Systematic Analysis of Differentially Expressed Maize ZmbZIP Genes between Drought and Rewatering Transcriptome Reveals bZIP Family Members Involved in Abiotic Stress Responses

Genome-wide profiling of bZIP transcription factors in Camelina sativa: implications for development and stress response

BACKGROUND

The bZIP transcription factor family, characterized by a bZIP domain, plays vital roles in plant stress responses and development. While this family has been extensively studied in various plant species, its specific functions in Camelina sativa (False Flax) remain underexplored.

METHODS AND RESULTS

This study identified 71 bZIP transcription factors in C. sativa, classified into nine distinct groups based on phylogenetic analysis. Subcellular localization predicted a nucleus-specific expression for these bZIPs. Analysis of GRAVY scores revealed a range from 0.469 to -1.256, indicating a spectrum from hydrophobic to hydrophilic properties. Motif analysis uncovered 10 distinct motifs, with one motif being universally present in all CsbZIPs. Conserved domain analysis highlighted several domains beyond the core bZIP domain. Protein-protein interaction predictions suggested a robust network involving CsbZIPs. Moreover, promoter analysis revealed over 60 types of cis-elements, including those responsive to stress. Expression studies through RNA-seq and Real-time RT-qPCR demonstrated high expression of CsbZIPs in roots, leaves, flowers, and stems. Specifically, CsbZIP01, CsbZIP02, CsbZIP44, and CsbZIP60 were consistently up-regulated under cold, salt, and drought stresses, whereas CsbZIP34 and CsbZIP35 were down-regulated.

CONCLUSION

This study presents the first comprehensive genome-wide profiling of bZIP transcription factors in Camelina sativa, providing novel insights into their roles in plant development and stress response mechanisms. By identifying and characterizing the bZIP gene family in C. sativa, this research offers new opportunities for improving stress tolerance and crop resilience through targeted genetic approaches, addressing key challenges in agriculture under changing environmental conditions.

Genetic, molecular and physiological crosstalk during drought tolerance in maize (Zea mays): pathways to resilient agriculture

MAIN CONCLUSION

This review comprehensively elucidates maize drought tolerance mechanisms, vital for global food security. It highlights genetic networks, key genes, CRISPR-Cas applications, and physiological responses, guiding resilient variety development. Maize, a globally significant crop, confronts the pervasive challenge of drought stress, impacting its growth and yield significantly. Drought, an important abiotic stress, triggers a spectrum of alterations encompassing maize's morphological, biochemical, and physiological dimensions. Unraveling and understanding these mechanisms assumes paramount importance for ensuring global food security. Approaches like developing drought-tolerant varieties and harnessing genomic and molecular applications emerge as effective measures to mitigate the negative effects of drought. The multifaceted nature of drought tolerance in maize has been unfolded through complex genetic networks. Additionally, quantitative trait loci mapping and genome-wide association studies pinpoint key genes associated with drought tolerance, influencing morphophysiological traits and yield. Furthermore, transcription factors like ZmHsf28, ZmNAC20, and ZmNF-YA1 play pivotal roles in drought response through hormone signaling, stomatal regulation, and gene expression. Genes, such as ZmSAG39, ZmRAFS, and ZmBSK1, have been reported to be pivotal in enhancing drought tolerance through diverse mechanisms. Integration of CRISPR-Cas9 technology, targeting genes like gl2 and ZmHDT103, emerges as crucial for precise genetic enhancement, highlighting its role in safeguarding global food security amid pervasive drought challenges. Thus, decoding the genetic and molecular underpinnings of drought tolerance in maize sheds light on its resilience and paves the way for cultivating robust and climate-smart varieties, thus safeguarding global food security amid climate challenges. This comprehensive review covers quantitative trait loci mapping, genome-wide association studies, key genes and functions, CRISPR-Cas applications, transcription factors, physiological responses, signaling pathways, offering a nuanced understanding of intricate mechanisms involved in maize drought tolerance.

