Genome wide identification, classification and functional characterization of heat shock transcription factors in cultivated and ancestral cottons (Gossypium spp.)

Polyploidization: A Biological Force That Enhances Stress Resistance

Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.

Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.

Genome-wide identification, classification, and expression analysis of heat shock transcription factor family in switchgrass (Panicum virgatum L.)

Switchgrass is one of the most promising bioenergy crops and is generally cultivated in arid climates and poor soils. Heat shock transcription factors (Hsfs) are key regulators of plant responses to abiotic and biotic stressors. However, their role and mechanism of action in switchgrass have not been elucidated. Hence, this study aimed to identify the Hsf family in switchgrass and understand its functional role in heat stress signal transduction and heat tolerance by using bioinformatics and RT-PCR analysis. Forty-eight PvHsfs were identified and divided into three main classes based on their gene structure and phylogenetic relationships: HsfA, HsfB, and HsfC. The results of the bioinformatics analysis showed a DNA-binding domain (DBD) at the N-terminal in PvHsfs, and they were not evenly distributed on all chromosomes except for chromosomes 8 N and 8 K. Many cis-elements related to plant development, stress responses, and plant hormones were identified in the promoter sequence of each PvHsf. Segmental duplication is the primary force underlying Hsf family expansion in switchgrass. The results of the expression pattern of PvHsfs in response to heat stress showed that PvHsf03 and PvHsf25 might play critical roles in the early and late stages of switchgrass response to heat stress, respectively, and HsfB mainly showed a negative response to heat stress. Ectopic expression of PvHsf03 in Arabidopsis significantly increased the heat resistance of seedlings. Overall, our research lays a notable foundation for studying the regulatory network in response to deleterious environments and for further excavating tolerance genes in switchgrass.

Genome-Wide Identification and Expression Analysis of HSF Transcription Factors in Alfalfa (Medicago sativa) under Abiotic Stress

Alfalfa (Medicago sativa) is one of the most important legume forage species in the world. It is often affected by several abiotic stressors that result in reduced yields and poor growth. Therefore, it is crucial to study the resistance of M. sativa to abiotic stresses. Heat shock transcription factors (HSF) are key players in a number of transcriptional regulatory pathways. These pathways play an essential role in controlling how plants react to different abiotic stressors. Studies on the HSF gene family have been reported in many species but have not yet undergone a thorough analysis in M. sativa. Therefore, in order to identify a more comprehensive set of HSF genes, from the genomic data, we identified 16 members of the MsHSF gene, which were unevenly distributed over six chromosomes. We also looked at their gene architectures and protein motifs, and phylogenetic analysis allowed us to divide them into 3 groups with a total of 15 subgroups. Along with these aspects, we then examined the physicochemical properties, subcellular localization, synteny analysis, GO annotation and enrichment, and protein interaction networks of amino acids. Finally, the analysis of 16 MsHSF genes' expression levels across all tissues and under four abiotic stresses using publicly available RNA-Seq data revealed that these genes had significant tissue-specific expression. Moreover, the expression of most MsHSF genes increased dramatically under abiotic stress, further validating the critical function played by the MsHSF gene family in abiotic stress. These results provided basic information about MsHSF gene family and laid a foundation for further study on the biological role of MsHSF gene in response to stress in M. sativa.

Functional Characterization of Heat Shock Factor (CrHsf) Families Provide Comprehensive Insight into the Adaptive Mechanisms of Canavalia rosea (Sw.) DC. to Tropical Coral Islands

Heat shock transcription factors (Hsfs) are key regulators in plant heat stress response, and therefore, they play vital roles in signal transduction pathways in response to environmental stresses, as well as in plant growth and development. Canavalia rosea (Sw.) DC. is an extremophile halophyte with good adaptability to high temperature and salt-drought tolerance, and it can be used as a pioneer species for ecological reconstruction on tropical coral islands. To date, very little is known regarding the functions of Hsfs in the adaptation mechanisms of plant species with specialized habitats, especially in tropical leguminous halophytes. In this study, a genome-wide analysis was performed to identify all the Hsfs in C. rosea based on whole-genome sequencing information. The chromosomal location, protein domain or motif organization, and phylogenetic relationships of 28 CrHsfs were analyzed. Promoter analyses indicated that the expression levels of different CrHsfs were precisely regulated. The expression patterns also revealed clear transcriptional changes among different C. rosea tissues, indicating that the regulation of CrHsf expression varied among organs in a developmental or tissue-specific manner. Furthermore, the expression levels of most CrHsfs in response to environmental conditions or abiotic stresses also implied a possible positive regulatory role of this gene family under abiotic stresses, and suggested roles in adaptation to specialized habitats such as tropical coral islands. In addition, some CrHsfAs were cloned and their possible roles in abiotic stress tolerance were functionally characterized using a yeast expression system. The CrHsfAs significantly enhanced yeast survival under thermal and oxidative stress challenges. Our results contribute to a better understanding of the plant Hsf gene family and provide a basis for further study of CrHsf functions in environmental thermotolerance. Our results also provide valuable information on the evolutionary relationships among CrHsf genes and the functional characteristics of the gene family. These findings are beneficial for further research on the natural ecological adaptability of C. rosea to tropical environments.

