Maize leaves drought-responsive genes revealed by comparative transcriptome of two cultivars during the filling stage

Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings

Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.

Transcriptional survey of abiotic stress response in maize (Zea mays) in the level of gene co-expression network and differential gene correlation analysis

Abstract. Maize may be exposed to several abiotic stresses in the field. Therefore, identifying the tolerance mechanisms of natural field stress is mandatory. Gene expression data of maize upon abiotic stress were collected, and 560 differentially expressed genes (DEGs) were identified through meta-analysis. The most significant gene ontology terms in up-regulated genes were 'response to abiotic stress' and 'chitinase activity'. 'Phosphorelay signal transduction system' was the most significant enriched biological process in down-regulated DEGs. The co-expression analysis unveiled seven modules of DEGs, with a notable positive correlation between the modules and abiotic stress. Furthermore, the statistical significance was strikingly high for the turquoise, green and yellow modules. The turquoise group played a central role in orchestrating crucial adaptations in metabolic and stress response pathways in maize when exposed to abiotic stress. Within three up-regulated modules, Zm.7361.1.A1_at, Zm.10386.1.A1_a_at and Zm.10151.1.A1_at emerged as hub genes. These genes might introduce novel candidates implicated in stress tolerance mechanisms, warranting further comprehensive investigation and research. In parallel, the R package glmnet was applied to fit a logistic LASSO regression model on the DEGs profile to select candidate genes associated with abiotic responses in maize. The identified hub genes and LASSO regression genes were validated on an independent microarray dataset. Additionally, Differential Gene Correlation Analysis (DGCA) was performed on LASSO and hub genes to investigate the gene-gene regulatory relationship. The P value of DGCA of 16 pairwise gene comparisons was lower than 0.01, indicating a gene-gene significant change in correlation between control and abiotic stress. Integrated weighted gene correlation network analysis and logistic LASSO analysis revealed Zm.11185.1.S1_at, Zm.2331.1.S1_x_at and Zm.17003.1.S1_at. Notably, these 3 genes were identified in the 16 gene-pair comparisons. This finding highlights the notable significance of these genes in the abiotic stress response. Additional research into maize stress tolerance may focus on these three genes.

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.

Functional Characterization of an Amaranth Natterin-4-Like-1 Gene in Arabidopsis thaliana

The functional characterization of an Amaranthus hypochondriacus Natterin-4-Like-1 gene (AhN4L-1) coding for an unknown function protein characterized by the presence of an aerolysin-like pore-forming domain in addition to two amaranthin-like agglutinin domains is herewith described. Natterin and nattering-like proteins have been amply described in the animal kingdom. However, the role of nattering-like proteins in plants is practically unknown. The results described in this study, obtained from gene expression data in grain amaranth and from AhN4L-1-overexpressing Arabidopsis thaliana plants indicated that this gene was strongly induced by several biotic and abiotic conditions in grain amaranth, whereas data obtained from the overexpressing Arabidopsis plants further supported the defensive function of this gene, mostly against bacterial and fungal plant pathogens. GUS and GFP AhN4L-1 localization in roots tips, leaf stomata, stamens and pistils also suggested a defensive function in these organs, although its participation in flowering processes, such as self-incompatibility and abscission, is also possible. However, contrary to expectations, the overexpression of this gene negatively affected the vegetative and reproductive growth of the transgenic plants, which also showed no increased tolerance to salinity and water-deficit stress. The latter despite the maintenance of significantly higher chlorophyll levels and photosynthetic parameters under intense salinity stress. These results are discussed in the context of the physiological roles known to be played by related lectins and AB proteins in plants.

