A ras-related small GTP-binding protein, RabE1c, regulates stomatal movements and drought stress responses by mediating the interaction with ABA receptors

BrMYB116 transcription factor enhances Cd stress tolerance by activating FIT3 in yeast and Chinese cabbage

Cd (cadmium) is a highly toxic heavy metal pollutant often present in soil and detrimentally impacting the production and quality of horticultural crops. Cd affects various physiological and biochemical processes in plants, including chlorophyll synthesis, photosynthesis, mineral uptake and accumulation, and hormonal imbalance, leading to cell death. The MYB family of transcription factors plays a significant role in plant response to environmental influences. However, the role of MYB116 in abiotic stress tolerance remains unclear. In this study, we reported that Chinese cabbage transcription factor BrMYB116 enhanced Cd stress tolerance in yeast. The expression level of BrMYB116 was increased by Cd stress in Chinese cabbage. Additionally, yeast cells overexpressing BrMYB116 showed improved Cd stress tolerance and reduced Cd accumulation. Moreover, we found that BrMYB116 interacted with facilitator of iron transport (FIT3) to enhance Cd stress tolerance. ChIP-qPCR results showed that ScFIT3 was activated through specific binding to its promoter. Additionally, the overexpression of ScFIT3 induced Cd stress tolerance and reduced Cd accumulation in yeast and Chinese cabbage. These results suggest new avenues for plant genomic modification to mitigate Cd toxicity and enhance the safety of vegetable production.

The role of Rab GTPase in Plant development and stress

Small GTPase is a type of crucial regulator in eukaryotes. It acts as a molecular switch by binding with GTP and GDP in cytoplasm, affecting various cellular processes. Small GTPase were divided into five subfamilies based on sequence, structure and function: Ras, Rho, Rab, Arf/Sar and Ran, with Rab being the largest subfamily. Members of the Rab subfamily play an important role in regulating complex vesicle transport and microtubule system activity. Plant cells are composed of various membrane-bound organelles, and vesicle trafficking is fundamental to the existence of plants. At present, the function of some Rab members, such as RabA1a, RabD2b/c and RabF2, has been well characterized in plants. This review summarizes the role of Rab GTPase in regulating plant tip growth, morphogenesis, fruit ripening and stress response, and briefly describes the regulatory mechanisms involved. It provides a reference for further alleviating environmental stress, improving plant resistance and even improving fruit quality.

Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes

Drought stress poses a severe threat to global wheat production, necessitating an in-depth exploration of the genetic basis for drought tolerance associated traits. This study employed a 90 K SNP array to conduct a genome-wide association analysis, unravelling genetic determinants of key traits related to drought tolerance in wheat, namely plant height, root length, and root and shoot dry weight. Using the mixed linear model (MLM) method on 125 wheat accessions subjected to both well-watered and drought stress treatments, we identified 53 SNPs significantly associated with stress susceptibility (SSI) and tolerance indices (STI) for the targeted traits. Notably, chromosomes 2A and 3B stood out with ten and nine associated markers, respectively. Across 17 chromosomes, 44 unique candidate genes were pinpointed, predominantly located on the distal ends of 1A, 1B, 1D, 2A, 3A, 3B, 4A, 6A, 6B, 7A, 7B, and 7D chromosomes. These genes, implicated in diverse functions related to plant growth, development, and stress responses, offer a rich resource for future investigation. A clustering pattern emerged, notably with seven genes associated with SSI for plant height and four genes linked to both STI of plant height and shoot dry weight, converging on specific regions of chromosome arms of 2AS and 3BL. Additionally, shared genes encoding polygalacturonase, auxilin-related protein 1, peptide deformylase, and receptor-like kinase underscored the interconnectedness between plant height and shoot dry weight. In conclusion, our findings provide insights into the molecular mechanisms governing wheat drought tolerance, identifying promising genomic loci for further exploration and crop improvement strategies.

