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Simple Summary: Colorectal cancer originates from benign growths in the colon known as adenomas. Understanding how these adenomas become malignant is crucial to the early detection and prevention of colorectal cancer. This study examines DNA methylation and genetic differences among various types of advanced adenomas to identify potential markers that indicate progression toward cancer. By analyzing DNA methylation patterns, gene copy-number changes, and mutations in these lesions, particular signals and pathways associated with each subtype were found. These discoveries can help refine screening methods to detect distinct adenomas lesions at an early stage. By providing new insights into the initial changes leading to colorectal cancer, these findings may significantly impact approaches to prevention and early intervention strategies. Background: Colorectal cancer (CRC) is characterized by the uncontrolled growth of malignant colonic or rectal crypt epithelium. About 85% of CRCs evolve through a stepwise progression from advanced precancerous adenoma lesions. A better understanding of the evolution from adenoma to carcinoma can provide a window of opportunity not only for early detection and therapeutic intervention but potentially also for cancer prevention strategies. Methods: This study investigates the heterogeneous methylation, copy-number alteration (CNA), and mutation signals of histological adenoma subtypes in the context of progression from normal colon to advanced precancerous lesions (APLs) and early-stage CRC. Results: Differential methylation analysis revealed 2321 significantly altered regions among APLs: 137 hypermethylated regions in serrated vs. tubular, 2093 in serrated vs. tubulovillous, and 91 in tubular vs. tubulovillous adenoma subtypes. The most differentiating pathways for serrated adenomas belonged to cAMP signaling and the regulation of pluripotency of stem cells, while regions separating tubular and tubulovillous subtypes were enriched for WNT signaling. CNA events were mostly present in tubular or tubulovillous adenomas, with the most frequent signals being seen in chromosomes 7, 12, 19, and 20. In contrast, early-stage CRC exhibited signals in chromosomes 7, 8, and 20, indicating different processes between APL and early-stage CRC. Mutations reinforce subtype-level differences, showing specific alterations in each subtype. Conclusions: These findings are especially important for developing early detection or cancer prevention tests trying to capture adenoma signatures. [ABSTRACT FROM AUTHOR]

The olive tree (Olea europaea L.), which characterizes the agriculture of the Mediterranean basin, faces challenges adapting to high-density orchards and mechanized cultivation. This study addresses a key issue: controlling tree size to enhance efficiency and manageability in olive cultivation. Utilizing genetic mapping methods, we have identified significant Quantitative Trait Loci (QTL) and candidate genes associated with low-vigor traits in olive trees. Our research on the 'Koroneiki' F2 progeny, which exhibits low vigor traits but remains underutilized in breeding programs, has pinpointed a QTL linked to trunk basal diameter—a trait correlated with plant height based on morphological measurements. Results underscore a strong genetic control of these traits, with a consistent correlation observed over time. We identified two candidate genes — Acid Phosphatase 1, Shikimate O-hydroxycinnamoyltransferase, and a SNP Marker likely associated with Calcium Responsive Proteins — each potentially interacting with plant hormones to influence growth. Controlling olive tree size presents several challenges, including the genetic complexity of polygenic traits like size and vigor, and limited rootstock options. By integrating reference genomes with our genetic analysis, we offer a conceptual advancement that could substantially accelerate breeding timelines compared to traditional approaches. Although genome editing is still a future possibility due to the complexity of olive genetics and the species' recalcitrance to transformation, our study lays a foundational understanding to guide future breeding programs. By targeting the identified candidate genes, this research represents a pivotal step toward selecting new low-vigor genotypes and rootstocks, contributing to innovations in olive cultivation. [ABSTRACT FROM AUTHOR]

The olive tree (Olea europaea subsp. europaea L.) is one of the most important perennial crops in the Mediterranean Basin. Olive Scab, caused by the fungal species Spilocaea oleagina, a member of the Venturiaceae family, is among the most significant diseases affecting olive cultivation, prompting farmers to spend millions of euros annually on fungicides for its control. The fungal genus Venturia includes highly specialized species responsible for diseases in other crops, such as Apple Scab, caused by V. inaequalis. One of the most effective control strategies for Apple Scab has been developing and using resistant varieties. However, in the case of Olive Scab, genetic resistance remains relatively underexplored. In apples, breeders have identified approximately 20 resistance genes against V. inaequalis, known as Rvi genes, over recent decades. In this study, we identified and characterized four homologous genes to the Rvi family in olive, analyzing their genomic organization and expression profiles in silico. A total of 14 homologous sequences were identified in the olive genome, all sharing conserved domains typical of the leucine-rich repeat (LRR) superfamily, widely associated with plant immune responses. Functional annotation using gene ontology indicated enrichment in categories related to stimulus response and diverse biological processes. Notably, homologous sequences corresponding to apple proteins linked to V. inaequalis resistance exhibited high expression levels in response to biotic and abiotic stresses. These results indicate that olive trees may harbor resistance mechanisms analogous to those observed in apples, providing a foundation for further research into olive disease resistance and breeding programs. [ABSTRACT FROM AUTHOR]

A circadian clock (CC) has evolved in plants that synchronizes their growth and development with daily and seasonal cycles. A properly functioning circadian clock contributes to increasing plant growth, reproduction, and competitiveness. In plants, continuous light treatment has been a successful approach for obtaining novel knowledge about the circadian clock. The olive tree (Olea europaea L.) is one of the most important crops in the Mediterranean area, and, so far, limited information is available on its CC gene network. Here, we studied the behavior of circadian rhythm genes under LD (light/darkness) and LL (light/light) conditions, the relationships in this network, and the ability of the treatments to modulate gene expression in the photoprotective pigment and lipid biosynthesis pathways. One month of LL conditions increased olive growth performance, but LL exposure also caused reductions in vegetative growth and chlorophyll accumulation. A panel was designed for a study of the transcription expression levels of the genes involved in light perception, the CC, and secondary metabolite and fatty acid biosynthesis. Our results revealed that the levels of 78% of the transcripts exhibited intraday differences under LD conditions, and most of them retained this rhythmicity after exposure to one and two months of LL conditions. Furthermore, co-regulation within a complex network among genes of photoreceptors, anthocyanidins, and fatty acids biosynthesis was orchestrated by the transcription factor HY5. This research enriches our knowledge on olive trees grown under prolonged irradiation, which may be attractive for the scientific community involved in breeding programs for the improvement of this species. [ABSTRACT FROM AUTHOR]