Multi-locus genome-wide association study for phosphorus use efficiency in a tropical maize germplasm

Phosphorus (P) is an essential macronutrient for maize (Zea mays L.) growth and development. Therefore, generating cultivars with upgraded P use efficiency (PUE) represents one of the main strategies to reduce the global agriculture dependence on phosphate fertilizers. In this work, genome-wide association studies (GWAS) were performed to detect quantitative trait nucleotide (QTN) and potential PUE-related candidate genes and associated traits in greenhouse and field trials under contrasting P conditions. The PUE and other agronomy traits of 132 maize inbred lines were assessed in low and normal P supply through the greenhouse and field experiments and Multi-locus GWAS was used to map the associated QTNs. Wide genetic variability was observed among the maize inbred lines under low and normal P supply. In addition, we confirm the complex and quantitative nature of PUE. A total of 306 QTNs were associated with the 24 traits evaluated using different multi-locus GWAS methods. A total of 186 potential candidate genes were identified, mainly involved with transcription regulator, transporter, and transference activity. Further studies are still needed to elucidate the functions and relevance of these genes regarding PUE. Nevertheless, pyramiding the favorable alleles pinpointed in the present study can be considered an efficient strategy for molecular improvement to increase maize PUE.

Expression of Foxtail Millet bZIP Transcription Factor SibZIP67 Enhances Drought Tolerance in Arabidopsis

Foxtail millet is a drought-tolerant cereal and forage crop. The basic leucine zipper (bZIP) gene family plays important roles in regulating plant development and responding to stresses. However, the roles of bZIP genes in foxtail millet remain largely uninvestigated. In this study, 92 members of the bZIP transcription factors were identified in foxtail millet and clustered into ten clades. The expression levels of four SibZIP genes (SibZIP11, SibZIP12, SibZIP41, and SibZIP67) were significantly induced after PEG treatment, and SibZIP67 was chosen for further analysis. The studies showed that ectopic overexpression of SibZIP67 in Arabidopsis enhanced the plant drought tolerance. Detached leaves of SibZIP67 overexpressing plants had lower leaf water loss rates than those of wild-type plants. SibZIP67 overexpressing plants improved survival rates under drought conditions compared to wild-type plants. Additionally, overexpressing SibZIP67 in plants displayed reduced malondialdehyde (MDA) levels and enhanced activities of antioxidant enzymes, including catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) under drought stress. Furthermore, the drought-related genes, such as AtRD29A, AtRD22, AtNCED3, AtABF3, AtABI1, and AtABI5, were found to be regulated in SibZIP67 transgenic plants than in wild-type Arabidopsis under drought conditions. These data suggested that SibZIP67 conferred drought tolerance in transgenic Arabidopsis by regulating antioxidant enzyme activities and the expression of stress-related genes. The study reveals that SibZIP67 plays a beneficial role in drought response in plants, offering a valuable genetic resource for agricultural improvement in arid environments.

Characterization of bZIP Transcription Factors in Transcriptome of Chrysanthemum mongolicum and Roles of CmbZIP9 in Drought Stress Resistance

bZIP transcription factors play important roles in regulating plant development and stress responses. Although bZIPs have been identified in many plant species, there is little information on the bZIPs in Chrysanthemum. In this study, bZIP TFs were identified from the leaf transcriptome of C. mongolicum, a plant naturally tolerant to drought. A total of 28 full-length bZIP family members were identified from the leaf transcriptome of C. mongolicum and were divided into five subfamilies based on their phylogenetic relationships with the bZIPs from Arabidopsis. Ten conserved motifs were detected among the bZIP proteins of C. mongolicum. Subcellular localization assays revealed that most of the CmbZIPs were predicted to be localized in the nucleus. A novel bZIP gene, designated as CmbZIP9, was cloned based on a sequence of the data of the C. mongolicum transcriptome and was overexpressed in tobacco. The results indicated that the overexpression of CmbZIP9 reduced the malondialdehyde (MDA) content and increased the peroxidase (POD) and superoxide dismutase (SOD) activities as well as the expression levels of stress-related genes under drought stress, thus enhancing the drought tolerance of transgenic tobacco lines. These results provide a theoretical basis for further exploring the functions of the bZIP family genes and lay a foundation for stress resistance improvement in chrysanthemums in the future.

