Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass.

BACKGROUND: Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. RESULTS: In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. CONCLUSION: Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

Bioprospecting of exopolysaccharides from the endophytic fungi Epicoccum sorghinum AMFS4, for its structure, composition, bioactivities and application in seed priming.

The endophytic fungi, Epicoccum sorghinum AMFS4 was investigated for its metabolic components and composition of bioactive exopolysaccharides (EPS). Metabolic analysis of the ethyl acetate extract majorly detected sugars derivatives such as, 4-Cholesten-3-one semicarbazone (20.9%), d-Fructose (18.96%), and α-d-Galactopyranosiduronicacid (1.71%). The growth curve and EPS yield were determined as 12.22 ± 1.02 g/L and 7.41 ± 0.32 g/L (dry weight) respectively on day 8. The deproteined EPS has been characterised with pyranose ring linked by α-glycosidic bonds, composing fructose, galactose and glucose monosaccharides validated by HPLC. Total sugar content was found to be 93.18 ± 0.81% with detection of proteins and uronate. The viscous EPS appeared filamentous under SEM observation and behaves as emulsifier with notable antioxidant properties. Priming of EPS on tomato seeds showed early induction of secondary rooting than in the control seedlings. Thus, E. sorghinum AMFS4 synthesises bioactive EPS with simple carbohydrate structure, good water absorption and significant metabolic influence on seed germination.

Tools and Techniques to Accelerate Crop Breeding.

As climate changes and a growing global population continue to escalate the need for greater production capabilities of food crops, technological advances in agricultural and crop research will remain a necessity. While great advances in crop improvement over the past century have contributed to massive increases in yield, classic breeding schemes lack the rate of genetic gain needed to meet future demands. In the past decade, new breeding techniques and tools have been developed to aid in crop improvement. One such advancement is the use of speed breeding. Speed breeding is known as the application of methods that significantly reduce the time between crop generations, thereby streamlining breeding and research efforts. These rapid-generation advancement tactics help to accelerate the pace of crop improvement efforts to sustain food security and meet the food, feed, and fiber demands of the world's growing population. Speed breeding may be achieved through a variety of techniques, including environmental optimization, genomic selection, CRISPR-Cas9 technology, and epigenomic tools. This review aims to discuss these prominent advances in crop breeding technologies and techniques that have the potential to greatly improve plant breeders' ability to rapidly produce vital cultivars.

Development of a Reference Transcriptome and Identification of Differentially Expressed Genes Linked to Salt Stress in Salt Marsh Grass (Sporobolus alterniflorus) along Delaware Coastal Regions.

Salt marsh grass (Sporobolus alterniflorus) plays a crucial role in Delaware coastal regions by serving as a physical barrier between land and water along the inland bays and beaches. This vegetation helps to stabilize the shoreline and prevent erosion, protecting the land from the powerful forces of the waves and tides. In addition to providing a physical barrier, salt marsh grass is responsible for filtering nutrients in the water, offering an environment for aquatic species and presenting a focal point of study for high salt tolerance in plants. As seawater concentrations vary along the Delaware coast from low to medium to high salinity, our study seeks to identify the impact of salt tolerance in marsh grass and to identify genes associated with salt tolerance levels. We developed more than 211,000 next-generation-sequencing (Illumina) transcriptomic reads to create a reference transcriptome from low-, medium-, and high-salinity marsh grass leaf samples collected from the Delaware coastline. Contiguous sequences were annotated based on a homology search using BLASTX against rice (Oryza sativa), foxtail millet (Setaria italica), and non-redundant species within the Viridiplantae database. Additionally, we identified differentially expressed genes related to salinity stress as candidates for salt stress qPCR analysis. The data generated from this study may help to elucidate the genetic signatures and physiological responses of plants to salinity stress, thereby offering valuable insight into the use of innovative approaches for gene expression studies in crops that are less salt tolerant.

