aBIOTECH最新文献

High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation. To address this need, we developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs. The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network (Mask R-CNN) achieved precision (measure of positive prediction accuracy), recall (sensitivity in detection), and F1 score values (harmonic mean of precision and recall) of 0.965, 0.958, and 0.961, respectively, for individual leaf segmentation. These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model. For silique segmentation, our enhanced DetectoRS model for silique segmentation attained precision, recall, and F1 scores of 0.954, 0.930, and 0.942, respectively. Notably, precision increased by 1%, while the F1 score improved by 2 percentage points. Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89% to 7.90%. We phenotyped 166 Arabidopsis accessions, using APTES, and subjected the resulting values to a genome-wide association study (GWAS), revealing 1,042 single-nucleotide polymorphisms (SNPs) as being significantly associated with 18 leaf and silique traits, and one significant SNP on chromosome 3 linked to silique number. Furthermore, we validated APTES across other public Arabidopsis databases and other plant species, with segmentation results demonstrating its applicability across diverse datasets. In conclusion, APTES is a valuable automated tool for leaf and silique segmentation and trait estimation, which should offer benefits to the broader plant science community.

The epigenomic landscape regulates gene expression and chromatin dynamics, with histone and RNA modifications playing crucial roles. Although studies have elucidated the interactions among chromatin modifications, DNA methylation, and mRNA modifications, the relationships among RNA modifications and their collective influence on RNA metabolism remain poorly understood. Grasping these epigenetic mechanisms is essential for improving crop resilience and productivity. In this study, we explored the co-occurrence and functional interactions of three significant mRNA modifications in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa): N⁴-acetylcytidine (ac⁴C), N⁶-methyladenosine (m⁶A), and 5-methylcytosine (m⁵C). Our results indicate that these modifications frequently coexist in the same transcripts, exhibiting distinct spatial distributions across species. Notably, the m⁶A modification enhances the ac⁴C-mediated destabilization of RNA secondary structures, especially when modifications are clustered, thereby promoting RNA stability. In Arabidopsis, the ac⁴C modification improved translational efficiency and the m⁶A modification amplified this effect in a distance-dependent manner; by contrast, in rice the influence of m⁶A is independent of distance. The m⁵C modification has minimal impact on RNA structure or stability but modulates m⁶A-associated transcript stability in a context-dependent manner. Our findings shed light on the dynamic regulatory code of combinatorial RNA modifications, highlighting species-specific mechanisms of post-transcriptional regulation. This research offers valuable insights into the intricate interplay of RNA modifications, with implications for advancing agricultural biotechnology through a deeper understanding of plant RNA functionality.

Defining how plant cell types are specified and regulated has been a central challenge in biology. Previous single-cell studies in plants, relying on either RNA-seq or ATAC-seq, provided valuable insights but could not directly connect chromatin state to transcriptional programs. Writing in Nature, Wang et al. present the first multi-organ single-cell multi-omics atlas of rice. Profiling more than 116,000 nuclei across eight tissues, they delineate 56 distinct cell types with high resolution. Joint analysis of gene expression and chromatin accessibility reveals sharper cell-type boundaries, transient developmental states, and regulatory networks with unprecedented clarity. Importantly, the study links cell-specific regulatory programs to key agronomic traits, identifying candidate regulators of root architecture, photosynthesis, nitrogen metabolism, and yield. This atlas establishes both a foundational resource for comparative plant biology and crop biotechnology, providing a roadmap for precision breeding and resilient agriculture driven by cell-type insights.

Genome editing has the potential to enhance yield and quality traits of crops. However, standard genetic transformation methods are not always applicable to modern germplasm. To tackle this challenge in the widely cultivated variety Ligena of the oilseed crop camelina (Camelina sativa (L.) Crantz), an only recently established principle of adventitious shoot formation from immature zygotic embryos was employed to further improve its fatty acid profile. In this approach, the three subgenomic homeologs of the FATTY ACID ELONGASE 1 (FAE1) gene were subjected to targeted mutagenesis. To pre-validate the Cas9-interacting, target motif-specific guide (g)RNAs, a robust protoplast-based DNA transfection method was established. This assay demonstrated that the preselected gRNAs were capable of eliciting mutations across all three camelina FAE1 homeologs. Likewise, targeted mutagenesis was successful at the whole-plant level. Triple-homozygous fae1 knockout mutants were identified amongst a segregating generation M₃ family. Gas chromatography of lipid extracts from M₄ seeds revealed a significant increase in all unsaturated C18 fatty acids including the particularly valuable α-linolenic acid. This was accompanied by a near elimination of the C20 and C22 very long-chain fatty acids including the nutritionally problematic erucic acid. Altogether, we have developed camelina elite lines with two significantly improved properties of high relevance for a health-promoting human nutrition.