Chitosan-fulvic acid nanoparticles enhance drought tolerance in maize via antioxidant defense and transcriptional reprogramming

Nanoparticles are promising alternatives to synthetic fertilizers in the context of climate change and sustainable agriculture. Maize plants were grown under gradient concentrations (50 μM, 100 μM, 200 μM, 500 μM, and 1 mM) of chitosan (Ch), fulvic acid (FA) or chitosan-fulvic acid nanoparticles (Ch-FANPs). Based on the overall phenotypic assessment, 100 μM was selected for downstream experiments. Maize plants grown under this optimized concentration were thereafter subjected to drought stress by water withholding for 14 days. Compared to the individual performances, the combined treatment of Ch-FANPs supported the best plant growth over chitosan, fulvic acid, or sole watered plants and alleviated the adverse effects of drought by enhancing root and shoot growth, and biomass by an average 20%. In addition, Ch-FANPs-treated plants exhibited a significant reduction in hydrogen peroxide (H2O2) content (~10%), with a concomitant increase in ascorbate peroxidase (APX) activity (>100%) while showing a reduced lipid peroxidation level observed by the decrease in malondialdehyde (MDA) content (~100%) and low electrolyte leakage level. Furthermore, chlorophyll content increased significantly (>100%) in maize plants treated with Ch-FANPs compared to Ch or FA and control in response to drought. The expression of drought-induced transcription factors, ZmDREB1A, ZmbZIP1, and ZmNAC28, and the ABA-dependent ZmCIPK3 was upregulated by Ch-FANPs. Owing to the above, Ch-FANPs are proposed as a growth-promoting agent and elicitor of drought tolerance in maize via activation of antioxidant machinery and transcriptional reprogramming of drought-related genes.

A teosinte-derived allele of ZmSC improves salt tolerance in maize

Maize, a salt-sensitive crop, frequently suffers severe yield losses due to soil salinization. Enhancing salt tolerance in maize is crucial for maintaining yield stability. To address this, we developed an introgression line (IL76) through introgressive hybridization between maize wild relatives Zea perennis, Tripsacum dactyloides, and inbred Zheng58, utilizing the tri-species hybrid MTP as a genetic bridge. Previously, genetic variation analysis identified a polymorphic marker on Zm00001eb244520 (designated as ZmSC), which encodes a vesicle-sorting protein described as a salt-tolerant protein in the NCBI database. To characterize the identified polymorphic marker, we employed gene cloning and homologous cloning techniques. Gene cloning analysis revealed a non-synonymous mutation at the 1847th base of ZmSCIL76 , where a guanine-to-cytosine substitution resulted in the mutation of serine to threonine at the 119th amino acid sequence (using ZmSCZ58 as the reference sequence). Moreover, homologous cloning demonstrated that the variation site derived from Z. perennis. Functional analyses showed that transgenic Arabidopsis lines overexpressing ZmSCZ58 exhibited significant reductions in leaf number, root length, and pod number, alongside suppression of the expression of genes in the SOS and CDPK pathways associated with Ca2+ signaling. Similarly, fission yeast strains expressing ZmSCZ58 displayed inhibited growth. In contrast, the ZmSCIL76 allele from Z. perennis alleviated these negative effects in both Arabidopsis and yeast, with the lines overexpressing ZmSCIL76 exhibiting significantly higher abscisic acid (ABA) content compared to those overexpressing ZmSCZ58 . Our findings suggest that ZmSC negatively regulates salt tolerance in maize by suppressing downstream gene expression associated with Ca2+ signaling in the CDPK and SOS pathways. The ZmSCIL76 allele from Z. perennis, however, can mitigate this negative regulatory effect. These results provide valuable insights and genetic resources for future maize salt tolerance breeding programs.

