Over-expression of rice R1-type MYB transcription factor confers different abiotic stress tolerance in transgenic Arabidopsis

Genetic diversity and adaptive evolutionary history of Sapindus in China: insights from whole-genome resequencing of 100 representative individuals

Sapindus is an important forest tree genus with utility in biodiesel, biomedicine, biochemistry and forestry. Similar to many perennial crop plants, its breeding is hampered by long generation times and lack of genetic resources. To understand the genome evolution underlying the important bioeconomic traits, we carried out a common garden experiment with 100 Sapindus core germplasm individuals representing three endemic species and 60 populations sampled throughout China. Whole genome sequencing identified a split into six populations according to species and geography. The previously uncharacterized S. delavayi and S. rarak are diploid species, and here we propose hypotheses for their speciation. Selective sweeps suggested stress responses as well as alleles of the genes CYP716A, CAMTA and HD-ZIP involved in triterpenoid saponin biosynthesis to have been under selection in natural populations, while genome-wide association analysis revealed several homologues of fatty acid biosynthesis genes to be associated with kernel fatty acid quality. Our findings elucidate the genetic structure of Sapindus in China, provide target loci for selection and suggest cultivar materials for genetic improvement.

OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice

Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.

Chromiomics: Chromium detoxification and approaches for engineering tolerance in plants

Chromium (Cr) is a heavy metal that poses a grave threat to the ecosystem including plants. Chromium is very harmful to plants due to its effects on many physiological and metabolic pathways culminating in a negative impact on plant's growth, development, and ability to take up nutrients. Plants have developed physiological, biochemical, and molecular ways of defense against Cr, such as by augmenting antioxidant potential to reduce reactive oxygen species (ROS). A number of genes have been discovered to play a significant role in the defense mechanisms of plants against Cr, for example, genes associated with the activation of phytochelatins, metallothioneins, and those of enzymes like glutathione-S-transferases. Along with this, a few miRNAs have been found to be associated in alleviating Cr stress and, to augment plant tolerance by controlling transcription factors, HSPs, and the expression of a few proteins and hormones. Defense pathway genes and miRNAs have been used for the generation of transgenic phytoremediator plants. Not only do the transgenic plants have a higher tolerance to Cr, but they also act as hyperaccumulators for Cr and have the potential to remediate other heavy metals. This article describes about environmental Cr contamination, Cr effects on plants, different genes and miRNAs involved in Cr stress mitigation and use of candidate genes, microRNAs for creating transgenic plant systems for phytoremediation, and the applications of CRISPR technology. It is expected that the integration of omics approach and advanced genomics will offer scope for more effective phytoremediation of Chromium in the coming years.

Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock 'Ruggeri' throughout Salinity

Salinity is one of the substantial threats to plant productivity and could be escorted by other stresses such as heat and drought. It impairs critical biological processes, such as photosynthesis, energy, and water/nutrient acquisition, ultimately leading to cell death when stress intensity becomes uncured. Therefore, plants deploy several proper processes to overcome such hostile circumstances. Grapevine is one of the most important crops worldwide that is relatively salt-tolerant and preferentially cultivated in hot and semi-arid areas. One of the most applicable strategies for sustainable viticulture is using salt-tolerant rootstock such as Ruggeri (RUG). The rootstock showed efficient capacity of photosynthesis, ROS detoxification, and carbohydrate accumulation under salinity. The current study utilized the transcriptome profiling approach to identify the molecular events of RUG throughout a regime of salt stress followed by a recovery procedure. The data showed progressive changes in the transcriptome profiling throughout salinity, underpinning the involvement of a large number of genes in transcriptional reprogramming during stress. Our results established a considerable enrichment of the biological process GO-terms related to salinity adaptation, such as signaling, hormones, photosynthesis, carbohydrates, and ROS homeostasis. Among the battery of molecular/cellular responses launched upon salinity, ROS homeostasis plays the central role of salt adaptation.

Deciphering the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) through genome-wide association studies

Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat.

The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites

Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.