Genome-Wide Identification and Expression Analysis Elucidates the Potential Role of PFK Gene Family in Drought Stress Tolerance and Sugar Metabolism in Cotton

Drought has been identified as a major threat for global crop production worldwide. Phosphofructokinase (PFK) is vital for sugar metabolism. During phosphorylation, plants have two enzymes: ATP-dependent phosphofructokinase (PFK) and pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP). Genome-wide identification led to the identification of 80 PFK genes, 26 genes in G. hirsutum and G. barbadense, and 14 genes in G. arboreum and G. raimondii. Phylogenetic, gene structure, and motif analyses showed that PFK genes were grouped into two main categories, namely, PFK and PFP, with 18 and 8 genes in the allotetraploid species and 10 PFK and 4 PFP genes in the diploid species, respectively. Using the RNA-seq expressions of 26 genes from GhPFK, a co-expression network analysis was performed to identify the hub genes. GhPFK04, GhPFK05, GhPFK09, GhPFK11, GhPFK13, GhPFK14, and GhPFK17 in leaves and GhPFK02, GhPFK09, GhPFK11, GhPFK15, GhPFK16, and GhPFK17 in root tissues were found as hub genes. RT-qPCR analysis validated the expressions of identified hub genes. Interestingly, GhPFK11 and GhPFK17 were identified as common hub genes, and these might be the true candidate genes involved in the drought stress tolerance. In the KEGG enrichment analysis, amino acids such as L-valine, L-histidine, L-glutamine, L-serine, L-homoserine, L-methionine, L-cysteine, and gluconic acid were significantly upregulated, whereas sugars, mainly fructose-1-phosphate, D-mannitol, D-sorbitol, dulcitol, and lactose, were significantly downregulated during drought stress. Genome-wide analysis paves the way for a deeper understanding of the PFK genes and establishes the groundwork for future research into PFK’s role in enhancing drought stress tolerance and sugar metabolism in cotton.

Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress

BACKGROUND

Common bean (Phaseolus vulgaris) is an essential crop with high economic value. The growth of this plant is sensitive to environmental stress. Heat shock factor (Hsf) is a family of antiretroviral transcription factors that regulate plant defense system against biotic and abiotic stress. To date, few studies have identified and bio-analyzed Hsfs in common bean.

RESULTS

In this study, 30 Hsf transcription factors (PvHsf1-30) were identified from the PFAM database. The PvHsf1-30 belonged to 14 subfamilies with similar motifs, gene structure and cis-acting elements. The Hsf members in Arabidopsis, rice (Oryza sativa), maize (Zea mays) and common bean were classified into 14 subfamilies. Collinearity analysis showed that PvHsfs played a role in the regulation of responses to abiotic stress. The expression of PvHsfs varied across different tissues. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PvHsfs were differentially expressed under cold, heat, salt and heavy metal stress, indicating that PvHsfs might play different functions depending on the type of abiotic stress.

CONCLUSIONS

In this study, we identified 30 Hsf transcription factors and determined their location, motifs, gene structure, cis-elements, collinearity and expression patterns. It was found that PvHsfs regulates responses to abiotic stress in common bean. Thus, this study provides a basis for further analysis of the function of PvHsfs in the regulation of abiotic stress in common bean.

Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview

Temperature is one of the decisive environmental factors that is projected to increase by 1. 5°C over the next two decades due to climate change that may affect various agronomic characteristics, such as biomass production, phenology and physiology, and yield-contributing traits in oilseed crops. Oilseed crops such as soybean, sunflower, canola, peanut, cottonseed, coconut, palm oil, sesame, safflower, olive etc., are widely grown. Specific importance is the vulnerability of oil synthesis in these crops against the rise in climatic temperature, threatening the stability of yield and quality. The natural defense system in these crops cannot withstand the harmful impacts of heat stress, thus causing a considerable loss in seed and oil yield. Therefore, a proper understanding of underlying mechanisms of genotype-environment interactions that could affect oil synthesis pathways is a prime requirement in developing stable cultivars. Heat stress tolerance is a complex quantitative trait controlled by many genes and is challenging to study and characterize. However, heat tolerance studies to date have pointed to several sophisticated mechanisms to deal with the stress of high temperatures, including hormonal signaling pathways for sensing heat stimuli and acquiring tolerance to heat stress, maintaining membrane integrity, production of heat shock proteins (HSPs), removal of reactive oxygen species (ROS), assembly of antioxidants, accumulation of compatible solutes, modified gene expression to enable changes, intelligent agricultural technologies, and several other agronomic techniques for thriving and surviving. Manipulation of multiple genes responsible for thermo-tolerance and exploring their high expressions greatly impacts their potential application using CRISPR/Cas genome editing and OMICS technology. This review highlights the latest outcomes on the response and tolerance to heat stress at the cellular, organelle, and whole plant levels describing numerous approaches applied to enhance thermos-tolerance in oilseed crops. We are attempting to critically analyze the scattered existing approaches to temperature tolerance used in oilseeds as a whole, work toward extending studies into the field, and provide researchers and related parties with useful information to streamline their breeding programs so that they can seek new avenues and develop guidelines that will greatly enhance ongoing efforts to establish heat stress tolerance in oilseeds.