Analysis of the molecular mechanisms regulating how ZmEREB24 improves drought tolerance in maize (Zea mays) seedlings

Drought stress is one of the most limiting factors of maize productivity and can lead to a sharp reduction in the total biomass when it occurs at the seedling stage. Improving drought tolerance at the seedling stage is of great importance for maize breeding. The AP2/ERF transcription factor family plays a critical role in plant response to abiotic stresses. Here, we used a preliminary previously-generated ranscriptomic dataset to identify a highly drought-stress-responsive AP2 gene, i.e., ZmEREB24. Compared to the wild type, the overexpression of ZmEREB24 in maize significantly promotes drought tolerance of transgenic plants at the seedling stage. CRISPR/Cas9-based ZmEREB24-knockout mutants showed a drought-sensitive phenotype. RNA-seq analysis and EMSA assay revealed AATGG.CT and GTG.T.GCC motifs as the main binding sites of ZmEREB24 to the promoters of downstream target genes. DAP-seq identified four novel target genes involved in proline and sugar metabolism and hormone signal transduction of ZmEREB24. Our data indicate that ZmEREB24 plays important biological functions in regulating drought tolerance by binding to the promoters of drought stress genes and modulating their expression. The results further suggest a role of ZmEREB24 in regulating drought adaptation in maize, indicating its potential importance for employing molecular breeding in the development of high-yield drought-tolerant maize cultivars.

Seed Priming with Reactive Oxygen Species-Generating Nanoparticles Enhanced Maize Tolerance to Multiple Abiotic Stresses

Climate change-induced extreme weather events (heat, cold, drought, and flooding) will severely affect crop production. Increasing the resilience of crops to fluctuating environmental conditions is critically important. Here, we report that nanomaterials (NMs) with reactive oxygen species (ROS)-generating properties can be used as seed priming agents to simultaneously enhance the tolerance of maize seeds and seedlings to diverse and even multiple stresses. Maize seeds primed with 40 mg/L silver nanoparticles (AgNPs) exhibited accelerated seed germination and an increased germination rate, greater seedling vigor, and better seedling growth under drought (10% and 20% PEG), saline (50 and 100 mM NaCl), and cold (15 °C) stress conditions, indicating enhanced resilience to diverse stresses. Importantly, maize resistance to simultaneous multiple stresses (drought and cold, drought and salt, and salt and cold) was markedly enhanced. Under drought conditions, seed priming significantly boosted root hair density and length (17.3-82.7%), which enabled greater tolerance to water deficiency. RNA-seq analysis reveals that AgNPs seed priming induced a transcriptomic shift in maize seeds. Plant hormone signal transduction and MAPK signaling pathways were activated upon seed priming. Importantly, low-cost and environmentally friendly ROS-generating Fe-based NMs (Fe2O3 and Fe3O4 NPs) were also demonstrated to enhance the resistance of seeds and seedlings to drought, salt, and cold stresses. These findings demonstrate that a simple seed priming strategy can be used to significantly enhance the climate resilience of crops through modulated ROS homeostasis and that this approach could be a powerful nanoenabled tool for addressing worsening food insecurity.

Molecular mechanism analysis of ZmRL6 positively regulating drought stress tolerance in maize

MYB-related genes, a subclass of MYB transcription factor family, have been documented to play important roles in biological processes such as secondary metabolism and stress responses that affect plant growth and development. However, the regulatory roles of MYB-related genes in drought stress response remain unclear in maize. In this study, we discovered that a 1R-MYB gene, ZmRL6, encodes a 96-amino acid protein and is highly drought-inducible. We also found that it is conserved in both barley (Hordeum vulgare L.) and Aegilops tauschii. Furthermore, we observed that overexpression of ZmRL6 can enhance drought tolerance while knock-out of ZmRL6 by CRISPR-Cas9 results in drought hypersensitivity. DAP-seq analyses additionally revealed the ZmRL6 target genes mainly contain ACCGTT, TTACCAAAC and AGCCCGAG motifs in their promoters. By combining RNA-seq and DAP-seq results together, we subsequently identified eight novel target genes of ZmRL6 that are involved in maize's hormone signal transduction, sugar metabolism, lignin synthesis, and redox signaling/oxidative stress. Collectively, our data provided insights into the roles of ZmRL6 in maize's drought response.