Characteristics and Functions of MYB (v-Myb avivan myoblastsis virus oncogene homolog)-Related Genes in Arabidopsis thaliana

The MYB (v-Myb avivan myoblastsis virus oncogene homolog) transcription factor family is one of the largest families of plant transcription factors which plays a vital role in many aspects of plant growth and development. MYB-related is a subclass of the MYB family. Fifty-nine Arabidopsis thaliana MYB-related (AtMYB-related) genes have been identified. In order to understand the functions of these genes, in this review, the promoters of AtMYB-related genes were analyzed by means of bioinformatics, and the progress of research into the functions of these genes has been described. The main functions of these AtMYB-related genes are light response and circadian rhythm regulation, root hair and trichome development, telomere DNA binding, and hormone response. From an analysis of cis-acting elements, it was found that the promoters of these genes contained light-responsive elements and plant hormone response elements. Most genes contained elements related to drought, low temperature, and defense and stress responses. These analyses suggest that AtMYB-related genes may be involved in A. thaliana growth and development, and environmental adaptation through plant hormone pathways. However, the functions of many genes do not occur independently but instead interact with each other through different pathways. In the future, the study of the role of the gene in different pathways will be conducive to a comprehensive understanding of the function of the gene. Therefore, gene cloning and protein functional analyses can be subsequently used to understand the regulatory mechanisms of AtMYB-related genes in the interaction of multiple signal pathways. This review provides theoretical guidance for the follow-up study of plant MYB-related genes.

Functional Study of Amorpha fruticosa WRKY20 Gene in Response to Drought Stress

The WRKY gene family in plants regulates the plant's response to drought through regulatory networks and hormone signaling. AfWRKY20 (MT859405) was cloned from Amorpha fruticosa (A. fruticosa) seedlings using RT-PCR. The binding properties of the AfWRKY20 protein and the W-box (a DNA cis-acting element) were verified both in vivo and in vitro using EMSA and Dual-Luciferase activity assays. RT-qPCR detected that the total expression level of AfWRKY20 in leaves and roots was 22 times higher in the 30% PEG6000 simulated drought treatment compared to the untreated group. Under the simulated drought stress treatments of sorbitol and abscisic acid (ABA), the transgenic tobacco with the AfWRKY20 gene showed enhanced drought resistance at the germination stage, with significantly increased germination rate, green leaf rate, fresh weight, and root length compared to the wild-type (WT) tobacco. In addition, the superoxide dismutase (SOD) activity, chlorophyll content, and Fv/Fm ratio of AfWRKY20 transgenic tobacco were significantly higher than those of the WT tobacco under natural drought stress, while the malondialdehyde (MDA) content and 3,3'-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) staining levels were lower. The expression levels of oxidation kinase genes (NbSOD, NbPOD, and NbCAT) in transgenic tobacco under drought stress were significantly higher than those in WT tobacco. This enhancement in gene expression improved the ability of transgenic tobacco to detoxify reactive oxygen species (ROS). The survival rate of transgenic tobacco after natural drought rehydration was four times higher than that of WT tobacco. In summary, this study revealed the regulatory mechanism of AfWRKY20 in response to drought stress-induced ABA signaling, particularly in relation to ROS. This finding provides a theoretical basis for understanding the pathways of WRKY20 involved in drought stress, and offers genetic resources for molecular plant breeding aimed at enhancing drought resistance.

A MYB-related transcription factor from peanut, AhMYB30, improves freezing and salt stress tolerance in transgenic Arabidopsis through both DREB/CBF and ABA-signaling pathways

Abiotic stresses such as salinity and low temperature have serious impact on peanut growth and yield. The present work investigated the function of a MYB-related transcription factor gene AhMYB30 obtained from peanut under salt and low temperature stresses by transgenic methods. The results indicated that the overexpression of AhMYB30 in Arabidopsis could enhance the resistance of transgenic plants to freezing and salt stresses. The expression of stress-response genes RD29A (Response-to-Dehydration 29A), COR15A (Cold-Regulated 15A), KIN1 (Kinesin 1) and ABI2 (Abscisic acid Insensitive 2) increased in transgenic plants compared with in wild-type. Subcellular localization and transcriptional autoactivation validation demonstrated that AhMYB30 has essential features of transcription factors. Therefore, AhMYB30 may increase salt and freezing stress tolerance as the transcription factor (TF) in Arabidopsis through both DREB/CBF and ABA-signaling pathways. Our results lay the theoretical foundation for exploring stress resistance mechanisms of peanut and offering novel genetic resources for molecular breeding.

