Leaf mold, one of the major diseases of tomato caused by Cladosporium fulvum (C. fulvum), can dramatically reduce the yield and cause multimillion dollar losses annually worldwide. Mapping the resistance genes (R genes) of C. fulvum and devising MAS based strategies for breeding new cultivars is an effective approach to improve the resistance in tomato. Up to now, many C. fulvum genes or QTLs have been mapped using different genetic materials, but few studies focused on Cf-10 gene positioning. In this study, we investigated the genetic rules for Cf-10 and used a novel combinatorial strategy to rapidly map the Cf-10 gene. Initially, the performance of F₁, F₂ and BC₁F₁ individuals after infection, demonstrated that the resistance against C. fulvum was controlled by a single dominant gene. Two pools of resistant and susceptible individuals from F₂ population were investigated, using mapping by sequencing approach and Cf-10 was found to be localized to 3.35 Mb and 3.74 Mb on chromosome 1, employing SNP/InDel index methods, respectively. After accounting for overlapping regions, these two algorithms yielded a total length of 3.29 Mb, narrowing down the target region. We further developed five serviceable KASP markers for this region based on sequencing data and conducted local QTL mapping using individuals from the F₂ population, except for mapping by sequencing as mentioned above. Finally Cf-10 gene was mapped spanning a region of 790 kb, where only one gene (Solyc01g007130.3) was annotated as probable receptor protein kinase TMK1 with a LRR motif, a common R gene characteristic. The RT-qPCR analysis further confirmed the localization and the relative expression of Solyc01g007130.3 in Ontario 792 and was found to be significantly higher than that in Moneymaker at 9 dpi and 12 dpi, respectively. This study proposed a novel combinatorial strategy by combining SNP-index, InDel-index analyses and local QTL mapping using KASP genotyping approach to rapidly map genes responsible for specific traits and provided a robust base for cloning the Cf-10 gene. Furthermore, these analyses suggest that Solyc01g007130.3 is a potential candidate to be regarded as Cf-10 gene.

In plants, alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that generates diverse mature transcripts from precursor mRNA, with the resulting functional proteins regulating a wide range of plant life activities. The regulation of AS is intricate and complex, playing pivotal roles in controlling plant biological processes like seed germination, flowering time control, growth, and development, as well as responses to abiotic and biotic stresses. The regulation of AS is a multilayered and intricately coordinated network system, primarily involving two core components: cis-regulatory elements and trans-acting factors on pre-mRNA. The precise execution of AS relies on the splicing factors by recognizing cis-elements to modulate splice site selection. Regulated by their own sequence variation, environmental cues, and identification of different spliceosomes, functional genes enable AS to achieve precise spatiotemporal regulation, thereby allowing plants to dynamically respond to developmental signals and environmental challenges. Here, we provide a comprehensive overview of AS patterns, functional genes, and splicing factors undergoing AS and its regulatory mechanisms during different processes, highlighting how AS-mediated gene regulation contributes to plant development and stress response, and offering potential strategies for improving plant adaptation by manipulation of AS-regulated genes.

Beet (Beta vulgaris L.) is an important economic crop widely cultivated across various regions worldwide. Its agricultural significance lies not only in its high sugar yield but also in its positive impact on agro-ecosystems and the economic value of its by-products. However, beet production and quality are adversely affected by multiple abiotic and biotic stresses, including pathogen infection, drought, salinity, and extreme temperatures. In recent years, numerous key stress-responsive genes have been identified, including BvPAL, BvPR, and Rz1-4, which mediate responses to biotic stresses, and BvM14-SAMS2, BvINT1;1, BvHMA3, BvCOLD1, and BvALKBH10B, which enhance tolerance to abiotic stresses. Meanwhile, core transcription factors such as bHLH, HSP, WRKY, and SPL show differential expression under stresses, suggesting that they may regulate stress-related genes and constitute major transcriptional modules enabling beet to withstand adverse conditions. In this study, we summarize the changes in beet under different stress conditions, combining gene information to reveal key regulatory changes in stress responses and how these molecular processes contribute to stress adaptation. This not only provides a theoretical basis for the improvement of beet stress tolerance and yield, but also offers potential directions for future breeding strategies in practical applications.

Transcriptome is a collection of mRNA transcripts in a specific physiological state which has become one of the hotspots in biological research to evaluate the genes and networks in different kinds of plants. Transcriptome sequencing technolog...

Invasion of Cladosporium fulvum causes the most serious diseases affecting the reproduction of tomatoes. Cf-10 gene carrying line showed remarkable resistance to C. fulvum. To exploit its defense response mechanism, we performed a multiple-omics profiling of Cf-10-carrying line and a susceptible line without carrying any resistance genes at control and 3 days postinoculation (dpi) of C. fulvum. We detected 54 differentially expressed miRNAs (DE-miRNAs) between the control and 3 dpi in the Cf-10-carrying line, which potentially regulated plant–pathogen interaction pathways and hormone signaling pathways. We also revealed 1,100 differentially expressed genes (DEGs) between the control and 3 dpi in the Cf-10-carrying line whose functions enriched in pathways that were potentially regulated by the DE-miRNAs. Integrating DE-miRNAs, gene expression and plant-hormone metabolites demonstrated a regulation network where the down-regulation of miRNAs at 3 dpi activated crucial resistance genes to trigger host hypersensitive cell death, improved hormone levels and upregulated the receptors/critical responsive transcription factors (TFs) of plant hormones, to shape immunity to the pathogen. Notably, we identified and expressionally validated that the downregulation of miR9472 would upregulate the expression of IAA-LEUCINE RESISTANT (ILR)-LIKE GENE 6 (ILL6), a gene that transforms JA to its major active component (+)-7-iso-jasmonoyl-l-isoleucine (JA-Ile), to improve the level of JA-Ile and activate JA-response genes in the Cf-10-carrying line. Our results demonstrated regulatory network and potential new pathway underlying the resistance to C. fulvum in Cf-10 gene carrying line, providing a more comprehensive genetic circuit and valuable gene targets for modulating resistance to the virus.

Climate change is intensifying environmental stresses, including drought, high temperature, and salinity, posing increasing challenges to plant growth and development. In addition to genetic variation, DNA methylation is an important epigenetic mechanism that regulates gene expression without altering the underlying DNA sequence through the addition of methyl groups to the fifth carbon of cytosine. Genome-wide dynamic changes in DNA methylation and demethylation at CG, CHG, and CHH sites contribute to the regulation of stress-responsive transcriptional networks, thereby shaping plant phenotypes and facilitating the establishment of stress memory. In recent years, advances in methylome profiling and molecular validation have shifted research from describing DNA methylation changes to elucidating their regulatory mechanisms. In this review, we summarize the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation, with a particular focus on its dynamic changes and regulatory roles in plant responses to cold, heat, drought, and salt stresses. It also compares the characteristics of DNA methylation responses across different types of stress and discusses their potential molecular mechanisms. Overall, DNA methylation represents an important regulatory layer in plant responses to abiotic challenges, and its dynamic changes are closely associated with plant adaptation, providing new insights into the mechanisms underlying stress adaptation.