Transcriptome-wide m6A methylation profile reveals its potential role underlying drought response in wheat (Triticum aestivum L.).

MAIN CONCLUSION: This study revealed the transcriptome-wide m6A methylation profile under drought stress and found that TaETC9 might regulate drought tolerance through mediating RNA methylation in wheat. Drought is one of the most destructive environmental constraints limiting crop growth and development. N6-methyladenosine (m6A) is a prevalent and important post-transcriptional modification in various eukaryotic RNA molecules, playing the crucial role in regulating drought response in plants. However, the significance of m6A in wheat (Triticum aestivum L.), particularly its involvment in drought response, remains underexplored. In this study, we investigated the transcriptome-wide m6A profile under drought stress using parallel m6A immunoprecipitation sequencing (MeRIP-seq). Totally, 4221 m6A peaks in 3733 m6A-modified genes were obtained, of which 373 methylated peaks exhibited differential expression between the control (CK) and drought-stressed treatments. These m6A loci were significantly enriched in proximity to stop codons and within the 3'-untranslated region. Integration of MeRIP-seq and RNA-seq revealed a positive correlation between m6A methylation and mRNA abundance and the genes displaying both differential methylation and expression were obtained. Finally, qRT-PCR analyses were further performed and the results found that the m6A-binding protein (TaETC9) showed significant up-regulation, while the m6A demethylase (TaALKBH10B) was significantly down-regulated under drought stress, contributing to increased m6A levels. Furthermore, the loss-of-function mutant of TaECT9 displayed significantly higher drought sensitivity compared to the wild type, highlighting its role in regulating drought tolerance. This study reported the first wheat m6A profile associated with drought stress, laying the groundwork for unraveling the potential role of RNA methylation in drought responses and enhancing stress tolerance in wheat through epigenetic approaches.

Mapping of afferent and efferent connections of phenylethanolamine N-methyltransferase-expressing neurons in the nucleus tractus solitarii.

OBJECTIVE: Phenylethanolamine N-methyltransferase (PNMT)-expressing neurons in the nucleus tractus solitarii (NTS) contribute to the regulation of autonomic functions. However, the neural circuits linking these neurons to other brain regions remain unclear. This study aims to investigate the connectivity mechanisms of the PNMT-expressing neurons in the NTS (NTSPNMT neurons). METHODS: The methodologies employed in this study included a modified rabies virus-based retrograde neural tracing technique, conventional viral anterograde tracing, and immunohistochemical staining procedures. RESULTS: A total of 43 upstream nuclei projecting to NTSPNMT neurons were identified, spanning several key brain regions including the medulla oblongata, pons, midbrain, cerebellum, diencephalon, and telencephalon. Notably, dense projections to the NTSPNMT neurons were observed from the central amygdaloid nucleus, paraventricular nucleus of the hypothalamus, area postrema, and the gigantocellular reticular nucleus. In contrast, the ventrolateral medulla, lateral parabrachial nucleus, and lateral hypothalamic area were identified as the primary destinations for axon terminals originating from NTSPNMT neurons. Additionally, reciprocal projections were evident among 21 nuclei, primarily situated within the medulla oblongata. CONCLUSION: Our research findings demonstrate that NTSPNMT neurons form extensive connections with numerous nuclei, emphasizing their essential role in the homeostatic regulation of vital autonomic functions.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.).

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

Design and verification of a high-gradient and high-power 2nd harmonic cavity for the China Spallation Neutron Source upgrade project.

Here, we report our recent progress in the design, fluid thermodynamics simulation, and high-power test of the2nd harmonic cavity for the China Spallation Neutron Source Phase II. A high-performance and large-size magnetic alloy (MA) core was developed as the load material for the radiofrequency cavity to achieve a high gradient of 40 kV/m. The water-cooling structure and cooling efficiency were studied and improved through numerical analysis and thermal experiments. The long-term stability of the cavity, especially the waterproofness of the MA cores with high heat load, was verified by high power tests.

Detection and characterization of spike architecture based on deep learning and X-ray computed tomography in barley.