Role of bZIP transcription factors in the regulation of plant secondary metabolism

MAIN CONCLUSION

This study provides an overview of the structure, classification, regulatory mechanisms, and biological functions of the basic (region) leucine zipper transcription factors and their molecular mechanisms in flavonoid, terpenoid, alkaloid, phenolic acid, and lignin biosynthesis. Basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors (TFs) in eukaryotic organisms. The bZIP TFs are widely distributed in plants and play important roles in plant growth and development, photomorphogenesis, signal transduction, resistance to pathogenic microbes, biotic and abiotic stress, and secondary metabolism. Moreover, the expression of bZIP TFs not only promotes or inhibits the accumulation of secondary metabolites in medicinal plants, but also affects the stress response of plants to the external adverse environment. This paper describes the structure, classification, biological function, and regulatory mechanisms of bZIP TFs. In addition, the molecular mechanism of bZIP TFs regulating the biosynthesis of flavonoids, terpenoids, alkaloids, phenolic acids, and lignin are also elaborated. This review provides a summary for in-depth study of the molecular mechanism of bZIP TFs regulating the synthesis pathway of secondary metabolites and plant molecular breeding, which is of significance for the generation of beneficial secondary metabolites and the improvement of plant varieties.

Potential of growth-promoting bacteria in maize (Zea mays L.) varies according to soil moisture

Climate change has caused irregularities in water distribution, which affect the soil drying-wetting cycle and the development of economically important agricultural crops. Therefore, the use of plant growth-promoting bacteria (PGPB) emerges as an efficient strategy to mitigate negative impacts on crop yield. We hypothesized that the use of PGPB (in consortium or not) had potential to promote maize (Zea mays L.) growth under a soil moisture gradient in both non-sterile and sterile soils. Thirty PGPB strains were characterized for direct plant growth-promotion and drought tolerance induction mechanisms and were used in two independent experiments. Four soil water contents were used to simulate a severe drought (30% of field capacity [FC]), moderate drought (50% of FC), no drought (80% of FC) and, finally, a water gradient comprising the three mentioned soil water contents (80%, 50%, and 30% of FC). Two bacteria strains (BS28-7 Arthrobacter sp. and BS43 Streptomyces alboflavus), in addition to three consortia (BC2, BC4 and BCV) stood out in maize growth performance in experiment 1 and were used in experiment 2. Overall, under moderate drought, inoculation with BS43 surpassed the control treatment in root dry mass and nutrient uptake. Considering the water gradient treatment (80-50-30% of FC), the greatest total biomass was found in the uninoculated treatment when compared to BS28-7, BC2, and BCV. The greatest development of Z. mays L. was only observed under constant water stress conditions in the presence of PGPB. This is the first report that demonstrated the negative effect of individual inoculation of Arthrobacter sp. and the consortium of this strain with Streptomyces alboflavus on the growth of Z. mays L. based on a soil moisture gradient; however, future studies are needed for further validation.

Identification of QTN-by-environment interactions for yield related traits in maize under multiple abiotic stresses

INTRODUCTION

Quantitative trait nucleotide (QTN)-by-environment interactions (QEIs) play an increasingly essential role in the genetic dissection of complex traits in crops as global climate change accelerates. The abiotic stresses, such as drought and heat, are the major constraints on maize yields. Multi-environment joint analysis can improve statistical power in QTN and QEI detection, and further help us to understand the genetic basis and provide implications for maize improvement.

