Plant Direct最新文献

Chorismate is an important branchpoint metabolite in the biosynthesis of lignin and a wide array of metabolites in plants. Chorismate mutase (CM), the enzyme responsible for transforming chorismate into prephenate, is a key regulator of metabolic flux towards the synthesis of aromatic amino acids and onwards to lignin. We examined three CM genes in hybrid poplar (Populus alba × grandidentata; P39, abbreviated as Pa×g) and used RNA interference (RNAi) to suppress the expression of Pa×gCM1, the most highly expressed isoform found in xylem tissue. Although this strategy was successful in disrupting Pa×gCM1 transcripts, there was also an unanticipated increase in lignin content, a shift towards guaiacyl lignin units, and more xylem vessels with smaller lumen areas, at least in the most severely affected transgenic line. This was accompanied by compensatory expression of the other two CM isoforms, Pa×gCM2 and Pa×gCM3, as well as widespread changes in gene expression and metabolism. This study investigates potential redundancy within the CM gene family in the developing xylem of poplar and highlights the pivotal role of chorismate in plant metabolism, development, and physiology.

Transcriptional master regulators are often targeted to improve plant traits, but antagonistic pleiotropic effects of these regulators can hamper this approach. The Myb-bHLH-WDR (MBW) complex is a broadly conserved transcriptional regulator affecting pigmentation, biotic stress resistance, and abiotic stress tolerance. We investigated the function of sorghum grain pigmentation regulator Tannin1, the ortholog of Arabidopsis pleiotropic WD40 regulator TTG1, to test for conserved pleiotropic regulatory effects and to better understand the evolution of the MBW complex in Poaceae. We characterized genome-wide differential expression of leaf tissue using RNA sequencing in near-isogenic lines (NILs) that contrasted wildtype Tan1 and loss-of-function tan1-b alleles, under optimal temperature and chilling stress. Notably, Gene Ontology analyses revealed no pathways with differential expression between Tan1 and tan1-b NILs, suggesting that, in contrast to Arabidopsis TTG1, Tannin1 has no pleiotropic regulatory role in leaves. Further, NILs had no visible difference in anthocyanin pigmentation, and no genes with known or expected function in flavonoid synthesis were differentially expressed. Genome-wide, only 18 total genes were differentially expressed between NILs, with six of these genes located inside the NIL introgression region, an observation most parsimoniously explained by cis-regulatory effects unrelated to Tannin1 regulation. Comparing our findings with known function of TTG1 orthologs in maize, rice, and Arabidopsis, we conclude that pleiotropic regulatory function in leaf tissue was likely lost in panicoid grass evolution before the sorghum-maize split. These findings inform future molecular breeding of MBW regulated traits and highlight the benefit of subfunctionalization to relieve pleiotropic constraints.

The need for more sustainable agricultural systems is becoming increasingly apparent. The global demand for agricultural products-food, feed, fuel and fiber-will continue to increase as the global population continues to grow. This challenge is compounded by climate change. Not only does a changing climate make it difficult to maintain stable yields but current agricultural systems are a major source of greenhouse gas emissions and continue to drive the problem further. Therefore, future agricultural systems must not only increase production but also significantly decrease negative environmental impacts. One approach to addressing this is to begin breeding and cultivating new plant species that have fundamental sustainability advantages over our existing crops. The Lemnaceae, commonly known as duckweeds, are one family of plants that have potential to increase output and reduce the negative environmental impacts of agricultural production. Herein we describe the Automated Lab-scale PHenotyping Apparatus, ALPHA, for high-throughput phenotyping of Lemnaceae. ALPHA is being used for selective breeding of one species, Lemna gibba, toward the goal of creating a new crop for use in sustainable agricultural systems. ALPHA can be used on many small aquatic plant species to assess growth rates in different environmental conditions. A proof of principle use case is demonstrated where ALPHA is used to determine saltwater tolerance of six different clones of L. gibba.

