and also demonstrated the possibility of P. persalinus as bio-indicator of nanomaterials in aquatic and potentials on bioremediation.

Genetic mechanisms of salt stress responses in halophytes

Abiotic stress is a major threat to plant growth and development, resulting in extensive crop loss worldwide. Plants react to abiotic stresses through physiological, biochemical, molecular, and genetic adaptations that promote survival. Exploring the molecular mechanisms involved in abiotic stress responses across various plant species is essential for improving crop yields in unfavorable environments. Halophytes are characterized as plants that survive to reproduce in soils containing high salt concentrations, and thus act as an ideal model to comprehend complicated genetic and physiological mechanisms of salinity stress tolerance. Plant ecologists classify halophytes into three main groups: euhalophytes, recretohalophytes, and pseudo-halophytes. Recent genetic and molecular research has showed complicated regulatory networks by which halophytes coordinate stress adaptation and tolerance. Furthermore, investigation of natural variations in these stress responses has supplied new perspectives on the evolution of mechanisms that regulate tolerance and adaptation. This review discusses the current understanding of the genetic mechanisms that contribute to salt-stress tolerance among different classes of halophytes.

Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties

To gain insight into the molecular mechanisms underpinning tobacco (Nicotiana tabacum) tolerance to drought stress, we integrated anatomical, physiological, and proteomic analyses of drought-tolerant (Yuyan6, [Y6]) and -sensitive (Yunyan87 [Y87]) varieties. In comparison to Y87, Y6 exhibited higher water retention capability, improved photosynthetic performance, delayed leaf-senescence, stable leaf ultrastructure, a stronger antioxidant defense, and lesser ROS accumulation when subjected to water stress. Using an iTRAQ-based proteomics approach, 405 and 1,560 differentially accumulated proteins (DAPs) were identified from Y6 and Y87 plants, respectively, of which 114 were found to be present in both cultivars. A subsequent functional characterization analysis revealed that these DAPs were significantly enriched in eight biological processes, six molecular functions, and six cellular components and displayed differential expression patterns in Y6 and Y87 plants, suggesting that the response to water stress between both varieties differed at the proteomic level. Furthermore, we constructed protein coexpression networks and identified hub proteins regulating tobacco defenses to water stress. Additionally, qPCR analysis indicated that the majority of genes encoding selected proteins showed consistency between mRNA levels and their corresponding protein expression levels. Our results provide new insights into the genetic regulatory mechanisms associated with drought response in tobacco plants.

Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms

Root systems play a pivotal role in coupling with drought stress, which is accompanied with a substantial transcriptome rebuilding in the root tissues. Here, we present the results of global gene expression profiling of roots of two barley genotypes with contrasting abilities to cope with drought that were subjected to a mild level of the stress. We concentrate our analysis on gene expression regulation processes, which allowed the identification of 88 genes from 39 families involved in transcriptional regulation in roots upon mild drought. They include 13 genes encoding transcription factors (TFs) from AP2 family represented by ERFs, DREB, or B3 domain-containing TFs, eight WRKYs, six NACs, five of the HD-domain, MYB or MYB-related, bHLH and bZIP TFs. Also, the representatives of C3H, CPP, GRAS, LOB-domain, TCP, Tiffy, Tubby, and NF-Ys TFs, among others were found to be regulated by the mild drought in barley roots. We found that drought tolerance is accompanied with a lower number of gene expression changes than the amount observed in a susceptible genotype. The better drought acclimation may be related to the activation of transcription factors involved in the maintenance of primary root growth and in the epigenetic control of chromatin and DNA methylation. In addition, our analysis pointed to fives TFs from ERF, LOB, NAC, WRKY and bHLH families that may be important in the mild but not the severe drought response of barley roots.

