Plant Direct最新文献

Post-translational modifications of histones (PTMs) play a crucial role in regulating chromatin function. These modifications are integral to numerous biological processes, including transcription, DNA repair, replication, and chromatin remodeling. Although several PTMs have been identified, enhancing our understanding of their roles in these processes, there is still much to discover given the potential for virtually any histone residue to be modified. In this study, we report the discovery of a novel PTM in the model diatom Phaeodactylum tricornutum, glutamate methylation identified by mass spectrometry at multiple positions on histone H4 and at position 96 on histone H2B. This modification was also detected in other model organisms, including Drosophila melanogaster, Caenorhabditis elegans, and humans, but not in Arabidopsis. Structural bioinformatics analyses, including molecular dynamics simulations, revealed that methylation of glutamate residues on histones induces displacement of these residues, exposing them to solvent and disrupting interactions with neighboring residues in associated histones. This disruption may interfere with histone complexes promoting histone eviction or facilitating interactions with regulatory proteins or complexes, which may compromise the overall nucleosome stability.

Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.

A robust symbiotic relationship between soybean and rhizobia can enhance the yield and quality of soybeans by reducing nitrogen fertilizer input, thereby contributing to sustainable agriculture. However, the genetic interplay between soybean cultivars and the rhizobial species colonizing their roots under natural conditions is yet to be sufficiently assessed. In this study, we build on previous observations that have revealed a significant variation in the prevalence of rhizobial species associated with the soybean cultivars "Peking" and "Tamahomare." Using recombinant inbred lines derived from a cross between Peking and Tamahomare, we performed quantitative trait loci (QTL) analysis of the proportion of Rhizobium species present in the root nodules of these cultivars and accordingly identified a major QTL on chromosome 18, accounting for 42% of the phenotypic variation, which was subsequently localized to a 240-kb region. RNA-seq analysis indicated that a single gene harboring nucleotide binding site-leucine-rich repeat domains exhibited markedly different expression within the QTL region in the parent cultivars. As this locus is distinct from the chromosomal regions containing known nodule-related genes, such as Rj and rj, we speculate that it represents a novel gene involved in the symbiosis between rhizobia and soybeans. Further research on the function and role of this new gene could potentially contribute to enhancing soybean yield, and hence sustainable agriculture, under low-nitrogen fertilization conditions.

Rice is a globally important crop and is particularly efficient at assimilating arsenic (As). Identifying QTLs and genes associated with grain As is essential for breeding low-As rice cultivars. In this study, data on As accumulation in grains of Rice Diversity Panel 1 in five field environments at four diverse geographic sites were reanalyzed to compare genome-wide association (GWA) methods. Two single-locus (EMMAX for single trait and GEMMA for multi-experiments) and six multi-locus (FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB, and FASTmrMLM) GWA methods were used. A total of 90 and 111 QTLs were detected using EMMAX and GEMMA, respectively. A total of 2, 11, 12, 19, 23, and 25 QTNs were identified by FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB, and FASTmrMLM, respectively. Among these, 22 QTLs/QTNs were co-detected by single-locus and multi-locus GWAS methods. From these QTLs/QTNs, a total of 10 candidate genes were identified. Analysis of the haplotype variants of one candidate genes, OsABCC1, and one cluster of the plasma membrane intrinsic proteins genes revealed that a greater than 10% reduction in grain As could be achieved. The QTLs/QTNs and candidate genes identified give insight into the molecular mechanisms regulating As accumulation in rice and serve as breeding targets for developing low grain As rice cultivars.

RNA-binding protein interactions with viral RNA are crucial in the context of viral infections, as viral RNAs can recruit and reprogram host RNA-binding proteins (RBPs) during disease progression. Despite their significance, the repertoire of RBPs involved in most viral infections remains inadequately characterized. In Africa, Sobemovirus Rice yellow mottle virus (Sobemovirus RYMV) is the most prevalent virus infecting rice, and its devastating impact has led to extensive research efforts worldwide. Comprehensive identification of host RBPs that are enriched under Sobemovirus RYMV-infected conditions through RNA-bound proteome (RBPome)-wide studies could provide novel strategies for developing Sobemovirus RYMV resistance. In this study, a silica-based acidic phase separation approach was employed to elucidate changes in the RBPome following Sobemovirus RYMV infection. The analysis demonstrated that Sobemovirus RYMV infection remodels the RBPome, with 11 non-viral RBPs identified as significantly enriched and two non-viral RBPs that were significantly less abundant following infection. This study provides a snapshot of the landscape of RBPome changes in response to Sobemovirus RYMV. Validating these RBPs to understand their biological involvement in Sobemovirus RYMV infection is crucial to developing Sobemovirus RYMV-resistant rice varieties.

