Plant Molecular Biology最新文献

Recent advances in genomic language models have improved the accuracy of in silico analyses, yet many rely on resource-intensive architectures. In this study, we focus on the impact of k-mer tokenization strategies-specifically varying window sizes (three to eight) and overlap schemes-on the performance of transformer-based genomic language models. Through extensive evaluation across multiple plant genomic tasks, including splice site and alternative polyadenylation site prediction, we show that thoughtful design of the k-mer tokenizer plays a critical role in model performance, often outweighing model scale. In particular, overlap-based tokenization generally enhances performance by preserving local sequence context, while certain non-overlap configurations achieve competitive accuracy with improved computational efficiency in some tasks. Despite using a smaller model, our approach performs on par with the state-of-the-art AgroNT model in many cases. These results emphasize that k-mer tokenization, not merely model size, is a key determinant of success in genomic sequence modeling. Our findings provide practical guidance for designing efficient genomic language models tailored to plant biology.

Root growth and modulation in plants is a highly dynamic yet strictly regulated process. Primary root development in Arabidopsis for example, is an intricate balance between cell division in the meristematic zone and cell elongation in the elongation zone, followed by subsequent differentiation. This process involves an orchestrated series of events that depend on environmental and developmental cues. Regulation is imparted by a complex network of hormone signaling primarily involving auxin, in crosstalk with cytokinin, abscisic acid, jasmonic acid, ethylene and others. In course of evolution, plants have developed an incredible array of mechanisms to address water scarcity, including modulation of root system architecture. During low to moderate water deficiency plants, adopt a "searching-for-water" strategy evoking growth-promoting responses. This is marked by elongation of the primary root for water exploration in deeper soil layers. However, during severe drought stress, plants resort to a "stop growth" strategy and restrict root growth, to conserve resources and energy for survival. The balance between these adaptive responses is critically regulated by key phytohormones which interact synergistically or antagonistically, to control root growth under varying levels of water shortage. Understanding these adaptation strategies as to how plants integrate environmental cues and associated hormone signaling to influence root growth generates a wide range of possibilities for agricultural innovation. This article aims to provide an overview of the mechanisms acquired by the root system at the morphological, physiological, and molecular levels, under optimum growth conditions and in response to varying degrees of water paucity.

Teak is a tropical forest tree of great commercial importance. This hardwood species has been considered the best decorative wood in the world with extraordinary qualities of color, density and durability. Despite its commercial importance, molecular mechanisms regulating wood formation in teak are still obscure. In plants, the MYB transcription factors (TFs) are the master switches in the regulation of secondary cell wall biosynthesis. Previous transcriptome analyses of the secondary xylem of teak trees have identified high expression of MYB in young tree stems. In the present work, the full-length coding sequence of the TgMYB2 gene was isolated from teak young stems, characterized, cloned and constitutively overexpressed in tobacco plants. Phylogenetic relationships and molecular analyses recognized TgMYB2 as a 3R-MYB protein, which contains conserved motifs identified as R1-R2-R3 MYB repeats. In transgenic tobacco plants, the overexpressed TgMYB2 protein was localized exclusively in the cell nucleus, as expected for a transcription factor. The overexpressed TgMYB2 significantly modified secondary plant growth and improved biomass. Furthermore, we provide evidence that TgMYB2 plays an important role in the coordinated regulation of cellulose, hemicellulose, and lignin biosynthetic pathways.

Garden pea is an important leguminous crop valued for its protein-rich food source for human nutrition and enhancing agricultural sustainability by fixing nitrogen biologically. However, its cultivation faces significant challenges from pests, diseases, and environmental stresses. Among these, Fusarium wilt (FW) caused by pathogen Fusarium oxysporum f. sp. pisi poses a severe threat, resulting in substantial yield losses globally. Four pathogenic races (1, 2, 5, and 6) of this fungus have been primarily identified, and its broad host range further complicates effective management. Traditional control methods including cultural practices, physical control, biological interventions, and chemical treatments have shown limited efficacy. Consequently, host-plant resistance has emerged as a sustainable and practical solution for managing FW. In this review, the advancements in genetics with modern molecular techniques such as SNP genotyping, QTL mapping, and marker-assisted selection for the development of FW resistant pea varieties were highlighted. Furthermore, we also discussed the omics techniques viz., transcriptomics, metabolomics and proteomics and innovative breeding techniques like CRISPR-mediated genome editing, speed breeding, and genomic selection for revolutionize FW resistance breeding programs in pea. Therefore, this review focuses on integrating cutting-edge molecular techniques with omics approaches to unravel Fusarium wilt defense mechanisms in garden pea, aiming to accelerate genetic gains and develop superior disease-resistant varieties for improved productivity and quality.

