Abstract Site-specific recombination systems originating from bacterium and yeast have been widely used for targeted DNA rearrangement in various heterologous species, yet the genome-wide off-target potential and biological effects of recombinases in the host remain poorly understood. Here, we investigated how sustained expression of two widely used bacteriophage recombinases, Cre and φC31 influences plant growth, abiotic stress responses, and transcriptome reprogramming, and examined the presence and activity of the putative cryptic recombinase target sites in a representative perennial grass species, creeping bentgrass (Agrostis stolonifera). Independent transgenic lines constitutively expressing Cre or φC31 all exhibited enhanced plant growth with the φC31 lines displaying the strongest and most coordinated increase in shoot and root biomass. The φC31 lines also exhibited improved drought and salt tolerance associated with sustained relative water content, cell membrane integrity, and proline accumulation, whereas the Cre lines did not show a significant difference from wild type in salt stress response, but exhibited increased drought susceptibility. Genome-wide in silico analysis identified numerous loxP-like and att-like putative Cre/φC31 targets in the creeping bentgrass genome. However, transient reporter assays only detected robust Cre-mediated DNA recombination on canonical loxP sites, not on the highest-scoring loxP-like putative Cre target candidates. No φC31-mediated DNA recombination was detected under the conditions tested. Transcriptome analysis revealed extensive transcriptional reprogramming in the φC31 lines, including enrichment of defense- and hormone-related processes, whereas the Cre lines showed enrichment mainly in growth-, photosynthesis-, and energy metabolism-associated processes without comparable immune-response activation.
Abstract Potato early blight, caused by Alternaria solani, poses a significant threat to global potato yield. While telomere-binding proteins (TBPs) are known to play critical roles in plant growth and development, their roles in potato responses to early blight remain unclear. Here, we report that StTBP4 compromises potato resistance to A. solani by suppressing the transcription of StLOX2, a key gene in the jasmonic acid (JA) biosynthetic pathway. StTBP4 expression was significantly induced upon A. solani infection. Functional characterization of StTBP4-silenced (TRV:StTBP4) in potato and tobacco knockout lines (CR-nttbp4) demonstrated enhanced disease resistance, whereas tobacco transgenic overexpression lines (StTBP4-OE) exhibited increased susceptibility. Physiological assays indicated that StTBP4 modulates resistance primarily by dampening JA accumulation; although abscisic acid (ABA) levels were also altered, exogenous hormone and inhibitor treatments confirmed that the resistance phenotype depended on JA rather than ABA. Mechanistically, StTBP4 binds directly to the StLOX2 promoter to repress its transcription, thereby blocking the downstream JA-mediated reactive oxygen species (ROS) burst and pattern-triggered immunity (PTI). Collectively, our findings elucidate a molecular mechanism by which the StTBP4-StLOX2 module compromises plant immunity, highlighting StTBP4 as a potential target for engineering early blight resistance in potato.
Abstract Powdery scab, caused by the soil-borne pathogen Spongospora subterranea f. sp. subterranea, is a destructive potato disease causing substantial yield losses and reduced marketability. However, tuber-specific resistance mechanisms remain poorly understood, largely due to phenotyping bottlenecks and the dynamic infection process. Here, we developed an integrated AI-omics pipeline combining deep-learning-based image analysis with machine-learning-driven transcriptomic modelling to dissect the genetic architecture of resistance. Automated disease quantification across 12 cultivars over a 118-day growth cycle revealed tuber initiation and expansion as the two critical infection windows. Integration of high-resolution phenotypic data with transcriptomic profiling and a consensus machine-learning framework prioritized 292 high-confidence candidate genes. Functional categorisation identified lignin biosynthesis as a core defence hub, with seven lignin-associated genes, including the rate-limiting enzyme CCR and three MYB transcription factors, consistently selected across complementary algorithms. Cross-dataset validation confirmed the directional robustness of the resistance signature (68.8% concordance). Virus-induced gene silencing of St4CL1 and StCCoAOMT1 compromised resistance and reduced lignin accumulation, functionally validating the pathway’s contribution to tuber defence. Beyond lignin, our pipeline ranked several poorly characterised genes, including EDNR2GH7 and DIV3B, as high-priority candidates, pointing to additional novel resistance components. This integrative framework enables objective, high-throughput resistance screening, eliminates observer bias, and provides a broadly applicable blueprint for accelerating molecular breeding in other crop–pathogen systems constrained by conventional phenotyping.
ABSTRACT Lignin is a crucial secondary metabolite that supports the structural integrity of fruit plants and improves their capacity to adapt to external factors, including both biotic and abiotic stresses. However, excessive lignin accumulation can cause lignification in fruit products, reducing their flavor and nutritional value. Therefore, it is important to maintain lignin content in fruit products at appropriate levels. Recently, the biosynthesis and regulation of lignin have attracted widespread interest among researchers, leading to substantial advances in understanding the mechanisms underlying lignin accumulation in fruit. This article focuses on recent research regarding lignin accumulation and its molecular regulation in fruit. It offers a comprehensive analysis of its potential applications and provides insights into future research directions that warrant further exploration. Additionally, the influence of various environmental and external stimuli on lignin accumulation was examined. This article offers innovative ideas for enhancing fruit quality.
Flavor-related compounds, particularly γ-decalactone—the key contributor to the characteristic ‘peach-like’ aroma—serve as essential indicators of peach fruit quality and strongly influence consumer purchasing decisions. However, excessive application of N fertilizers has led to a significant decline in the flavor quality of peaches, posing a major obstacle to the sustainable development of the peach industry. Although this remains a critical challenge, the molecular mechanisms linking N to flavor compound biosynthesis are still not well characterized. In this study, we discovered that excessive N application reduced the biosynthesis of γ-decalactone in peach, based on multi-year field observations. Correlation analysis and expression profiling under N treatments revealed that two NAC (NAM-ATAF1/2-CUC2) transcription factors (TFs), PpNAC6 and PpNAC36, were involved in regulating γ-decalactone biosynthesis in response to N signaling. Genetic analyses indicated that PpNAC6 and PpNAC36 positively regulated the accumulation of γ-decalactone. Both yeast one-hybrid (Y1H) assays and dual-luciferase reporter assays consistently showed that PpNAC6 and PpNAC36 directly interact with the promoter regions of γ-decalactone biosynthesis-related genes (PpAAT2, PpAAT3, PpLOX1, PpLOX6, and PpFAD3) and significantly enhance their transcriptional activity. Furthermore, transgene verification demonstrated that the α subunit of peach SNF-related Kinase 1 (PpSnRK1α) suppresses γ-decalactone biosynthesis. Notably, we found that PpSnRK1α interacts with PpNAC6/PpNAC36 and selectively phosphorylates PpNAC36 in response to N, thus regulating γ-decalactone production. Our study uncovers the transcriptional regulatory network involved in PpSnRK1α-mediated phosphorylation of PpNAC6/PpNAC36, linking N signaling to γ-decalactone synthesis in peach, and provides insights for molecular breeding and precision fertilization to enhance peach flavor.
