Genome-wide identification and abiotic stress response patterns of abscisic acid stress ripening protein family members in Triticum aestivum L

Genome-Wide Identification and Expression Profiling of ABA-Stress-Ripening (ASR) Gene Family in Barley (Hordeum vulgare L.)

Abscisic acid (ABA)-stress-ripening, or ABA-, stress-, and ripening-induced (ASR) proteins play an important role in responses to environmental stimuli. A total of ten barley HvASRs were identified in this study, which were unevenly distributed on three chromosomes. ASRs from barley, wheat, Brachypodium distachyon, rice, maize, foxtail millet, and tomato were classified into two distinct clusters based on phylogenetic analysis. Notably, ASRs from Poaceae were evenly distributed between these two clusters. HvASRs contained a typical ABA/WDS domain, and exhibited similar motif arrangements. Two gene pairs of tandem duplicates (HvASR4/5/6/7 and HvASR8/9) were identified among HvASRs. Cis-acting elements involved in hormone and stress responses, including ABRE, MYB, ARE, and STRE, were consistently identified in the promoters of HvASRs. The expression of HvASRs was substantially influenced by salt, osmotic, and ABA treatments in the roots and leaves of barley seedlings. HvASR2 acts as a transcriptional repressor, whereas HvASR3 serves as a transcriptional activator. These results enhance our understanding of the HvASR family and provide a foundation for further functional characterization.

Development History, Structure, and Function of ASR (Abscisic Acid-Stress-Ripening) Transcription Factor

Abiotic and biotic stress factors seriously affect plant growth and development. The process of plant response to abiotic stress involves the synergistic action of multiple resistance genes. The ASR (Abscisic acid stress-ripening) gene is a plant-specific transcription factor that plays a central role in regulating plant senescence, fruit ripening, and response to abiotic stress. ASR family members are highly conserved in plant evolution and contain ABA/WBS domains. ASR was first identified and characterized in tomatoes (Solanum lycopersicum L.). Subsequently, the ASR gene has been reported in many plant species, extending from gymnosperms to monocots and dicots, but lacks orthologues in Arabidopsis (Arabidopsis thaliana). The promoter regions of ASR genes in most species contain light-responsive elements, phytohormone-responsive elements, and abiotic stress-responsive elements. In addition, ASR genes can respond to biotic stresses via regulating the expression of defense genes in various plants. This review comprehensively summarizes the evolutionary history, gene and protein structures, and functions of the ASR gene family members in plant responses to salt stress, low temperature stress, pathogen stress, drought stress, and metal ions, which will provide valuable references for breeding high-yielding and stress-resistant plant varieties.

Insights into Salinity Tolerance in Wheat

Salt stress has a detrimental impact on food crop production, with its severity escalating due to both natural and man-made factors. As one of the most important food crops, wheat is susceptible to salt stress, resulting in abnormal plant growth and reduced yields; therefore, damage from salt stress should be of great concern. Additionally, the utilization of land in coastal areas warrants increased attention, given diminishing supplies of fresh water and arable land, and the escalating demand for wheat. A comprehensive understanding of the physiological and molecular changes in wheat under salt stress can offer insights into mitigating the adverse effects of salt stress on wheat. In this review, we summarized the genes and molecular mechanisms involved in ion transport, signal transduction, and enzyme and hormone regulation, in response to salt stress based on the physiological processes in wheat. Then, we surveyed the latest progress in improving the salt tolerance of wheat through breeding, exogenous applications, and microbial pathways. Breeding efficiency can be improved through a combination of gene editing and multiple omics techniques, which is the fundamental strategy for dealing with salt stress. Possible challenges and prospects in this process were also discussed.

Identification and analysis of BAHD superfamily related to malonyl ginsenoside biosynthesis in Panax ginseng

Introduction

The BAHD (benzylalcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase and deacetylvindoline 4-O-acetyltransferase), has various biological functions in plants, including catalyzing the biosynthesis of terpenes, phenolics and esters, participating in plant stress response, affecting cell stability, and regulating fruit quality.

Methods

Bioinformatics methods, real-time fluorescence quantitative PCR technology, and ultra-high-performance liquid chromatography combined with an Orbitrap mass spectrometer were used to explore the relationship between the BAHD gene family and malonyl ginsenosides in Panax ginseng.