Light is one of the most critical ecological cues controlling plant growth and development. Plants have evolved complex mechanisms to cope with fluctuating light signals. In Arabidopsis, bHLH transcription factors MYC2, MYC3, and MYC4 have been shown to play a vital role in protecting plants against herbivory and necrotrophic pathogens. While the role of MYC2 in light-mediated seedling development has been studied in some detail, the role of MYC3 and MYC4 still needs to be discovered. Here, we show that MYC4 negatively regulates seedling photomorphogenesis, while the MYC3 function seems redundant. However, the genetic analysis reveals that MYC3/MYC4 together act as positive regulators of seedling photomorphogenic growth as the myc3myc4 double mutants showed exaggerated hypocotyl growth compared to the myc3 and myc4 single mutants and Col-0. Intriguingly, the loss of MYC2 function in the myc3myc4 double mutant background (myc2myc3myc4) resulted in further enhancement in the hypocotyl growth than myc3myc4 double mutants in WL, BL and FRL, suggesting that MYC2/3/4 together play an essential and positive role in meditating optimal seedling photomorphogenesis. Besides, MYC3/MYC4 genetically and physically interact with HY5 to partially inhibit its function in controlling hypocotyl and photo-pigment accumulation. Moreover, our results suggest that COP1 physically interacts and degrades MYC3 and MYC4 through the 26S proteasomal pathway and controls their response to dark and light for fine-tuning HY5 function and seedling photomorphogenesis.

The health and productivity of plants, particularly those in agricultural and horticultural industries, are significantly affected by timely and accurate disease detection. Traditional manual inspection methods are labor-intensive, subjective, and often inaccurate, failing to meet the precision required by modern agricultural practices. This research introduces an innovative deep transfer learning method utilizing an advanced version of the Xception architecture, specifically designed for identifying plant diseases in roses, mangoes, and tomatoes. The proposed model introduces additional convolutional layers following the base Xception architecture, combined with multiple trainable dense layers, incorporating advanced regularization and dropout techniques to optimize feature extraction and classification. This architectural enhancement enables the model to capture complex, subtle patterns within plant leaf images, contributing to more robust disease identification. A comprehensive dataset comprising 5491 images across four distinct disease categories was employed for the training, validation, and testing of the model. The experimental results showcased outstanding performance, achieving 98% accuracy, 99% precision, 98% recall, and a 98% F1-score. The model outperformed traditional techniques as well as other deep learning-based methods. These results emphasize the potential of this advanced deep learning framework as a scalable, efficient, and highly accurate solution for early plant disease detection, providing substantial benefits for plant health management and supporting sustainable agricultural practices.

Stomatal aperture is driven by changes in turgor of the guard cells that surround the stomatal pore. Epidermal cells immediately surrounding the guard cells are thought to contribute to the kinetics of aperture changes through changes in their turgor that opposes the guard cells and thought their putative roles in solute storage for use by the guard cells. Nonetheless, our knowledge remains fragmentary of surrounding cell mechanics, in large part because the tools and strategies needed to target the surrounding cells independent of the guard cells are limited. Here, we have analyzed sets of promoters for Arabidopsis, Brassica, and barley that will allow physiological studies of the roles of epidermal cells and also surrounding cells in the case of barley in stomatal behavior. These tissue-specific promoters offer distinct advantages over widely used, constitutive promoters by enabling precise and targeted gene expression within guard cells and the adjacent epidermal cells. As genetic tools, the promoters will have applications in strategies centered on physiological analyses and differential comparisons following expression targeted between the guard cells and the foliar epidermis as a whole. As such, they are well suited to questions around the mechanics of solute and water flux that will advance an understanding of the stomatal complex in these model species.

The presence of a selection marker in transgenic plants has raised public concerns regarding health safety. We have developed a CRISPR/Cas9-based DNA delivery system termed transgenic selection-associated fragment elimination (T-SAFE). The T-SAFE system comprises four cassettes: the selection marker, CRISPR/Cas9, spacer-plus-protospacer adjacent motif (SP), and the cargo. The first two cassettes, the selection marker and CRISPR/Cas9, are collectively referred to as SCC. The SCC is flanked by two identical SPs derived from the fruit fly Ebony gene, which efficiently facilitate the SCC cleavage and subsequently lead to self-elimination of the selection marker upon integration of exogenous DNA into the plant genome. To inhibit the production of a functional Cas9 protein in bacteria, the IV2 intron of the potato ST-LS1 gene has been incorporated into the Cas9 gene. Additionally, the Cas9 gene is driven by a reproductive cell-specific or inducible promoter to avoid SCC cleavage in nonreproductive plant cells. These innovative features allow the T-SAFE system to achieve an elimination efficiency of the selection marker ranging from 10%-30% in Arabidopsis and 5%-8% in rice, with a DNA delivery capacity of approximately 10 kb. This approach offers a safe means for genetically modifying plants.