METHODS

In this study, 3VmrMLM was applied to identify QTNs and QEIs for three yield-related traits (grain yield, anthesis date, and anthesis-silking interval) of 300 tropical and subtropical maize inbred lines with 332,641 SNPs under well-watered and drought and heat stresses.

RESULTS

Among the total 321 genes around 76 QTNs and 73 QEIs identified in this study, 34 known genes were reported in previous maize studies to be truly associated with these traits, such as ereb53 (GRMZM2G141638) and thx12 (GRMZM2G016649) associated with drought stress tolerance, and hsftf27 (GRMZM2G025685) and myb60 (GRMZM2G312419) associated with heat stress. In addition, among 127 homologs in Arabidopsis out of 287 unreported genes, 46 and 47 were found to be significantly and differentially expressed under drought vs well-watered treatments, and high vs. normal temperature treatments, respectively. Using functional enrichment analysis, 37 of these differentially expressed genes were involved in various biological processes. Tissue-specific expression and haplotype difference analysis further revealed 24 candidate genes with significantly phenotypic differences across gene haplotypes under different environments, of which the candidate genes GRMZM2G064159, GRMZM2G146192, and GRMZM2G114789 around QEIs may have gene-by-environment interactions for maize yield.

DISCUSSION

All these findings may provide new insights for breeding in maize for yield-related traits adapted to abiotic stresses.

Functional analysis of a late embryogenesis abundant protein ZmNHL1 in maize under drought stress

Maize is an important feed and industrial cereal crop and is crucial for global food security. The development of drought-tolerant genotypes is a major aim of breeding programs to fight water scarcity and maintain sustainable maize production. Late embryogenesis abundant (LEA) proteins are a family of proteins related to osmotic regulation that widely exist in organisms. Here, we implemented a previously generated maize transcriptomic dataset to identify a drought-responsive gene designated ZmNHL1. Bioinformatics analysis of ZmNHL1 showed that the protein encoded by ZmNHL1 belongs to the LEA-2 protein family. Tissue specific expression analysis showed that ZmNHL1 is relatively abundant in stems and leaves, highly expressed in tassels and only slightly expressed in roots, pollens and ears. Moreover, the activity of SOD and POD of plants from three 35S::ZmNHL1 transgenic lines under either the induced drought stress conditions (by 20% PEG6000) or the natural water deficit treatment (by water withholding) were higher than that of the WT plants, while the electrolyte leakage of the 35S::ZmNHL1 transgenic plants was lower than that of the WT plants under both drought treatments. Our data further revealed that ZmNHL1 promotes maize tolerance to drought stress in 35S::ZmNHL1 transgenic plants by improving ROS scavenging and maintaining the cell membrane permeability. Overall, our data revealed that ZmNHL1 promotes maize tolerance to drought stress and contributes to provide elite germplasm resources for maize drought tolerance breeding programs.

Genome-wide identification of HD-ZIP transcription factors in maize and their regulatory roles in promoting drought tolerance

Drought is the main limiting factor of maize productivity, therefore improving drought tolerance in maize has potential practical importance. Cloning and functional verification of drought-tolerant genes is of great importance to understand molecular mechanisms under drought stress. Here, we employed a bioinformatic pipeline to identify 42 ZmHDZ drought responsive genes using previously reported maize transcriptomic datasets. The coding sequences, exon-intron structure and domain organization of all the 42 genes were identified. Phylogenetic analysis revealed evolutionary conservation of members of the ZmHDZ genes in maize. Several regulatory elements associated with drought tolerance were identified in the promoter regions of ZmHDZ genes, indicating the implication of these genes in plant response to drought stress. 42 ZmHDZ genes were distributed unevenly on 10 chromosomes, and 24 pairs of gene duplications were the segmental duplication. The expression of several ZmHDZ genes was upregulated under drought stress, and ZmHDZ9 overexpressing transgenic plants exhibited higher SOD and POD activities and higher accumulation of soluble proteins under drought stress which resulted in enhanced developed phenotype and improved resistance. The present study provides evidence for the evolutionary conservation of HD-ZIP transcription factors homologs in maize. The results further provide a comprehensive insight into the roles of ZmHDZ genes in regulating drought stress tolerance in maize.