An R2R3-MYB FtMYB11 from Tartary buckwheat has contrasting effects on abiotic tolerance in Arabidopsis

R2R3-MYB transcription factors play important roles in response to abiotic stresses in planta, such as salt, drought, and osmotic stress. However, the role of FtMYB11 in Tartary buckwheat (Fagopyrum tataricum) in drought and osmotic tolerance has not yet been elucidated. In this study, we found that FtMYB11 was markedly induced by exogenous abscisic acid (ABA), salinity, and mannitol. Further, FtMYB11-overexpressing Arabidopsis showed hypersensitivity to ABA-mediated seed germination and seedling establishment through regulating transcripts of AtCBF1, AtDREB2A, and AtRD20, compared with wild type, indicating that FtMYB11 plays a positive role in ABA signaling. In contrast, transgenic lines overexpressing FtMYB11 were sensitive to mannitol and NaCl treatments, suggesting that FtMYB11 plays a negative role in osmotic tolerance. Intriguingly, the transcripts of ABA biosynthetic enzyme genes were significantly elevated in plants overexpressing FtMYB11 after exposure to osmotic stresses, such as AtABA3 and AtNCED3. In addition, flavonoid biosynthesis genes were also upregulated in transgenic Arabidopsis under ABA, salt, and drought treatments, including AtC4H, AtF3H, AtANS, AtFLS, and At4CL. The drought tolerance assay showed that plants overexpressing FtMYB11 displayed greater tolerance to water deficit through regulating MDA and proline content. Taken together, FtMYB11 has opposite roles in response to abiotic stresses, but it may mediate flavonoid biosynthesis through regulation of related enzyme genes.

MYB transcription factors-master regulators of phenylpropanoid biosynthesis and diverse developmental and stress responses

Phenylpropanoids, the largest class of natural products including flavonoids, anthocyanins, monolignols and tannins perform multiple functions ranging from photosynthesis, nutrient uptake, regulating growth, cell division, maintenance of redox homeostasis and biotic and abiotic stress responses. Being sedentary life forms, plants possess several regulatory modules that increase their performance in varying environments by facilitating activation of several signaling cascades upon perception of developmental and stress signals. Of the various regulatory modules, those involving MYB transcription factors are one of the extensive groups involved in regulating the phenylpropanoid metabolic enzymes in addition to other genes. R2R3 MYB transcription factors are a class of plant-specific transcription factors that regulate the expression of structural genes involved in anthocyanin, flavonoid and monolignol biosynthesis which are indispensable to several developmental pathways and stress responses. The aim of this review is to present the regulation of the phenylpropanoid pathway by MYB transcription factors via Phospholipase D/phosphatidic acid signaling, downstream activation of the structural genes, leading to developmental and/or stress responses. Specific MYB transcription factors inducing or repressing specific structural genes of anthocyanin, flavonoid and lignin biosynthetic pathways are discussed. Further the roles of MYB in activating biotic and abiotic stress responses are delineated. While several articles have reported the role of MYB's in stress responses, they are restricted to two or three specific MYB factors. This review is a consolidation of the diverse roles of different MYB transcription factors involved both in induction and repression of anthocyanin, flavonoid, and lignin biosynthesis.

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.