The jasmonate signaling pathway coordinates plant defenses and growth, thereby enhancing fitness in changing conditions. Jasmonate-mediated responses are triggered by the recognition of external signals via pattern recognition receptors (PRRs) located on the cell membrane. Following signal perception, cells rapidly activate jasmonic acid (JA) biosynthesis, resulting in the accumulation of the bioactive jasmonate, jasmonoyl-isoleucine (JA-Ile). In the nucleus, the coronatine insensitive 1–jasmonate-ZIM-domain (COI1–JAZ) complex recognizes JA-Ile and triggers JAZ ubiquitination and proteasomal degradation. Consequently, transcription factors (e.g., MYC2) bound by JAZ are released, enabling the activation and amplification of JA responses. In parallel to this activation, feedback regulation orchestrated by transcription factors terminates transcription, preventing overcommitment to JA signaling. In this review, we summarize recent advances in understanding JA signaling, emphasizing the connection between PRR activation and JA biosynthesis, and the feedback regulatory mechanisms that ensure precision and robustness of the JA signaling pathway. Finally, we discuss how these mechanistic insights can be leveraged to optimize JA signaling for crop genetic improvement.

GABA, a non-proteinogenic amino acid with anti-hypertensive properties, holds health-beneficial potential when enriched in crops. Previous studies have established that targeted disruption of the calmodulin-binding domain (CaMBD) of the tomato glutamate decarboxylase 3 (SlGAD3) enhances GABA biosynthesis. In this study, we used CRISPR/Cas9-mediated gene editing to precisely modify the CaMBD coding sequence of SlGAD3 in three elite tomato varieties (SFT1, SFT2, and SFT3). Under our experimental conditions, targeted editing of SlGAD3 led to substantial accumulation of GABA in all three varieties without compromising key agronomic traits such as fruit size and number. Although flowering was delayed in SFT2 and SFT3 mutants, SFT1 mutants had higher GABA levels but also maintained a wild-type flowering time. This result highlights the critical importance of selecting specific varieties, such as SFT1, to minimize pleiotropic effects. By identifying varieties that can accumulate high levels of GABA without major reductions in growth and yield potential, this work bridges a critical gap between plant metabolic-engineering research and practical applications in commercial crop-improvement programs.

Symbiotic nitrogen fixation (SNF) between legumes and rhizobia contributes to sustainable agriculture. In root nodules, infected cells (ICs) are the primary sites of rhizobial colonization and nitrogen fixation. However, the function of the neighboring uninfected cells (UCs) has received little attention and is poorly understood. In this study, we employed a symplastic tracing approach to elucidate the role of UCs in nutrient storage and transport within root nodules. We uncovered an extensive network of plasmodesmata connecting ICs and UCs, while direct IC–IC connections were absent. By artificially inducing callose deposition at plasmodesmata, we demonstrate that plasmodesmata permeability between ICs and UCs regulates nutrient import into ICs, thereby influencing nutrient homeostasis and the SNF ability of nodules. Furthermore, high nitrogen levels triggered callose deposition at plasmodesmata, restricting nutrient transport, which may represent one mechanism by which excessive nitrogen inhibits SNF. These findings provide insights into the regulatory mechanisms of SNF and underscore the crucial role of UCs in optimizing nitrogen fixation efficiency.

Plants can produce compounds with extraordinary chemical structures and a wide range of applications in the treatment of human diseases. The biosynthesis of such compounds in plants is often complex and limited to specific tissues and specialized cells, resulting in low yields. Unlike many medicinal plants, Nicotiana benthamiana is easy to grow and is amenable to genetic manipulation. Indeed, many metabolic pathways for valuable medicinal compounds have been elucidated and reconstructed in N. benthamiana through Agrobacterium tumefaciens-mediated transient expression of the relevant metabolic genes. Here, we review different aspects to consider when characterizing candidate metabolic genes and their products, as well as reconstructing their biosynthetic pathways in N. benthamiana. We discuss how high yields from ectopically expressed pathways may benefit from boosting precursor levels, as well as from eliminating competing enzymatic activities and various detoxification reactions. Finally, we discuss innovative approaches to studying the export of compounds through the plasma membrane and cell wall and explain how these approaches may influence the industrial-scale production of valuable compounds in N. benthamiana.

Peanut (Arachis hypogaea) is widely cultivated worldwide as an important source of edible vegetable oil and protein. Peanut seed pods develop below ground from a gynophore that forms above ground and then penetrates the soil surface to bury the developing pod. Numerous studies have explored transcriptional regulation during peanut pod development. Here, we explored post-transcriptional regulation, including polyadenylation, alternative splicing, and RNA adenosine methylation (m⁶A), in peanut pods across four developmental stages by performing direct RNA sequencing. This produced 70.43 million long reads with average lengths of 890–1,136 nucleotides (nt) from 12 samples across four developmental stages, yielding a total of 14,627 newly identified transcripts. We detected a negative relationship between poly(A) tail lengths and transcript abundance, with the shortest poly(A) tails at the subterranean peg and expanded pod 1 stages, and longest poly(A) tails at the aerial gynophore and expanded pod 2 stages. Moreover, throughout pod development, from the penetration of the gynophore into the soil to pod enlargement, the splicing machinery utilized more proximal than distal alternative polyadenylation sites in the transcripts. The date showed no correlation between m⁶A modification and gene expression in peanut, but found more transcripts with alternative first and last exon types of alternative splicing events. Transcripts that were differentially abundant across developmental stages were primarily enriched in the Gene Ontology terms photosynthesis, response to oxidative stress, response to auxin, plant-type cell wall organization, and lignin catabolism. This study lays a foundation for revealing the roles of epigenetics and post-transcriptional regulation in pod development in peanut.