Crop Design最新文献

Over the past decade, bulk RNA sequencing (RNA-seq) has become an indispensable tool in molecular biology, and have made the novel development, with two innovative methodologies being developed, single-cell RNA sequencing (scRNA-seq) technology and spatial transcriptome (ST) technology. The scRNA-seq technology allows researchers to analyze gene expression in individual cells, providing more detailed information relative to the past technologies. Meanwhile, ST technology overcomes the limitations of single-cell sequencing in terms of loss of spatial information, enabling scientists to better understand the spatial distribution of gene expression within tissues. These advancements of transcriptomics technologies revolutionize the field of genomics and have been widely used in disease diagnosis and medicine. However, they are less utilized in plant research. This review describes the development, advantage and limitations of three transcriptomics technologies, and presents their applications in plant sciences.

Salinity is a significant challenge for agriculture, negatively impacting soil health and crop yields worldwide. Coping with salinity stress is intricate due to its multifaceted nature, making it challenging to fully grasp. Mangroves, recognized for their salt tolerance, thrive in diverse salinity levels, spanning from freshwater to seawater. They play a vital role in coastal ecosystems, thriving in areas where many other plants struggle. For a thorough knowledge of the salinity stress signaling and tolerance mechanism in mangroves, a variety of “omics” techniques have been explored. Recent research has illuminated crucial pathways, transcription factors, microRNAs, and signaling components in mangroves exposed to salty conditions. This knowledge holds promise for developing salt-tolerant crop plants through genetic modification techniques, which can help address the increasing issue of soil salinity. Our review encompasses genomics and transcriptomics studies that identify crucial genes and pathways in mangroves' response to salinity. Since the transcriptome lacks a direct correlation with the protein expression dynamics, we have also emphasized mangrove proteomics and metabolomics studies. The review also outlines the different strategies that can be used to enhance the salinity tolerance of crops using mangroves as models.

Finger Millet (Eleusine coracana - (L.) Gaertn), is an important nutraceutical crop with the potential for imparting food and nutritional security. These plants have a comparatively higher tolerance for several abiotic stresses like drought, salinity, and heat. Several players including Transcription Factor (TF) like Nuclear Factor Y (NF-Y) might be associated with this enhanced level of tolerance. Further, it is unclear how phytohormones like Abscisic acid (ABA) regulate the expression of NF-Y, whether in ABA-dependent or ABA-Independent pathway. The interaction of PYL (Pyrabactin resistance1-like) receptor proteins with Nuclear Factor Y (NF-Y) Transcription Factor in the presence of phytohormones like abscisic acid (ABA) provides one insight related to the enhanced tolerance towards abiotic stresses under ABA-dependent signaling in finger millet crop. A total of three PYL receptors of finger millet designated as EcPYL1, EcPYL5, and EcPYL9 were retrieved in the finger millet genome. These receptors were modeled through the SWISS-MODEL using templates 5gwo and 3wg8 and docked with ABA. The best-docked protein-ligand complex PYL5-ABA (binding energy ΔG ​= ​-8.8 kcal mol^-1) was found to be most stable at the 50ns MD simulation study. Further protein-protein interaction between PYL5 and NF-YA2/B3/C1 sub-family members showed a good interaction. This clearly indicates the possibility of the NF-Y-PYL module in the ABA transduction pathway, which performs a crucial role in the expression of stress-responsive genes. These studies reveal the intricate relationship between the ABA, PYL receptors of finger millet, and NF-Y transcription factor in regulating the stress-responsive genes and provide an insight into the abiotic stress tolerance mechanisms, which can be targeted for crop improvement.

Sucrose nonfermenting 2 (Snf2) family proteins function as the ATP-dependent catalytic engines of chromatin remodeling complexes, which harness ATP hydrolysis energy to alter chromatin structure and nucleosome positioning, enabling regulatory factor access to DNA. Plant genomes contain numerous Snf2 family proteins, several of which have been demonstrated to act as key developmental regulators at different stages in model plants like Arabidopsis and rice. Despite their vital roles, the Snf2 genes in Triticum aestivum remain largely uncharacterized. Here, we report the identification of 112 wheat Snf2 genes that were unevenly distributed across the 21 chromosomes, with 40 genes on the A subgenome, 33 on the B subgenome, and 39 on the D subgenome, and phylogenetically classified these Snf2 genes into 18 subfamilies related to the 6 Snf2 groups in Arabidopsis. Evolutionary analysis revealed that purifying selection has largely driven the evolution of Snf2 genes, acting as the primary selective force shaping the Snf2 gene family in wheat, while segmental duplications have served as the main mechanism for expanding the gene family. All identified Snf2 proteins contained at least one Helicase_C and SNF2_N domain among 10 conserved domains, and their gene structures consisted of 3–38 exons. Tissue-specific expression analysis uncovered distinct expression patterns among Snf2 gene family members, including some with enhanced reproductive tissue expression, while analysis under various abiotic and biotic stresses revealed differential regulation of specific family members in response to these conditions. Overall, these systematic analyses including identification, evolutionary relationships, and expression profiling provide valuable insights into the wheat Snf2 family while establishing a genomic framework to elucidate Snf2 functional roles in wheat growth, development, and stress responses.

