Genome-Wide Analysis of Heat Shock Transcription Factors in Ziziphus jujuba Identifies Potential Candidates for Crop Improvement Under Abiotic Stress

Characterization of the Heat Shock Transcription Factor Family in Lycoris radiata and Its Potential Roles in Response to Abiotic Stresses

Heat shock transcription factors (HSFs) are an essential plant-specific transcription factor family that regulates the developmental and growth stages of plants, their signal transduction, and their response to different abiotic and biotic stresses. The HSF gene family has been characterized and systematically observed in various species; however, research on its association with Lycoris radiata is limited. This study identified 22 HSF genes (LrHSFs) in the transcriptome-sequencing data of L. radiata and categorized them into three classes including HSFA, HSFB, and HSFC, comprising 10, 8, and 4 genes, respectively. This research comprises basic bioinformatics analyses, such as protein sequence length, molecular weight, and the identification of its conserved motifs. According to the subcellular localization assessment, most LrHSFs were present in the nucleus. Furthermore, the LrHSF gene expression in various tissues, flower developmental stages, two hormones stress, and under four different abiotic stresses were characterized. The data indicated that LrHSF genes, especially LrHSF5, were essentially involved in L. radiata development and its response to different abiotic and hormone stresses. The gene-gene interaction network analysis revealed the presence of synergistic effects between various LrHSF genes' responses against abiotic stresses. In conclusion, these results provided crucial data for further functional analyses of LrHSF genes, which could help successful molecular breeding in L. radiata.

Response Mechanisms of Woody Plants to High-Temperature Stress

High-temperature stress is the main environmental stress that restricts the growth and development of woody plants, and the growth and development of woody plants are affected by high-temperature stress. The influence of high temperature on woody plants varies with the degree and duration of the high temperature and the species of woody plants. Woody plants have the mechanism of adapting to high temperature, and the mechanism for activating tolerance in woody plants mainly counteracts the biochemical and physiological changes induced by stress by regulating osmotic adjustment substances, antioxidant enzyme activities and transcription control factors. Under high-temperature stress, woody plants ability to perceive high-temperature stimuli and initiate the appropriate physiological, biochemical and genomic changes is the key to determining the survival of woody plants. The gene expression induced by high-temperature stress also greatly improves tolerance. Changes in the morphological structure, physiology, biochemistry and genomics of woody plants are usually used as indicators of high-temperature tolerance. In this paper, the effects of high-temperature stress on seed germination, plant morphology and anatomical structure characteristics, physiological and biochemical indicators, genomics and other aspects of woody plants are reviewed, which provides a reference for the study of the heat-tolerance mechanism of woody plants.

Evaluation of drought-tolerant endophytic fungus Talaromyces purpureogenus as a bioinoculant for wheat seedlings under normal and drought-stressed circumstances

The present work is aimed to hypothesize that fungal endophytes associated with wheat (Triticum aestivum L.) plants can play a variety of roles in biotechnology including plant growth. Out of 67 fungal isolates, five maximum drought-tolerant isolates were used to check their various plant growth-promoting traits, antioxidants, and antifungal activities under secondary screening. Fungal isolate #8TAKS-3a exhibited the maximum drought tolerance capacity and potential to produce auxin, gibberellic acid, ACC deaminase, phosphate, zinc solubilization, ammonia, siderophore, and extracellular enzyme activities followed by #6TAKR-1a isolate. In terms of antioxidant activities, #8TAKS-3a culture also showed maximum DPPH scavenging, total antioxidant, and NO-scavenging activities. However, #6TAKR-1a exhibited maximum total flavonoid content, total phenolic content, and Fe-reducing power and also the highest growth inhibition of Aspergillus niger (ITCC 6152) and Colletotrichum sp. (ITCC 6152). Based on morphological characters and multi-locus phylogenetic analysis of the nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS), β-tubulin (TUB 2), and RNA polymerase II second largest subunit (RPB2) genes, potent fungal isolate #8TAKS-3a was identified as Talaromyces purpureogenus. Under the in vitro conditions, T. purpureogenus (#8TAKS-3a) was used as a bioinoculant that displayed a significant increase in various physio-biochemical growth parameters under normal and stressed conditions (p < 0.05). Our results indicate that drought stress-tolerant T. purpureogenus can be further used for field testing as a growth promoter.

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.

Genome-wide analysis of the heat shock transcription factor gene family in Sorbus pohuashanensis (Hance) Hedl identifies potential candidates for resistance to abiotic stresses

Heat shock transcription factors (Hsfs) are essential regulators of plant responses to abiotic stresses, growth, and development. However, all the Hsf family members have not been identified in Sorbus pohuashanensis. Therefore, the aim of this study was to identify the Hsf family members in S. pohuashanensis and examine their expression under abiotic stress conditions through the integration of gene structure, phylogenetic relationships, chromosome location, and expression patterns. Bioinformatics-based methods, identified 33 Hsfs in S. pohuashanensis. Phylogenetic analysis of Hsfs from S. pohuashanensis and other species revealed that they were more closely related to apples and white pears, followed by Populus trichocarpa, and most distantly related to Arabidopsis. Moreover, the Hsfs were clustered into three major groups: A, B, and C. Gene structure and conserved motif analysis revealed a high degree of conservation among members of the same class. Collinearity analysis revealed that segmental duplication played an essential role in increasing the size of the SpHsfs gene family in S. pohuashanensis. Additionally, several cis-acting elements associated with growth and development, hormone response, and stress were found in the promoter region of SpHsfs genes. Furthermore, expression analysis in various tissues of S. pohuashanensis showed that the genes were closely associated with heat, drought, salt stress, growth, and developmental processes. Overall, these results provide valuable information on the evolutionary relationships of the Hsf gene family. These genes stand as strong functional candidates for further studies on the resistance of S. pohuashanensis to abiotic stresses.

Genome-Wide Analysis and Expression Profile of Nuclear Factor Y (NF-Y) Gene Family in Z. jujuba

Nuclear factor-Y (NF-Y) is an important transcription factor in the plant species, which potentially provides a higher level of functional diversity including for abiotic stress tolerance. The genome-wide study and expression analysis of NF-Y gene family in Ziziphus, an elite abiotic stress-tolerant species, assist bioprospecting of genes. Here, a total of 32 NF-Y (8 NF-YA, 15 NF-YB, and 9 NF-YC) genes were identified in genome-wide search of Z. jujuba genome. Physicochemical properties, cellular localization, gene structure, chromosomal location, and protein motifs were analyzed for structural and functional understanding. Identified 12 NF-Ys were responsible for the expansion of NF-Y gene family by tandem duplication in Z. jujuba. Phylogenetic and comparative physical mapping of Z. jujuba NF-Ys with its orthologs illustrated evolutionary and functional insights into NF-Y gene family. A total of 45 perfect microsatellites (20bp to 40bp) were extracted across the ZjNF-Y genes. The promoter and gene ontology study suggested that Z. jujuba NF-Y gene family is functionally diverse and could play a wide-ranging role in plant abiotic stress, development, and cellular processes. An expression study revealed that large numbers of the NF-Ys are differentially expressed in response to drought and salinity. The total 15 and 18 ZjNF-Y genes that are upregulated under drought and salinity stress, respectively, are the potential candidates for further functional analysis for development of climate-resilient crops. The present study established a base for understanding the role of NF-Ys in Z. jujuba under abiotic stress conditions and paved a way for further research.