Carrageenan kappa (CK), a polysaccharide obtained from marine red algae, oligo-carragenan kappa (OCK), an oligosaccharide obtained by acid hydrolysis of CK, and oligo-ulvans (OU), an oligosaccharide obtained by acid hydrolysis of ulvans from marine green algae, were sprayed on leaves of Arabidopsis thaliana at a concentration of 1 mg mL^- 1, five times, every two days, and plants were cultivated for ten additional days. Plants treated with water (control) or with an aqueous solution of CK, OCK and OU showed an increase in fresh weight (FW) and dry weight (DW), mainly in those treated with OCK and OU. Plants treated with OCK and OU showed an increase in rosette diameter and length of the primary root, but not those treated with CK. Plants treated with OCK and OU showed an increase in the level of transcripts encoding enzymes such as rubisco, glutamine synthase and O-acetyl thiol lyase, but not those treated with CK. Plants treated with CK, OCK and OU showed an increase in transcripts encoding an enzyme involved in gibberellin A₃ synthesis whereas plants treated with OCK and OU showed increased transcript encoding an enzyme involved in epi-brassinolide synthesis, but not those treated with CK. Plants treated with OCK and OU showed increased transcripts encoding cyclin A, cyclin D and CDPKB, which regulate the cell cycle, but not those treated with CK. Plants treated with OCK and OU showed an increase in the number of cells per leaf area and in the content of total proteins. Thus, OCK and OU better stimulate growth of A. thaliana compared to CK by increasing the expression of genes involved in primary metabolism, phytohormone synthesis and cell division and act on different cellular pathways compared with CK. Therefore, these oligosaccharides can be useful for biotechnological purposes by increasing plant growth and productivity.

Rice is a major food crop and serves as the primary food source for over half of the world's population, particularly in Asia. However, its cultivation is constrained by several abiotic stresses, notably sodicity, which significantly reduces productivity and is expected to worsen in the near future. In this study, a genome-wide association study (GWAS) was conducted to identify genomic regions and candidate genes associated with sodicity tolerance in rice. A rice association mapping panel consisting of 150 genotypes was evaluated for sodicity tolerance traits across four environments and genome-wide single nucleotide polymorphisms (SNPs) obtained using genotyping-by-sequencing (GBS) approach. The results revealed high phenotypic variation and heritability for six sodicity tolerance traits across the evaluated environments. The high-quality SNPs obtained were subjected to linkage disequilibrium (LD) block construction, resulting in 5,459 tag-SNPs, which were used for population structure and GWAS analyses. Population structure analysis revealed nine distinct sub-populations (k = 9) within the panel. GWAS, using three multi-locus models, identified 27 consistent and stable marker-trait associations (MTAs) for six sodicity tolerance traits across 10 chromosomes. A candidate gene search within the corresponding LD block regions identified 57 putative candidate genes associated with sodicity tolerance. Furthermore, gene-based haplotype analysis was conducted for these candidates and revealed that four genes-encoding ADP-glucose pyrophosphorylase, phenolics efflux transporter, DUF1296 family proteins, and F-box domain-containing proteins-exhibited significant differences among their haplotype groups. These candidate genes may serve as valuable resources for rice genetic improvement programs aimed at developing sodicity-tolerant rice cultivars.

Scutellaria baicalensis, a traditional medicinal plant originating in China, is widely cultivated for its therapeutic properties. The main bioactive substances in S. baicalensis are flavonoids, which exhibit extensive antibacterial and antiviral activities. However, the contents of these valuable natural product ingredients are relatively low in the plant. MYB transcription factors play crucial roles in regulating plant secondary metabolism, including flavonoid biosynthesis. While the regulation of MYB transcription factors has been extensively studied in various species, research on their role in S. baicalensis remains relatively scarce. In this study, we identified SbMYB111, belonging to the S7 subgroup of R2R3-MYB transcription factors, which functions as a transcriptional activator and is localized in the nucleus. Through heterologous overexpression of SbMYB111 in Arabidopsis thaliana and suppression expression in S. baicalensis, we demonstrated that SbMYB111 acts as a positive regulator in the biosynthesis of flavonoids. Furthermore, the yeast one-hybrid and dual-luciferase reporter gene assays validated that SbMYB111 activates the expression of SbC4H2, a key enzyme gene in the flavonoid biosynthesis pathway. This study provides a theoretical basis for understanding the transcriptional regulation mechanism of flavonoid synthesis and further developing medicinal resources of S.baicalensis.

Zanthoxylum armatum DC. fruit is a traditional spicy condiment and medicinal herb, and the prickly ash industry has developed into a pillar industry for specialty agricultural products in many regions of China. As one of the main components of Z. armatum, isoquinoline alkaloids have good biological activity and play an important role in the formation of flavor quality. In this study, we investigated the metabolites and genes involved in the biosynthesis of isoquinoline alkaloids in Z. armatum fruits during three developmental periods. A total of 1167 metabolites and 5204 differentially expressed genes were detected by combining metabolome, SMRT sequencing and Illumina sequencing. The annotation results of KEGG database showed that four metabolites (levodopa, dopamine, tyramine, and magnoflorine) and eight differentially expressed genes were involved in the biosynthesis of isoquinoline alkaloids in Z. armatum fruits. Specifically, metabolites Dopamine and Tyramine decreased with the development of Z. armatum, and the expression of the genes related to their regulation, Zardc00988 and Zardc23209, showed the same trend. This study contributes to our understanding of the biosynthesis and accumulation of Z. armatum isoquinoline alkaloids and provides a reference for the development of the medicinal value of Z. armatum.