Finger millet (Eleusine coracana L.) has gained notable interest in recent times for its capacity to tackle global challenges related to nutritional security and sustainability. This review delves into the critical issue of global nutritional security by focusing on Finger millet, as an essential staple crop known for its rich nutraceutical content. However, due to the expanding global population and the imperative for sustainable food sources, there is an urgent need to elevate the nutritional content of crops such as Finger millet. This review also utilizes molecular breeding and omics methodologies, encompassing genomics, transcriptomics, proteomics, and metabolomics, to thoroughly examine the molecular dimensions involved in enhancing the nutraceutical content and other crucial agronomic traits in Finger millet. These cutting-edge techniques provide insights into the genetic makeup and expression of key genes related to nutrient accumulation and distribution during grain development, as well as for other important agronomic traits. Moreover, this review also emphasizes the importance of sustainable agricultural practices to ensure the long-term availability of nutrient-rich crops like Finger millet. However, by harnessing the power of genetics and advanced analytical genomic tools, researchers can pave the way for the development of Finger millet varieties, contributing to a more sustainable and nutritious food security for the growing world population.

The variations in climatic factors can lead to morphological changes like male sterility, self-incompatibility, embryo abortions, poor seed setting, low nutrient content, growth retardation, yield loss and even crop failure of agricultural or horticultural crops under open land ecosystem. The traditional agricultural systems involve using a large quantity of water on a large arable land, along with a lot of agro chemicals, which can lead to leaching of nutrients and chemical residues into the soil and water bodies, insect competition, weed emergence, or soil erosion. The controlled environment plant growth chamber reserves 80 ​% land use, 90 ​% water use and runs off or translocates nutrients more efficiently than traditional agriculture. The controlled environment plant growth chamber utilizes standard nutrient diffusion for plant growth and regulates stable nutrient use efficiency, water use efficiency, photosynthetic assimilation product, metabolic use efficiency, climatic factors, greenhouse gases emission, carbon sequestration, carbon foot print with the mechanistic model with machine learning examines critical or non critical levels, dynamics and influences of water, climate and nutrient in controlled environment system. The controlled environment plant growth chamber enables production of outstanding physical and chemical quality enriched plants. The controlled environment witnesses the combat against climate change and the restoration or conservation of natural resources, as well as the generation of research, employment, and industrial development. More comparative investigations are required to understand and justify climate combating with major plants in controlled environment ecosystem and natural environment ecosystem with or without soil.

Meiotic recombination is essential for the generation of genetic diversity in natural and breeding context. The chromosome axis comprises cohesin, HORMA-domain containing proteins and coiled coil proteins and is crucial for the establishment of meiotic recombination. These proteins form a complex during meiosis of Brassica oleracea but information about their respective localisation and dynamic on meiotic chromosomes remain sparse. Our study reveals that the HORMA-protein ASY1 aggregates on the chromatin and forms domains of high and low abundances. The regions enriched for ASY1 are also highly enriched for the axis proteins ASY3, SMC3 and SCC3, although to varying degrees between leptotene and pachytene stages. At later stages, when most DNA double strand breaks are repaired and the chromosome axis disassemble, ASY1, ASY3, SCC3 and SMC3 co-localise and form large aggregates on the discontinuous axis structures. As the axis structures reduce in length, we found that all four axis proteins relocalise in the nucleoplasm and further aggregates. Moreover, we found that ZYP1, the transverse filament of the synaptonemal complex, forms numerous chromosomic aggregates that are sometimes associated with MLH1 and can form ectopic synaptic interactions. Overall, our study indicates that axis proteins have a high propensity to aggregate. This property is important for assembling the chromosome axis but the association of axis proteins with the chromatin must be tightly regulated to limit polycomplex formation.

High-throughput sequencing technologies at single-cell resolution have great potential to reveal a new landscape of plant cells. Single-cell/nucleus RNA (scRNA/snRNA), single-cell/nucleus assay for transposase accessible chromatin (scATAC/snATAC) and spatial transcriptome sequencing have been applied in multiple plant tissues. Consequently, a significant increase in publications on plant single-cell transcriptomics was seen in the recent two years. In this review, we will summarize the advantages and weaknesses of these single-cell sequencing approaches, offer a glimpse of their developments in cell biology, bioinformatic tools and databases in the latest two years.

Heavy metals, drought, salinity, cold stress, and heat stress are some of the main abiotic stresses that adversely affect plant growth and crop productivity generally. For crop production systems to be sustainable in the face of abiotic environmental constraints, effective strategies must be used in conjunction with technological advancement to achieve this goal. In recent times, the emergence of nanotechnology as an intriguing field of study with application potential in the field of agriculture needs to be given the necessary attention to address some of the abiotic stresses. Due to their environmental friendliness, affordability, special physicochemical properties, and increased plant productivity, the use of nanoparticles (NPs) as nano fertilizers has enormous potential and much interest has developed in the field in recent times. Abiotic stress management involves NPs, according to several studies. In order to create a practical and environmentally responsible plan for the long-term sustainability of agriculture, this review focuses on the effects of abiotic stress on plants, synthesis, and the roles of NPs in managing abiotic stresses, and future prospects.