A bZIP transcription factor VabZIP12 from blueberry induced by dark septate endocyte improving the salt tolerance of transgenic Arabidopsis

Dark septate endophytes (DSEs) have attracted much attention due to their positive roles in plant growth as well as resistance to various abiotic stresses. However, there are no reports on the molecular mechanisms of DSE fungi to improve salt tolerance in plants. In this study, the blueberry seedlings inoculated with T010, a beneficial DSE fungus reported previously, grew more vigorously than the non-inoculated control under salt stress. Physiological indicators showed that T010 inoculation increased antioxidant activities of blueberry roots. To explore its molecular mechanism, we focused on the bZIP TFs VabZIP12, who was highly up-regulated with T010 inoculation under salt stress. Further studies showed that VabZIP12, as a transcription activator, could combine both G-Box 1 and G-Box 2 motifs. Moreover, overexpression of VabZIP12 enhanced salt stress tolerance through increasing the activities of the enzymatic antioxidants in the transgenic Arabidopsis with up-regulation the related genes. These results indicated that the induction of VabZIP12 contribute to improving the tolerance of blueberry to salt stress by T010 inoculation.

Overexpression of ZmPP2C55 positively enhances tolerance to drought stress in transgenic maize plants

Serine/threonine protein phosphatases play essential roles in plants. PP2C has diverse functions related to development and stress response, while little is known about the functions of PP2C genes with respect to a variety of stresses in maize. In the present study, three ZmPP2C genes, ZmPP2C55, ZmPP2C28, and ZmPP2C71, were identified. Subcellular localization demonstrated that ZmPP2C28 and ZmPP2C71 were nuclear proteins, and ZmPP2C55 was located in both the nucleus and cytoplasm. qRT-PCR analysis showed that ZmPP2C55, ZmPP2C28, and ZmPP2C71 were expressed in roots, leaves and stems, and the three genes were responsive to drought, salt, high-temperature stress and exogenous ABA treatment. To explore the function of the ZmPP2C gene, ZmPP2C55-overexpressing transgenic lines were generated. The transgenic plants exhibited higher RWC, proline content, POD and SOD activities, GSH content and GSH/GSSG ratio and lower MDA content, electrolyte leakage and GSSG content compared with WT plants under natural stress treatment when seedlings were at the three-leaf. Our results illustrated that the overexpression of ZmPP2C55 positively enhanced tolerance to drought stress.

Systematic analysis of differentially expressed ZmMYB genes related to drought stress in maize

MYB transcription factors play pivotal roles in hormone conduction signaling and abiotic stress response. In this study, 54 differentially expressed ZmMYB genes were identified and comprehensive analyses were conducted including gene's structure, chromosomal localization, phylogenetic tree, motif prediction, cis-elements and expression patterns. The results showed that 54 genes were unevenly distributed on 10 chromosomes and classified into eleven main subgroups by phylogenetic analysis, supported by motif and exon/intron analyses. The mainly stress-related cis-elements were ABRE, ARE, MBS and DRE-core. In addition, 8 core ZmMYB genes were identified by co-expression network. qRT-PCR results showed that the 8 ZmMYB genes exhibited different expression levels under different abiotic stresses, indicating that they were responsive to various abiotic stress. These results will provide insight for further functional investigation of ZmMYB genes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01013-2.