The influence of cold stress during the reproductive phase can lead to substantial yield losses in sorghum. In order to extend cultivation into temperate regions, a better understanding of reproductive cold tolerance is essential for breeding progress. To further elucidate the mechanisms responsible for cold tolerance, a cold-tolerant and a cold-sensitive parental line, along with their reciprocal F1 hybrids, were subjected to cold stress at various stages of reproductive development, with a focus on pollen fertility and receptivity of female floral organs. For this purpose, pollen measurements were conducted using impedance flow cytometry, and the panicle harvest index was determined post-maturation. While existing literature primarily attributes reduced pollen fertility as the cause of decreased seed set, this study provides evidence that female floral organs might be more affected than previously assumed. We found that the onset of generative tissue formation until BBCH39 (flag leaf visible) is the most cold-sensitive developmental stage and that there is no predominance of maternal or paternal effects associated with the inheritance of cold tolerance in reciprocal F1 hybrids. These findings offer valuable insights for the development of cold-tolerant sorghum varieties to enable cultivation in colder regions and enhance yield stability in temperate climates. Further studies should aim at validating and expanding these findings from the limited number of representative genotypes analyzed in the present manuscript to global sorghum diversity.

Sustainable agriculture holds the key in meeting food production requirements for a rapidly growing population without exacerbating environmental degradation. Plant leaf diseases pose a critical threat to crop yield and quality. Existing inspection methods are labor-intensive and prone to human errors, while lacking support for large-scale agriculture. This research aims to enhance plant health by developing advanced deep learning models for the detection and classification of plant diseases across a variety of species. A deep learning model based on the paradigm of the MobileNet architecture is proposed, which employs a dedicated design through deeper convolutional layers, dropout regularization, and fully connected layers. This results in significant improvements in disease classification in tomato, bean, and chili plants, with accuracy rates of 97.90%, 98.12%, and 97.95%, respectively. Moreover, Grad-CAM is used to shed light on the decision-making process of the proposed model. The work contributes to the advancement of precision farming and sustainable agricultural practices, supporting timely and accurate plant disease diagnosis.

Various environmental factors control the plant flowering time. However, the specific effects of ultraviolet (UV)-B radiation on flowering remain unclear. UV-B irradiation delays flowering in Arabidopsis during short-day (SD) photoperiods. In contrast, UV-B irradiation causes a variety of flowering phenotypes during long-day (LD) photoperiods, including unchanged, delayed, and accelerated flowering. We hypothesized that variations in UV-B intensity are responsible for the phenotypic changes under LD photoperiods. Therefore, in this study, Arabidopsis plants were exposed to two distinct UV-B intensities: a low UV-B intensity that activates UVR8-dependent pathways and high UV-B intensity that activates both UVR8-dependent and -independent pathways. Under LD photoperiods, neither the wild-type (WT) nor the uvr8 mutant showed any change in flowering time at either UV-B irradiation intensity. Under the SD photoperiod, UV-B irradiation delayed WT flowering. The expression of flowering locus T (FT) increased after UV-B irradiation under the LD photoperiod in a UVR8-dependent manner. However, despite the increased expression of FT, expression levels of floral meristem identity genes in shoot apical meristem (SAM) were not increased by UV-B irradiation. As UV-B irradiation is known to suppress flowering in SAM in a UVR8-dependent manner, increase in FT expression induced by UV-B irradiation possibly antagonized the suppressive effect of UV-B irradiation. Overall, these results suggest that flowering phenotypes do not change with UV-B intensity but with the balance between the inhibitory and promotive effects of UVR8 activated by UV-B irradiation.

Plant growth and development rely on a delicate balance between cell proliferation and cell differentiation. The root apical meristem (RAM) of Arabidopsis thaliana is an excellent model to study the cell cycle due to the coordinated relationship between nucleus shape and cell size at each stage, allowing for precise estimation of the cell cycle duration. In this study, we present a method for high-resolution visualization of RAM cells. This is the first protocol that allows for simultaneous high-resolution imaging of cellular and nuclear stains, being compatible with DNA replication markers such as EdU, including fluorescent proteins (H2B::YFP), SYTOX DNA stains, and the cell wall stain SR2200. This protocol includes a clarification procedure that enables the acquisition of high-resolution 3D images, suitable for detailed subsequent analysis.

Plants exhibit strong plasticity in growth and development, seen clearly in lateral and adventitious root development from differentiated tissues in response to environmental stresses. Previous studies have demonstrated the role of both auxin-dependent and auxin-independent signaling pathways in regulating the de novo formation of adventitious roots (ARs) from differentiated tissues, such as leaf petiole in Arabidopsis. One important question is how the auxin-dependent and auxin-independent pathways are coordinated. To investigate this question, we used a combined approach of inducible gene expression, mutant, and signaling reporter gene analysis during AR regeneration in the Arabidopsis petiole to understand regulatory relationships. Auxin signaling components AXR1 and AXR3 are each required for both AR and subsequent lateral root (LR) initiation, as is the ethylene signaling repressor POLARIS, but not EIN2. The PIN trafficking SNARE protein VAMP714 is required for LR rather than AR formation, through effects on auxin-induced gene expression. We identify the RNA splicing regulator MDF and the transcription factor RAP2.7 as new positive regulators of both the auxin-independent and auxin-dependent pathways, and show that MDF regulates RAP2.7, WOX5, and NAC1 while RAP2.7 regulates WOX5 but not NAC1 or YUC1. NAC1 is required for de novo root formation in a pathway independent of YUC1, WOX5, or RAP2.7. We propose a model in which MDF represents a point of molecular crosstalk between auxin-dependent and auxin-independent regeneration processes.