Overexpression of cowpea NAC transcription factors promoted growth and stress tolerance by boosting photosynthetic activity in Arabidopsis

ATAF-like NAC transcription factors are bonafide regulators of stress-signaling. However, their overexpression often exerts growth-retardation by activating ABA-hypersensitivity, chloroplast-degradation, or carbon-starvation. To improve tolerance to multiple stress complying with growth sustainability, we examined two ATAF orthologs, VuNAC1 and VuNAC2, isolated from a drought-hardy cowpea genotype, for a harmonized regulation of stress and growth signaling. The genes were induced by dehydration, NaCl, polyethylene glycol, heat, cold, ABA, and light. Analysis of the promoter-elements and regulatory network corroborated the integration of circadian, hormonal, stress, developmental, and nutrition signals, being VuNAC1/2 the central transcriptional-switch interfacing growth and stress responses. The constitutive gene overexpression in Arabidopsis resulted in an improved embryonic, rosette, and inflorescence growth, under optimum as well as limiting nutrition, in association with increased photosynthetic activity and stomatal-density. The transgenic seedlings manifested tolerance to dehydration, salinity, aluminum, cadmium, and H₂O₂ toxicity, in addition to ABA-mediated seed dormancy and hypersensitivity. The soil-grown plants survived severe drought and hypersalinity by maintaining the water-status and membrane integrity through the accumulation of stress protectants, such as proline, glutathione, and ascorbate. Unlike their orthologs from other species, VuNAC1/2 conferred tolerance to multiple abiotic stresses in line with improved growth attributes via regulation of photosynthetic controls and nutritional balance, suggesting growth being a crucial component of stress-tolerance and recovery. Such unique stress-responsive transcription factors, which also confer photosynthetic gain, could be sustainable biotechnological tools for developing stress-tolerant crops and translating the improved growth into yield without unintended trade-offs.

BcGR1.1, a Cytoplasmic Localized Glutathione Reductase, Enhanced Tolerance to Copper Stress in Arabidopsis thaliana

Copper is a mineral element, which is necessary for the normal growth and development of plants, but high levels of copper will seriously damage plants. Studies have shown that AtGR1 improves the tolerance of Arabidopsis to aluminum and cadmium stress. However, the role of GR in the copper stress response of plants is still unclear. Here, we identified four genes (named BcGR1.1, BcGR1.2, BcGR2.1 and BcGR2.2, respectively) encoding glutathione reductase (GR) in non-heading Chinese cabbage (Brassica campestris (syn. Brassica rapa) ssp. chinensis), which could be divided into two types based on the subcellular localization. Among them, BcGR1.1, which belonged to the cytoplasmic localization type, was significantly upregulated under copper stress. Compared to WT (the wild type), Arabidopsis thaliana heterologously overexpressed BcGR1.1 had longer roots, higher fresh weight, higher GSH levels and GSH/GSSG (oxidized form of GSH) ratio, and accumulated more superoxide dismutase and peroxidase under copper stress. However, in the AsA-GSH cycle under copper stress, the contents of AsA and AsA/DHA were significantly downregulated, and the contents of DHA and T-AsA (total AsA) were upregulated, in the BcGR1.1-overexpressing Arabidopsis. Therefore, BcGR1.1 could improve the scavenging ability of reactive oxygen species (ROS) by increasing the activity of GR, antioxidant enzymes and the utilization of AsA, and then enhance the copper stress tolerance of plants.

Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid

Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane.

Validating ADME QSAR Models Using Marketed Drugs

Problems with drug ADME are responsible for many clinical failures. By understanding the ADME properties of marketed drugs and modeling how chemical structure contributes to these inherent properties, we can help new projects reduce their risk profiles. Kinetic aqueous solubility, the parallel artificial membrane permeability assay (PAMPA), and rat liver microsomal stability constitute the Tier I ADME assays at the National Center for Advancing Translational Sciences (NCATS). Using recent data generated from in-house lead optimization Tier I studies, we update quantitative structure-activity relationship (QSAR) models for these three endpoints and validate in silico performance against a set of marketed drugs (balanced accuracies range between 71% and 85%). Improved models and experimental datasets are of direct relevance to drug discovery projects and, together with the prediction services that have been made publicly available at the ADME@NCATS web portal (https://opendata.ncats.nih.gov/adme/), provide important tools for the drug discovery community. The results are discussed in light of our previously reported ADME models and state-of-the-art models from scientific literature.Graphical Abstract[Figure: see text].