BACKGROUND: Spike is the grain-bearing organ in cereal crops, which is a key proxy indicator determining the grain yield and quality. Machine learning methods for image analysis of spike-related phenotypic traits not only hold the promise for high-throughput estimating grain production and quality, but also lay the foundation for better dissection of the genetic basis for spike development. Barley (Hordeum vulgare L.) is one of the most important crops globally, ranking as the fourth largest cereal crop in terms of cultivated area and total yield. However, image analysis of spike-related traits in barley, especially based on CT-scanning, remains elusive at present. RESULTS: In this study, we developed a non-invasive, high-throughput approach to quantitatively measuring the multitude of spike architectural traits in barley through combining X-ray computed tomography (CT) and a deep learning model (UNet). Firstly, the spikes of 11 barley accessions, including 2 wild barley, 3 landraces and 6 cultivars were used for X-ray CT scanning to obtain the tomographic images. And then, an optimized 3D image processing method was used to point cloud data to generate the 3D point cloud images of spike, namely 'virtual' spike, which is then used to investigate internal structures and morphological traits of barley spikes. Furthermore, the virtual spike-related traits, such as spike length, grain number per spike, grain volume, grain surface area, grain length and grain width as well as grain thickness were efficiently and non-destructively quantified. The virtual values of these traits were highly consistent with the actual value using manual measurement, demonstrating the accuracy and reliability of the developed model. The reconstruction process took 15 min approximately, 10 min for CT scanning and 5 min for imaging and features extraction, respectively. CONCLUSIONS: This study provides an efficient, non-invasive and useful tool for dissecting barley spike architecture, which will contribute to high-throughput phenotyping and breeding for high yield in barley and other crops.

Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement.

Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.

A review of plants strategies to resist biotic and abiotic environmental stressors.

Plants exposed to a variety of abiotic and biotic stressors including environmental pollution and global warming pose significant threats to biodiversity and ecosystem services. Despite substantial literature documenting how plants adapt to distinct stressors, there still is a lack of knowledge regarding responses to multiple stressors and how these affects growth and development. Exposure of plants to concurrent biotic and abiotic stressors such as cadmium and drought, leads to pronounced inhibition in above ground biomass, imbalance in oxidative homeostasis, nutrient assimilation and stunted root growth, elucidating the synergistic interactions of multiple stressors culminating in adverse physiological outcomes. Impact of elevated heavy metal and water deficit exposure extends beyond growth and development, influencing the biodiversity of the microenvironment including the rhizosphere nutrient profile and microbiome. These findings have significant implications for plant-stress interactions and ecosystem functioning that prompt immediate action in order to eliminate effect of pollution and address global environmental issues to promote sustainable tolerance for multiple stress combinations in plants. Here, we review plant tolerance against stress combinations, highlighting the need for interdisciplinary approaches and advanced technologies, such as omics and molecular tools, to achieve a comprehensive understanding of underlying stress tolerance mechanisms. To accelerate progress towards developing stress-tolerance in plants against multiple environmental stressors, future research in plant stress tolerance should adopt a collaborative approach, involving researchers from multiple disciplines with diverse expertise and resources.

Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii.

N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops.

BarleyExpDB: an integrative gene expression database for barley.

BACKGROUND: RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources. RESULTS: We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations. CONCLUSIONS: BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.

Genome-wide identification, evolution and expression analysis of NAC gene family under salt stress in wild emmer wheat (Triticum dicoccoides. L).

The NAC transcription factor (TF) family is one of the largest plant-specific gene families, playing the vital roles in plant growth and development as well as stress response. Although it has been extensively characterized in many plants, the significance of NAC family in wild emmer wheat is not well understood up to now. Here, a total of 200 NAC transcription factors were identified in wild emmer (TdNACs) through a genome-search method, which were classified into 12 subfamilies based on phylogenetic relationship. And the members in the subfamily shared similar exon-intron structure and conversed domain organization. Collinearity analysis revealed that segmental duplication and polyploidization contributed mainly to the expansion of TdNACs. Furthermore, the genetic variations of TdNACs were investigated using the re-sequencing data and genetic bottleneck has occurred on NAC genes when wild emmer domesticated to cultivated emmer wheat. Finally, the expression patterns of these TdNACs were investigated using RNA-seq data of the salt-tolerant genotype under salt stress to obtain salt-responsive TdNACs, and 10 out of which were further validated using QPCR analysis. This study provided the targets for further functional study of TdNAC genes, and also contributed to mine novel genes for improving the salt tolerance in wheat and other crops.