Overexpression of NtabDOG1L promotes plant growth and enhances drought tolerance in Nicotiana tabacum

Drought is one of the major environmental stresses limiting crop growth and production. It is very important to exploit and utilize drought-tolerance genes to improve crop drought-resistance. In this study, we identified two homoeologs of a Nicotiana tabacum (Ntab) DELAY OF GERMINATION (DOG) 1 like gene, named as NtabDOG1L-T and NtabDOG1L-S, respectively. The NtabDOG1L genes were preferentially expressed in roots and their expression levels were induced by polyethylene glycol, high salt, cold, and abscisic acid treatments. Subcellular localization results indicated that NtabDOG1L-T was localized in the nucleus, cytoplasm and cell membrane. Overexpression of NtabDOG1L-T in tobacco resulted in roots growth enhancement in transgenic plants. Furthermore, overexpression of NtabDOG1L-T enhanced drought stress tolerance in transgenic tobacco. The transgenic tobacco lines exhibited lower leaf water loss and electrolyte leakage, lower content of malondialdehyde and reactive oxygen species (ROS), and higher antioxidant enzymes activities after drought treatment when compared with wild type (WT) plants. In addition, the expression levels of several genes encoding key antioxidant enzymes and drought-related proteins were higher in the transgenic plants than in the WT plants under drought stress. Taken together, our results showed that NtabDOG1L functions as a novel regulator that improves plant growth and drought tolerance in tobacco.

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat

Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)

Perennial ryegrass (Lolium perenne) is a forage and amenity grass species widely cultivated in temperate regions worldwide. As such, perennial ryegrass populations are exposed to a range of environmental conditions and stresses on a seasonal basis and from year to year. One source of potential stress is limitation on water availability. The ability of these perennial grasses to be able to withstand and recover after periods of water limitation or drought can be a key component of grassland performance. Thus, we were interested in looking at changes in patterns of gene expression associated with increasing water stress. Clones of a single genotype of perennial ryegrass were grown under non-flowering growth room conditions in vermiculite supplemented with nutrient solution. Leaf and root tissue was sampled at 4 times in quadruplicate relating to estimated water contents of 35%, 15%, 5% and 1%. RNA was extracted and RNAseq used to generate transcriptome profiles at each sampling point. Transcriptomes were assembled using the published reference genome sequence and differential gene expression analysed using 3 different programmes, DESeq2, edgeR and limma (with the voom transformation), individually and in combination, deriving Early, Middle and Late stage comparisons. Identified differentially expressed genes were then associated with enriched GO terms using BLAST2GO. For the leaf, up-regulated differentially expressed genes were strongly associated with GO terms only during the Early stage and the majority of GO terms were associated with only down-regulated genes at the Middle or Late stages. For the roots, few differentially expressed genes were identified at either Early or Middle stages. Only one replicate at 1% estimated water content produced high quality data for the root, however, this indicated a high level of differential expression. Again the majority of enriched GO terms were associated with down-regulated genes. The performance of the different analysis programmes and the annotations associated with identified differentially expressed genes is discussed.

A Gene Regulatory Network Controlled by BpERF2 and BpMYB102 in Birch under Drought Conditions

Gene expression profiles are powerful tools for investigating mechanisms of plant stress tolerance. Betula platyphylla (birch) is a widely distributed tree, but its drought-tolerance mechanism has been little studied. Using RNA-Seq, we identified 2917 birch genes involved in its response to drought stress. These drought-responsive genes include the late embryogenesis abundant (LEA) family, heat shock protein (HSP) family, water shortage-related and ROS-scavenging proteins, and many transcription factors (TFs). Among the drought-induced TFs, the ethylene responsive factor (ERF) and myeloblastosis oncogene (MYB) families were the most abundant. BpERF2 and BpMYB102, which were strongly induced by drought and had high transcription levels, were selected to study their regulatory networks. BpERF2 and BpMYB102 both played roles in enhancing drought tolerance in birch. Chromatin immunoprecipitation combined with qRT-PCR indicated that BpERF2 regulated genes such as those in the LEA and HSP families, while BpMYB102 regulated genes such as Pathogenesis-related Protein 1 (PRP1) and 4-Coumarate:Coenzyme A Ligase 10 (4CL10). Multiple genes were regulated by both BpERF2 and BpMYB102. We further characterized the function of some of these genes, and the genes that encode Root Primordium Defective 1 (RPD1), PRP1, 4CL10, LEA1, SOD5, and HSPs were found to be involved in drought tolerance. Therefore, our results suggest that BpERF2 and BpMYB102 serve as transcription factors that regulate a series of drought-tolerance genes in B. platyphylla to improve drought tolerance.

Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity

In this study, high-throughput sequencing (RNA-Seq) was utilized to evaluate differential expression of transcripts and their related genes involved in response to terminal drought in root tissues of bread wheat landrace (L-82) and drought-sensitive genotype (Marvdasht). Subsets of 460 differentially expressed genes (DEGs) in drought-tolerant genotype and 236 in drought-sensitive genotype were distinguished and functionally annotated with 105 gene ontology (GO) terms and 77 metabolic pathways. Transcriptome profiling of drought-resistant genotype “L-82” showed up-regulation of genes mostly involved in Oxidation-reduction process, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. On the other hand, down-regulated genes mostly involved in signaling, oxidation-reduction process, secondary metabolite biosynthesis, auxin-responsive protein and lipid metabolism. We hypothesized that the drought tolerance in “L-82” was a result of avoidance strategies. Up-regulation of genes related to the deeper root system and adequate hydraulic characteristics to allow water uptake under water scarcity confirms our hypothesis. The transcriptomic sequences generated in this study provide information about mechanisms of acclimation to drought in the selected bread wheat landrace, “L-82”, and will help us to unravel the mechanisms underlying the ability of crops to reproduce and keep its productivity even under drought stress.

De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation

Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54.84%, and the HiSeq reads were assembled into 91,543 high-confidence protein-coding transcripts, 2,404 low-confidence protein-coding transcripts, and 13,181 non-coding transcripts with the completeness of >90%. Combining the FLX and HiSeq assemblies, we assembled a root transcriptome of 92,335 ORF-containing transcripts. Approximately 7% of the coding transcripts and ~2% non-coding transcripts are not present in the current wheat genome assembly. Functional annotation of both assemblies showed similar gene ontology patterns and that ~7% coding and >5% non-coding transcripts are root-specific. Transcription quantification identified 1,728 differentially expressed transcripts between root tips and maturation zone, and functional annotation of these transcripts captured a transcriptional signature of longitudinal development of wheat root. With the transcriptomic resources developed, this study provided the first view of wheat root transcriptome under different developmental zones and laid a foundation for molecular studies of wheat root development and growth using a reverse genetic approach.

Correlations between Phytohormones and Drought Tolerance in Selected Brassica Crops: Chinese Cabbage, White Cabbage and Kale

Drought is one of the major abiotic stresses affecting the productivity of Brassica crops. To understand the role of phytohormones in drought tolerance, we subjected Chinese cabbage (B. rapa ssp. pekinensis), white cabbage (B. oleracea var. capitata), and kale (B. oleracea var. acephala) to drought and examined the stress response on the physiological, biochemical and hormonal levels. The phytohormones abscisic acid (ABA), auxin indole-3-acetic acid (IAA), brassinosteroids (BRs), cytokinins (CKs), jasmonates (JAs), and salicylic acid (SA) were analyzed by ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS). Based on the physiological and biochemical markers the Chinese cabbage exhibited the lowest tolerance, followed by the white cabbage, while the kale appeared to be the most tolerant to drought. The drought tolerance of the kale correlated with increased levels of SA, ABA, IAA, CKs iP(R) and cZ(R), and typhasterol (TY), a precursor of active BRs. In contrast, the drought sensitivity of the Chinese cabbage correlated with a significant increase in ABA, JAs and the active BRs castasterol (CS) and brassinolide (BL). The moderately tolerant white cabbage, positioned between the kale and Chinese cabbage, showed more similarity in terms of the phytohormone patterns with the kale. We concluded that the drought tolerance in Brassicaceae is mostly determined by the increased endogenous levels of IAA, CKs, ABA and SA and the decreased levels of active BRs.