The strong correlation between reproductive life cycle type and chromosome numbers in green plants has been a long-standing mystery in evolutionary biology. Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which three lineages are extant. In all green plant lineages where heterospory has emerged, there has been a significant downsizing in chromosome numbers. This dynamic has been investigated without clear answers for many decades. In this study, we combine known ideas from existing literature with novel methods, tools, and data to generate fresh insights into an old question. Using gene family evolution models and selection analyses, we identified gene families that have undergone significant expansion, contraction, or selection in heterosporous lineages. Alongside lineage-specific genomic changes, our results revealed shared genomic changes/trends among heterosporous lineages. We found expansions in gene families related to developmental regulation, signaling pathways, and stress responses across heterosporous groups. Notably, the MATE efflux family showed consistent expansion and evidence of selection in heterosporous lineages, suggesting a potentially conserved role in heterospory evolution. These findings could provide novel avenues to investigate and probe the underlying mechanism that may underpin the association between heterospory and genomic changes. The general importance of chromosome numbers, structure, and sizes in cellular biology notwithstanding, the association between the emergence of heterosporous reproduction and chromosome number reduction/genome downsizing is not fully understood. It remains unclear why there exists an association between aspects of biology at such disparate levels as reproductive life cycles and chromosome numbers/genome size. Exploring and answering this conundrum of evolutionary biology can add to our broader understanding of life sciences and of biology at different levels. Applying the novel tools and methods emerging from ongoing progress in biotechnology and computational sciences presents an opportunity to make new inroads into this long-standing question.

Currently in wheat breeding, genome wide association studies (GWAS) have successfully revealed the genetic basis of complex traits such as nitrogen use efficiency (NUE) and its biological processes. In the GWAS model, thresholding is common strategy to indicate deviation of expected range of p-value(s), and it can be used to find the distribution of true positive associations under or over of test statistics. Therefore, the threshold plays a critical role to identify reliable and significant associations in wide genome, while the proportion of false positive results is relatively low. The problem of multiple comparisons arises when a statistical analysis involves multiple simultaneous statistical tests, each of them has the potential to be a discovery. There are several ways to address this problem, including the family-wise error rate and false discovery rate (FDR), raw and adjusted p-value(s), consideration of threshold coherence and consonance, and the properties of proportional hypothesis tests in the threshold definition. We encountered some limitations in the definition of FDR threshold, particularly in the upper bounds of linear and nonlinear approaches. We emphasize that empirical null distributions based on permutation test can be useful when the assumption of linear or parametric FDR approaches do not hold. Nevertheless, we believe that it is necessary to utilize modern statistical optimization techniques to evaluate the stability and performance of our results and to select significant FDR threshold. By incorporating the neural network algorithm, it is possible to improve the reliability of FDR threshold and increase the probability of identifying true genetic associations while minimizing the risk of false positives in GWAS results.

The plant shikimate pathway directs a significant portion of photosynthetically assimilated carbon into the downstream biosynthetic pathways of aromatic amino acids (AAA) and aromatic natural products. 3-Deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase (hereafter DHS) catalyzes the first step of the shikimate pathway, playing a critical role in controlling the carbon flux from central carbon metabolism into the AAA biosynthesis. Previous biochemical studies suggested the presence of manganese- and cobalt-dependent DHS enzymes (DHS-Mn and DHS-Co, respectively) in various plant species. Unlike well-studied DHS-Mn, however, the identity of DHS-Co is still unknown. Here, we show that all three DHS isoforms of Arabidopsis thaliana exhibit both DHS-Mn and DHS-Co activities in vitro. A phylogenetic analysis of various DHS orthologs and related sequences showed that Arabidopsis 3-deoxy-D-manno-octulosonate-8-phosphate synthase (KDOPS) proteins were closely related to microbial Type I DHSs. Despite their sequence similarity, these Arabidopsis KDOPS proteins showed no DHS activity. Meanwhile, optimization of the DHS assay conditions led to the successful detection of DHS-Co activity from Arabidopsis DHS recombinant proteins. Compared with DHS-Mn, DHS-Co activity displayed the same redox dependency but distinct optimal pH and cofactor sensitivity. Our work provides biochemical evidence that the DHS isoforms of Arabidopsis possess DHS-Co activity.