Analysis on the salt tolerance of Nitraria sibirica Pall. based on Pacbio full-length transcriptome sequencing

KEY MESSAGE

Nitraria sibirica Pall. regulates its tolerance to salt stress mainly by adjusting ion balance, modifying cell wall structure, and activating signal transduction pathways. N. sibirica, as a typical halophyte, can not only effectively restore saline-alkali land, but also has high economic value. However, studies on its salt tolerance at combining molecular and physiological levels were limited. In this study, the salt tolerance of N. sibirica was analyzed based on Pacbio full-length transcriptome sequencing, and the salt tolerance in the physiological level was verified by key genes. The results showed that 89,017 full-length transcripts were obtained, of which 84,632 sequences were annotated. A total of 86,482 coding sequences (CDS) were predicted and 6561 differentially expressed genes (DEGs) were identified. DEGs were significantly enriched in "sodium ion homeostasis", "response to osmotic stress", "reactive oxygen species metabolic process", "defense response by cell wall thickening", "signal transduction", etc. The expression levels for most of these DEGs increased under salt stress. A total of 69 key genes were screened based on weighted gene co-expression network analysis (WGCNA), of which 33 were first reported on salt tolerance. Moreover, NsRabE1c gene with the highest expression level was selected to verify its salt tolerance. Over-expression of NsRabE1c gene enhanced the germination potential and root length of transgenic Arabidopsis thaliana plants without salt treatment as compared to those of Col-0 and AtRabE1c mutant. The expression levels of NsRabE1c decreased in the growth stagnation phase, while significantly increased in the growth recovery phase under salt stress. We predicted that NsRabE1c gene help N. sibirica resist salt stress through the regulation of plant growth. The results of this study deepen the understanding of salinity resistance in N. sibirica.

Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance

Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.

Genome-wide identification and expression analysis of the HD2 protein family and its response to drought and salt stress in Gossypium species

Histone deacetylase 2 (HD2) proteins play an important role in the regulation of gene expression. This helps with the growth and development of plants and also plays a crucial role in responses to biotic and abiotic stress es. HD2s comprise a C₂H₂-type Zn²⁺ finger at their C-terminal and an HD2 label, deacetylation and phosphorylation sites, and NLS motifs at their N-terminal. In this study, a total of 27 HD2 members were identified, using Hidden Markov model profiles, in two diploid cotton genomes (Gossypium raimondii and Gossypium arboretum) and two tetraploid cotton genomes (Gossypium hirsutum and Gossypium barbadense). These cotton HD2 members were classified into 10 major phylogenetic groups (I-X), of which group III was found to be the largest with 13 cotton HD2 members. An evolutionary investigation showed that the expansion of HD2 members primarily occurred as a result of segmental duplication in paralogous gene pairs. Further qRT-PCR validation of nine putative genes using RNA-Seq data suggested that GhHDT3D.2 exhibits significantly higher levels of expression at 12h, 24h, 48h, and 72h of exposure to both drought and salt stress conditions compared to a control measure at 0h. Furthermore, gene ontology, pathways, and co-expression network study of GhHDT3D.2 gene affirmed their significance in drought and salt stress responses.

Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS

Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar 'Chinese Spring' detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci.

Pinpointing genomic loci for drought-induced proline and hydrogen peroxide accumulation in bread wheat under field conditions

BACKGROUND

Proline (Pro) and hydrogen peroxide (H₂O₂) play a critical role in plants during drought adaptation. Genetic mapping for drought-induced Pro and H₂O₂ production under field conditions is very limited in crop plants since their phenotyping with large populations is labor-intensive. A genome-wide association study (GWAS) of a diversity panel comprised of 184 bread wheat cultivars grown in natural field (control) and rain-out shelter (drought) environments was performed to identify candidate loci and genes regulating Pro and H₂O₂ accumulation induced by drought.

RESULTS

The GWAS identified top significant marker-trait associations (MTAs) on 1A and 2A chromosomes, respectively for Pro and H₂O₂ in response to drought. Similarly, MTAs for stress tolerance index (STI) of Pro and H₂O₂ were identified on 5B and 1B chromosomes, respectively. Total 143 significant MTAs were identified including 36 and 71 were linked to drought and 2 and 34 were linked to STI for Pro and H₂O_2, respectively. Next, linkage disequilibrium analysis revealed minor alleles of significant single-markers and haplotypes were associated with higher Pro and H₂O₂ accumulation under drought. Several putative candidate genes for Pro and H₂O₂ content encode proteins with kinase, transporter or protein-binding activities.

CONCLUSIONS

The identified genetic factors associated with Pro and H₂O₂ biosynthesis underlying drought adaptation lay a fundamental basis for functional studies and future marker-assisted breeding programs.