Maize ZmbZIP33 Is Involved in Drought Resistance and Recovery Ability Through an Abscisic Acid-Dependent Signaling Pathway

Analyzing the transcriptome of maize leaves under drought stress and rewatering conditions revealed that transcription factors were involved in this process, among which ZmbZIP33 of the ABSCISIC ACID-INSENSITIVE 5-like protein 5 family was induced to significantly up-regulated. The functional mechanism of ZmbZIP33 in Abscisic acd (ABA) signaling pathway and its response to drought stress and rewatering has not been studied yet. The present study found that ZmbZIP33 contains a DNA-binding and dimerization domain, has transcriptional activation activity, and is highly homologous to SbABI1,SitbZIP68 and OsABA1. The expression of ZmbZIP33 is strongly up-regulated by drought, high salt, high temperature, and ABA treatments. Overexpression of ZmbZIP33 remarkably increased chlorophyll content and root length after drought stress and rewatering, and, moreover, cause an accumulation of ABA content, thereby improving drought resistance and recovery ability in Arabidopsis. However, silencing the expression of ZmbZIP33 (BMV-ZmbZIP33) remarkably decreased chlorophyll content, ABA content, superoxide dismutase and peroxidase activities, and increased stomatal opening and water loss rate compared with BMV (control). It showed that silencing ZmbZIP33 lead to reduced drought resistance and recovery ability of maize. ABA sensitivity analysis found that 0.5 and 1 μmol/L treatments severely inhibited the root development of overexpression ZmbZIP33 transgenic Arabidopsis. However, the root growth of BMV was greatly inhibited for 1 and 5μmol/L ABA treatments, but not for BMV-ZmbZIP33. Subcellular localization, yeast two-hybrid and BIFC further confirmed that the core components of ABA signaling pathways ZmPYL10 and ZmPP2C7 interacted in nucleus, ZmPP2C7 and ZmSRK2E as well as ZmSRK2E and ZmbZIP33 interacted in the plasma membrane. We also found that expression levels of ZmPYL10 and ZmSRK2E in the BMV-ZmbZIP33 mutant were lower than those of BMV, while ZmPP2C7 was the opposite under drought stress and rewatering. However, expression of ZmPYL10 and ZmSRK2E in normal maize leaves were significantly up-regulated by 3-4 folds after drought and ABA treatments for 24 h, while ZmPP2C7 was down-regulated. The NCED and ZEP encoding key enzymes in ABA biosynthesis are up-regulated in overexpression ZmbZIP33 transgenic line under drought stress and rewatering conditions, but down-regulated in BMV-ZmbZIP33 mutants. Together, these findings demonstrate that ZmbZIP33 played roles in ABA biosynthesis and regulation of drought response and rewatering in Arabidopsis and maize thought an ABA-dependent signaling pathway.

Using single-plant-omics in the field to link maize genes to functions and phenotypes

Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

Genome-Wide Analyses and Prediction of Resistance to MLN in Large Tropical Maize Germplasm

Maize lethal necrosis (MLN), caused by co-infection of maize chlorotic mottle virus and sugarcane mosaic virus, can lead up to 100% yield loss. Identification and validation of genomic regions can facilitate marker assisted breeding for resistance to MLN. Our objectives were to identify marker-trait associations using genome wide association study and assess the potential of genomic prediction for MLN resistance in a large panel of diverse maize lines. A set of 1400 diverse maize tropical inbred lines were evaluated for their response to MLN under artificial inoculation by measuring disease severity or incidence and area under disease progress curve (AUDPC). All lines were genotyped with genotyping by sequencing (GBS) SNPs. The phenotypic variation was significant for all traits and the heritability estimates were moderate to high. GWAS revealed 32 significantly associated SNPs for MLN resistance (at p < 1.0 × 10⁻⁶). For disease severity, these significantly associated SNPs individually explained 3–5% of the total phenotypic variance, whereas for AUDPC they explained 3–12% of the total proportion of phenotypic variance. Most of significant SNPs were consistent with the previous studies and assists to validate and fine map the big quantitative trait locus (QTL) regions into few markers’ specific regions. A set of putative candidate genes associated with the significant markers were identified and their functions revealed to be directly or indirectly involved in plant defense responses. Genomic prediction revealed reasonable prediction accuracies. The prediction accuracies significantly increased with increasing marker densities and training population size. These results support that MLN is a complex trait controlled by few major and many minor effect genes.