The SlTPL3-SlWUS module regulates multi-locule formation in tomato by modulating auxin and gibberellin levels in the shoot apical meristem

Genome-Wide Identification of GH17s Family Genes and Biological Function Analysis of SlA6 in Tomato

Glycoside hydrolases (GHs), enzymes that break down glycosidic bonds in carbohydrates and between carbohydrates and non-carbohydrates, are prevalent in plants, animals, microorganisms, and other organisms. The tomato is a significant crop that contains the GH17 gene family. However, its role in tomatoes has yet to be fully investigated. In this study, we identified 43 GH17 genes from the tomato genome, distributed unevenly across 12 chromosomes. We further analyzed their gene structure, phylogenetic relationships, promoter elements, and expression patterns. The promoter element analysis indicated their potential roles in response to biotic and abiotic stresses as well as phytohormone effects on growth and development. The expression studies across different tomato tissues revealed that 10 genes were specifically expressed in floral organs, with SlA6 prominently expressed early during bud formation. By using CRISPR/Cas9 gene-editing technology, SlA6 knockout plants were generated. Phenotypic characterization showed that pollen viability, pollen tube germination, fruit weight, and seed number were significantly reduced in the Sla6 mutant, but the soluble solids content (TSS) was significantly higher in the Sla6 mutant, suggesting that SlA6 affects pollen development and fruit quality.

Transcriptome profiling reveals key regulatory factors and metabolic pathways associated with curd formation and development in broccoli

Broccoli, a cruciferous vegetable, has a unique indeterminate inflorescence structure known as curds. It is the main edible organ of broccoli and has a rich nutritional value and health benefits. However, the formation and development mechanism of the curd is still not well understood. In the present study, the shoot apical meristem (SAM) stage and three different development stages of curd (formation stage (FS), expansion stage (ES), and maturation stage (MS)) were identified and subjected to transcriptome sequencing to uncover the potential genes and regulatory networks involved in curd formation and development. The results indicated that the genes associated with the development of SAM such as BolAP1A, BolAP1C, BolCAL, and BolAGL6 play an important role in the abnormal differentiation of the curd apical buds. The genes, BolFRI, BolbHLH89, BolKAN4, BolAGL12, and BolAGL24, displayed significantly differential expression patterns in curd development may function in the regulation of the transition from inflorescence meristem (IM) to floral meristem (FM). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes (DEGs) indicate that phytohormones, such as auxin (AUX), gibberellins (GA), and abscisic acid (ABA) also play an important role in SAM proliferation and the transition from SAM to IM. In addition, the genes regulating photosynthetic reaction (BolLHCA1, BolLHCB1, BolPsbO, etc.) have a key involvement in the differentiation of secondary IMs during curd expansion. The genes associated with the metabolism of starch and sucrose (e.g., BolSPS4, BolBAM4) were significantly upregulated at the MS should contribute to the maturation of the curd. These findings provide new insights into the potential key regulatory factors and metabolic pathways involved in the formation and development of broccoli curds.

Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening

Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.

Cold stress induces malformed tomato fruits by breaking the feedback loops of stem cell regulation in floral meristem

Fruit malformation is a major constrain in fruit production worldwide resulting in substantial economic losses. The farmers for decades noticed that the chilling temperature before blooming often caused malformed fruits. However, the molecular mechanism underlying this phenomenon is unclear. Here we examined the fruit development in response to cold stress in tomato, and demonstrated that short-term cold stress increased the callose accumulation in both shoot apical and floral meristems, resulting in the symplastic isolation and altered intercellular movement of WUS. In contrast to the rapidly restored SlWUS transcription during the recovery from cold stress, the callose removal was delayed due to obstructed plasmodesmata. The delayed reinstatement of cell-to-cell transport of SlWUS prevented the activation of SlCLV3 and TAG1, causing the interrupted feedback inhibition of SlWUS expression, leading to the expanded stem cell population and malformed fruits. We further showed that the callose dynamics in response to short-term cold stress presumably exploits the mechanism of bud dormancy during the seasonal growth, involving two antagonistic hormones, abscisic acid and gibberellin. Our results provide a novel insight into the cold stress regulated malformation of fruit.