Comprehensive Proteomic Analysis of Common Bean (Phaseolus vulgaris L.) Seeds Reveal Shared and Unique Proteins Involved in Terminal Drought Stress Response in Tolerant and Sensitive Genotypes.

This study identified proteomic changes in the seeds of two tolerant (SB-DT3 and SB-DT2) and two sensitive (Merlot and Stampede) common bean genotypes in response to terminal drought stress. Differentially expressed proteins (DEPs) were abundant in the susceptible genotype compared to the tolerant line. DEPs associated with starch biosynthesis, protein-chromophore linkage, and photosynthesis were identified in both genotypes, while a few DEPs and enriched biological pathways exhibited genotype-specific differences. The tolerant genotypes uniquely showed DEPs related to sugar metabolism and plant signaling, while the sensitive genotypes displayed more DEPs involved in plant-pathogen interaction, proteasome function, and carbohydrate metabolism. DEPs linked with chaperone and signal transduction were significantly altered between both genotypes. In summary, our proteomic analysis revealed both conserved and genotype-specific DEPs that could be used as targets in selective breeding and developing drought-tolerant common bean genotypes.

Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean (Phaseolus vulgaris L.) in Response to Terminal Drought Stress.

We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.

Comparative Analysis of Untargeted Metabolomics in Tolerant and Sensitive Genotypes of Common Bean (Phaseolus vulgaris L.) Seeds Exposed to Terminal Drought Stress.

Many environmental stresses can affect the accumulation of metabolites in plants, including drought. In the present study, we found a great deal of variability in the seed metabolic profiles of the tolerant (Matterhorn, SB-DT2 and SB-DT3) common bean genotypes in comparison to the sensitive genotypes (Sawtooth, Merlot and Stampede) using ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS). The genotypes were grown in the field and subjected to drought stress after flowering (terminal drought stress). We aimed to investigate the accumulation of genotype-specific metabolites and related pathways under terminal drought stress by comparing tolerant and sensitive genotypes within a race. A total of 26 potential metabolites were identified across genotype comparisons. Significant metabolic pathways, including monobactam biosynthesis, flavone and flavonol biosynthesis, pentose phosphate pathway, C5-branched dibasic acid metabolism, cysteine and methionine metabolism, vitamin B6 metabolism and flavonoid biosynthesis, were derived from the enriched metabolites. Many of these metabolic pathways were specific and varied with genotype comparisons. SB-DT2 vs. stampede revealed more significant metabolites and metabolic pathways compared to Matterhorn vs. Sawtooth and SB-DT3 vs. Merlot under terminal drought stress. Our study provides useful information regarding the metabolite profiles of seeds and their related pathways in comparisons of tolerant and sensitive common bean genotypes under terminal drought conditions. Further research, including transcriptomic and proteomic analyses, may contribute to a better understanding of molecular mechanisms and nutritional differences among seeds of common bean genotypes grown under terminal drought conditions.

Characterization and Expression Analysis of Common Bean Histone Deacetylase 6 during Development and Cold Stress Response.

Histone deacetylases (HDACs) are important regulators of gene transcription thus controlling multiple cellular processes. Despite its essential role in plants, HDA6 is yet to be validated in common bean. In this study, we show that HDA6 is involved in plant development and stress response. Differential expression of HDA6 was determined in various tissues and the expression was seen to be upregulated with plant age (seedling < flowering < maturity). Higher expression was observed in flowers and pods than in stem, leaf, and root. Upregulation of HDA6 gene during cold stress implies its prominent role in abiotic stress. Furthermore, the HDA6 gene was isolated from three common bean genotypes and sequence analyses revealed homology with functionally characterized homologs in model species. The 53 kDa translated product was detected using an HDA6 specific antibody and recombinant protein overexpressed in Escherichia coli showed HDAC activity in vitro. To our knowledge, this is the first report in the agriculturally important crop common bean describing the functional characterization and biological role of HDA6.