AtHD2D, a plant-specific histone deacetylase involved in abscisic acid response and lateral root development

In eukaryotes, histone acetylation levels directly regulate downstream gene expression. As a plant-specific histone deacetylase (HDAC), HD2D is involved in plant development and abiotic stress. However, the response of HD2D to drought stress and its interacting proteins, is still unclear. In this study, we analysed HD2D gene expression patterns in Arabidopsis, revealing that HD2D gene was highly expressed in roots and rosette leaves, but poorly expressed in other tissues such as stems, flowers, and young siliques. The HD2D gene expression was induced by d-mannitol. We investigated the responses to drought stress in the wild-type plant, HD2D overexpression lines, and hd2d mutants. HD2D-overexpressing lines showed abscisic acid (ABA) hypersensitivity and drought tolerance, and these phenotypes were not present in hd2d mutants. RNA-seq analysis revealed the transcriptome changes caused by HD2D under drought stress, and showed that HD2D responded to drought stress via the ABA signalling pathway. In addition, we demonstrated that CASEIN KINASE II (CKA4) directly interacted with HD2D. The phosphorylation of Ser residues on HD2D by CKA4 enhanced HD2D enzymatic activity. Furthermore, the phosphorylation of HD2D was shown to contribute to lateral root development and ABA sensing in Arabidopsis, but, these phenotypes could not be reproduced by the overexpression of Ser-phospho-null HD2D lines. Collectively, this study suggests that HD2D responded to drought stress by regulating the ABA signalling pathway, and the expression of drought stress-related genes. The regulatory mechanism of HD2D mediated by CKII phosphorylation provides new insights into the ABA response and lateral root development in Arabidopsis.

Growth-Defense Trade-Offs Induced by Long-term Overgrazing Could Act as a Stress Memory

Long-term overgrazing (OG) is one of the key drivers of global grassland degradation with severe loss of productivity and ecosystem functions, which may result in stress memory such as smaller stature of grassland plants. However, how the OG-induced stress memory could be regulated by phytohormones is unknown. In this study, we investigated the changes of four phytohormones of cloned offspring of Leymus chinensis that were developed from no-grazing (NG) plants and OG plants with a grazing history of 30 years. The concentrations of auxin (IAA) and gibberellic acid (GA) in OG plant leaves were 45% and 20% lower than control, respectively. Meanwhile, the level of abscisic acid (ABA) in OG leaves nearly doubled compared with that in NG leaves. The situation was quite similar in roots. Unexpectedly, no significant changes in the jasmonic acid (JA) level were observed between OG and NG plants. The changes in gene expression patterns between OG and NG plants were also investigated by transcriptomic analysis. In total, 302 differentially expressed genes (DEGs) were identified between OG and NG plants, which were mainly classified into the functions of synthesis, receptor, and signal transduction processes of phytohormones. The expression of 24 key genes related to the biosynthesis and signal transduction of IAA and GA was downregulated in OG plants. Among them, OASA1 and AO1 (regulating the biosynthesis of IAA and ABA, respectively) were reduced significantly by 88 and 92%, respectively. In addition, the content of secondary metabolites related to plant defense such as flavonoids and phenols was also increased in leaves. Taken together, the decrease of positive plant growth-related hormones (IAA and GA) together with the increase of plant stress-related hormones or factors (ABA, flavonoids, and phenols) induced the growth-defense trade-offs for L. chinensis adaptation to long-term OG stress. The findings reported in this study shed new light on the mechanism of plant-animal interaction in the grassland ecosystem and provide a deeper insight into optimizing grazing management and sustainable utilization of grassland.

Transcriptome Characterization of the Roles of Abscisic Acid and Calcium Signaling during Water Deficit in Garlic

Garlic (Allium sativum L.) is one of the most important vegetable crops, and breeding drought-tolerant varieties is a vital research goal. However, the underlying molecular mechanisms in response to drought stress in garlic are still limited. In this study, garlic seedlings were subjected to 15% PEG6000 for 0, 1, 4, and 12 h, respectively, to simulate drought stress. Changes of transcriptomes as a result of drought stress in garlic leaves were determined by de novo assembly using the Illumina platform. In total, 96,712 unigenes and 11,936 differentially expressed genes (DEGs) were identified in the presence of drought conditions. Transcriptome profiling revealed that the DEGs were mainly enriched in the biosynthesis of secondary metabolites, MAPK signaling pathway, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction. Genes involved in abscisic acid and calcium signaling were further investigated and discussed. Our results indicated that a coordinated interplay between abscisic acid and calcium is required for drought-induced response in garlic.