Perfluorooctanoic acid (PFOA) exposure induces splenic atrophy via overactivation of macrophages in male mice

Perfluorooctanoic acid (PFOA), a synthetic and widely used chemical, has aroused wide public concern due to its persistence, bioaccumulation, and potential toxicity. To investigate splenic atrophy induced by PFOA, male mice were exposed to 0, 0.4, 2, or 10 mg/kg/d PFOA for 28 d. Results demonstrated that spleen weight and relative spleen weight (RSW) decreased in the 2 and 10 mg/kg/d PFOA exposure groups. Iron levels in the spleen and serum were also reduced in all PFOA exposure groups. Weighted gene co-expression network analysis (WGCNA) of 7 043 genes highlighted enrichment in cell cycle, autoimmunity, and anemia in the spleen. In addition, changes in the levels of hemoglobin, platelets, bilirubin, and heme oxygenase-1 were consistent with anemia. The ratio of total macrophages to M1 macrophages in the spleen, phagocytic ability of macrophages, and levels of cytokines such as TNF-α, IL-1β, and IL-6 all increased, thus suggesting the occurrence of autoimmune disorder. Therefore, we concluded that overactivation of macrophages may be an important reason for splenic atrophy induced by PFOA exposure.

Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities

Non-invasive X-ray computed tomography (XRCT) is increasingly used in rhizosphere research to visualize development of soil-root interfaces in situ. However, exposing living systems to X-rays can potentially impact their processes and metabolites. In order to evaluate these effects, we assessed the responses of rhizosphere processes 1 and 24 h after a low X-ray exposure (0.81 Gy). Changes in root gene expression patterns occurred 1 h after exposure with down-regulation of cell wall-, lipid metabolism-, and cell stress-related genes, but no differences remained after 24 h. At either time point, XRCT did not affect either root antioxidative enzyme activities or the composition of the rhizosphere bacterial microbiome and microbial growth parameters. The potential activities of leucine aminopeptidase and phosphomonoesterase were lower at 1 h, but did not differ from the control 24 h after exposure. A time delay of 24 h after a low X-ray exposure (0.81 Gy) was sufficient to reverse any effects on the observed rhizosphere systems. Our data suggest that before implementing novel experimental designs involving XRCT, a study on its impact on the investigated processes should be conducted.

Comparative transcriptomic and physiological analyses of contrasting hybrid cultivars ND476 and ZX978 identify important differentially expressed genes and pathways regulating drought stress tolerance in maize

BACKGROUND

Drought is the major abiotic stress factor that negatively influences growth and yield in cereal grain crops such as maize (Zea mays L.). A multitude of genes and pathways tightly modulate plant growth, development and responses to environmental stresses including drought. Therefore, crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought responses.

OBJECTIVE

Here, we sought to elucidate the molecular and physiological mechanisms underpinning maize drought stress tolerance.

METHODS

We therefore applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at the late vegetative (V12) growth stage and performed a large-scale RNA sequencing (RNA-seq) transcriptome analysis of the leaf tissues.

RESULTS

A comparative analysis of the two genotypes leaf transcriptomes and physiological parameters revealed the key differentially expressed genes (DEGs) and metabolic pathways that respond to drought in a genotype-specific manner. A total of 3114 DEGs were identified, with 21 DEGs being specifically expressed in tolerant genotype ND476 in response to drought stress. Of these, genes involved in secondary metabolites biosynthesis, transcription factor regulation, detoxification and stress defense were highly expressed in ND476. Physiological analysis results substantiated our RNA-seq data, with ND476 exhibiting better cell water retention, higher soluble protein content and guaiacol peroxidase activity, along with low lipid peroxidation extent than the sensitive cultivar ZX978 under drought conditions.

CONCLUSION

Our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Additionally, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.

Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature

Drought is the leading cause of agricultural yield loss among all abiotic stresses, and the link between water deficit and phloem protein contents is relatively unexplored. Here we collected phloem exudates from Solanum lycopersicum leaves during periods of drought stress and recovery. Our analysis identified 2558 proteins, the most abundant of which were previously localized to the phloem. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggests that the protein content of phloem sap is complex, and includes proteins that function in chaperone systems, branched-chain amino acid synthesis, trehalose metabolism, and RNA silencing. We observed 169 proteins whose abundance changed significantly within the phloem sap, either during drought or recovery. Proteins that became significantly more abundant during drought include members of lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are decreased during drought. Our experiment has achieved an in-depth profiling of phloem sap protein contents during drought stress and recovery that supports previous findings and provides new evidence that multiple biological processes are involved in drought adaptation.