Results

In this study, 103 BAHD genes were identified in P. ginseng, mainly distributed in three major clades. Most PgBAHDs contain cis-acting elements associated with abiotic stress response and plant hormone response. Among the 103 genes, 68 PgBAHDs are WGD (whole-genome duplication) genes. The significance of malonylation in biosynthesis has garnered considerable attention in the study of malonyltransferases. The phylogenetic tree results showed 34 PgBAHDs were clustered with genes that have malonyl characterization. Among them, seven PgBAHDs (PgBAHD4, 45, 65, 74, 90, 97, and 99) showed correlations > 0.9 with crucial enzyme genes involved in ginsenoside biosynthesis and > 0.8 with malonyl ginsenosides. These seven genes were considered potential candidates involved in the biosynthesis of malonyl ginsenosides.

Discussion

These results help elucidate the structure, evolution, and functions of the P. ginseng BAHD gene family, and establish the foundation for further research on the mechanism of BAHD genes in ginsenoside biosynthesis.

Wheat Omics: Advancements and Opportunities

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.

Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

C-repeat binding factors (CBFs) are transcription factors that are known to play important roles in plant cold acclimation. They are highly conserved in most higher plants. Taraxacum kok-saghyz (TKS) is an herb native to China and Kazakhstan and is well-known for its production of rubber silk with industrial and economic value. To understand cold acclimation mechanisms, we conducted a genome-wide discovery of the CBF family genes in TKS and revealed ten CBF genes. A bioinformatic analysis of the CBF genes was carried out to analyze the phylogenetic relationship, protein conservative motifs, protein physicochemical properties, gene structure, promoter cis-acting elements, and the gene expression patterns under cold acclimation and control conditions. It was found that most of these genes were highly responsive at the late stage of cold acclimation, indicating that they play important roles in the cold acclimation processes of TKS. This study provides a theoretical basis for the study of the molecular functions of the CBF gene family in TKS, and a useful guidance for the genetic improvement of the cold tolerance traits of TKS and other plants, including crops.

Genetic Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.)

Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first domesticated crop and is the most popular cereal crop in the world. Because of a lack of systematic research on cold signaling pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway under cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic processes and elements. This review also highlights possible strategies for improving cold tolerance in wheat.

The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.

TaASR1-D confers abiotic stress resistance by affecting ROS accumulation and ABA signalling in transgenic wheat

Cultivating new crop cultivars with multiple abiotic stress tolerances is important for crop production. The abscisic acid-stress-ripening (ASR) protein has been shown to confer abiotic stress tolerance in plants. However, the mechanisms of ASR function under stress condition remain largely unclear. In this study, we characterized all ASR family members in common wheat and constitutively overexpressed TaASR1-D in a commercial hexaploid wheat cultivar Zhengmai 9023. The transgenic wheat plants exhibited increased tolerance to multiple abiotic stresses and increased grain yields under salt stress condition. Overexpression of TaASR1-D conferred enhanced antioxidant capacity and ABA sensitivity in transgenic wheat plants. Further, RNA in situ hybridization results showed that TaASR1-D had higher expression levels in the vascular tissues of leaves and the parenchyma cells around the vascular tissues of roots and stems. Yeast one-hybrid and electrophoretic mobility shift assays revealed that TaASR1-D could directly bind the specific cis-elements in the promoters of TaNCED1 and TaGPx1-D. In conclusion, our findings suggest that TaASR1-D can be used to breed new wheat cultivars with increased multiple abiotic stress tolerances, and TaASR1-D enhances abiotic stress tolerances by reinforcing antioxidant capacity and ABA signalling.

Adaptation Strategies of Halophytic Barley Hordeum marinum ssp. marinum to High Salinity and Osmotic Stress

The adaptation strategies of halophytic seaside barley Hordeum marinum to high salinity and osmotic stress were investigated by nuclear magnetic resonance imaging, as well as ionomic, metabolomic, and transcriptomic approaches. When compared with cultivated barley, seaside barley exhibited a better plant growth rate, higher relative plant water content, lower osmotic pressure, and sustained photosynthetic activity under high salinity, but not under osmotic stress. As seaside barley is capable of controlling Na⁺ and Cl⁻ concentrations in leaves at high salinity, the roots appear to play the central role in salinity adaptation, ensured by the development of thinner and likely lignified roots, as well as fine-tuning of membrane transport for effective management of restriction of ion entry and sequestration, accumulation of osmolytes, and minimization of energy costs. By contrast, more resources and energy are required to overcome the consequences of osmotic stress, particularly the severity of reactive oxygen species production and nutritional disbalance which affect plant growth. Our results have identified specific mechanisms for adaptation to salinity in seaside barley which differ from those activated in response to osmotic stress. Increased knowledge around salt tolerance in halophytic wild relatives will provide a basis for improved breeding of salt-tolerant crops.