Plant cuticular wax plays an important role in resistance to environmental stresses. Eceriferum (CER) genes are involved in wax synthesis. However, little information is available for tomato species. In this study, 26 SlCER genes were identified in tomato (S. lycopersicum), and they were classified into four clades. The physicochemical properties and conserved motifs of their proteins were predicted. These SlCERs were mainly expressed in leaves, flowers or fruits, and most SlCERs played roles in response to abiotic stresses, especially drought stress. Furthermore, the changes in haplotypes indicated that SlCERs might have been involved in adapting to the environments for wild species S. pimpinellifolium before domestication. These findings would lay a foundation for future functional studies of SlCERs and also provide insights for anti-stress improvement in tomato in the near future.

Late blight is a destructive disease affecting tomato production. The identification and characterization of resistance (R) genes are critical for the breeding of late blight-resistant cultivars. The incompletely dominant gene Ph-2 confers resistance against the race T₁ of Phytophthora infestans in tomatoes. Herein, we identified Solyc10g085460 (RGA1) as a candidate gene for Ph-2 through the analysis of sequences and post-inoculation expression levels of genes located within the fine mapping interval. The RGA1 was subsequently validated to be a Ph-2 gene through targeted knockout and complementation analyses. It encodes a CC-NBS-LRR disease resistance protein, and transient expression assays conducted in the leaves of Nicotiana benthamiana indicate that Ph-2 is predominantly localized within the nucleus. In comparison to its susceptible allele (ph-2), the transient expression of Ph-2 can elicit hypersensitive responses (HR) in N. benthamiana, and subsequent investigations indicate that the structural integrity of the Ph-2 protein is likely a requirement for inducing HR in this species. Furthermore, ethylene and salicylic acid hormonal signaling pathways may mediate the transmission of the Ph-2 resistance signal, with PR1- and HR-related genes potentially involved in the Ph-2-mediated resistance. Our results could provide a theoretical foundation for the molecular breeding of tomato varieties resistant to late blight and offer valuable insights into elucidating the interaction mechanism between tomatoes and P. infestans.

Although the effects of soil type, plant genotype, and pathogen invasion on plant rhizosphere microbiomes have been preliminarily explored, their relative contributions and interactive influences on rhizobacterial community assembly remain unclear. In this study, we used tomato as a model to evaluate the individual and combined impacts of these three factors on rhizosphere bacterial community structure and function within a unified experimental framework. Microbiome-based analyses revealed that soil type was the predominant driver, explaining 53.1% of structural and 49.6% of functional variation, followed by tomato genotype (15.6% and 36.1%, respectively) and Fusarium oxysporum f. sp. lycopersici (Fol) inoculation (2.1% and 0.9%). Notably, the interaction between soil type and tomato genotype exerted a stronger influence than any other factor combination. Total nitrogen emerged as the key abiotic factor shaping the taxonomic composition of rhizobacterial communities, whereas soil pH played a dominant role in determining their functional profiles. Distinct tomato genotypes harbored rhizobacterial communities with divergent taxonomic and functional compositions. Although pathogen inoculation triggered the recruitment of beneficial microbes by the host plants, its impact on rhizobacterial community assembly was considerably weaker compared with the effects of soil type and tomato genotype. These findings provide a framework for understanding how soil, host, and pathogen collectively shape rhizobacterial communities and offer insights for optimizing microbiome management in crop production.

The root parasitic weed Phelipanche aegyptiaca (Pers.) Pomel poses a serious threat to solanaceous crops, leading to yield losses of up to 80% in tomato (Solanum lycopersicum L.). Strigolactones (SLs), derived from the carotenoid metabolic pathway, serve as key host-recognition signals for root-parasitic plants. This study investigated the molecular mechanisms of host resistance, focusing on the suppression of SL biosynthesis through altered carotenoid metabolism in the high-pigment tomato mutants hp-1 and og^c. Both pot experiment and in vitro seed germination assays demonstrated that the mutants exhibited reduced susceptibility to P. aegyptiaca and triggered lower germination rates in broomrape seeds compared to the wild-type cultivar AC. Quantitative RT-PCR analysis revealed a significant downregulation of SL biosynthesis genes (SlD27, SlCCD7, SlCCD8, SlMAX1, SlP450, SlDI4) in hp-1 at various parasitic stages post-inoculation, with a more pronounced suppression observed in hp-1 than in og^c. Notably, the extent of downregulation correlated with the enhanced resistance phenotype in hp-1. These findings highlight a synergistic resistance mechanism involving the coordinated regulation of carotenoid metabolism and SL biosynthesis, providing new insights into the molecular defense network underlying tomato-broomrape interactions.

Chloroplasts drive photosynthesis and regulate cellular signaling and phytohormone biosynthesis processes that greatly influence crop yield and quality traits. In this study, we identified a recessive chlorophyll-deficient mutant, reduced chlorophyll mutant 1t (rcm1t), from an advanced-generation tomato inbred line. Genetic and phenotypic characterization confirmed that chloroplast degradation accelerates rapidly and chlorosis occurs during late leaf development in the rcm1t mutant. Subsequently, we fine-mapped rcm1t to an approximately 60 kb region on chromosome 8. This interval encompasses Lutescent (L1)/SlRCM1, a well-characterized gene essential for chloroplast biogenesis and developmental maintenance. An allelism test between rcm1t and the previously characterized ethyl methanesulfonate (EMS)-induced rcm1 mutant revealed non-complementation. Moreover, transgenic complementation with the wild-type SlRCM1 coding sequence rescued the chloroplast premature senescence phenotype in rcm1t, providing definitive genetic evidence that rcm1t is a loss-of-function allele of SlRCM1. Resequencing identified a ~4.8 kb retrotransposon insertion in the first exon of the gene, which disrupts normal transcription and results in a premature stop codon. Quantification of abscisic acid (ABA) revealed significantly higher ABA levels in the rcm1t mutant than in the wild type. Protein–protein interaction analyses demonstrate that SlRCM1 interacts with SlNCED2. Osmotic stress assays showed that the rcm1t near-isogenic line exhibited enhanced tolerance under osmotic stress. This study successfully mapped the natural allele rcm1t of SlRCM1, preliminarily explored its potential application in enhancing plant tolerance to osmotic stress, and provided valuable insights for further elucidation of SlRCM1 function.

Tomato fruit firmness is a critical determinant of postharvest quality, dictating storage, ultimate shelf-life, and market value. While previous research on tomato fruit firmness has largely confined to wild or heirloom accessions, the genetic basis underlying this trait in modern elite breeding lines remains largely unexplored. In this study, we dissect the genetic architecture of fruit firmness using a recombinant inbred line (RIL) population derived from a cross between the modern inbred line CF-1 and the conventional cultivar Moneymaker. Quantitative trait locus (QTL) mapping revealed three firmness-associated loci on chromosomes 3, 4, and 5. The major-effect QTL qFF3.1 on chromosome 3 accounted for 11.55% of the phenotypic variation and was further confirmed by bulked segregant analysis (BSA-seq). Fine-mapping in the F _2:3 population delimited qFF3.1 to a 111 kb interval containing 26 predicted gene models. Combined analysis of functional annotations and RNA-seq data from near-isogenic lines (NILs), we prioritized six candidate genes associated with cell wall development and ethylene responsive, and four of which exhibiting differential expression patterns across fruit ripening stages. To our knowledge, qFF3.1 is the first major-effect QTL for fruit firmness identified in a modern tomato breeding line. Our findings offer molecular insights into the regulation of fruit firmness, and provide a strategy for improving shelf-life and other postharvest traits.