Integrative Analysis of Transcriptomic Profiles and Physiological Responses Provide New Insights into Drought Stress Tolerance in Oil Palm (Elaeis guineensis Jacq.).

Oil palm (Elaeis guineensis Jacq.) is a highly productive crop economically significant for food, cosmetics, and biofuels. Abiotic stresses such as low water availability, salt accumulation, and high temperatures severely impact oil palm growth, physiology, and yield by restricting water flux among soil, plants, and the environment. While drought stress's physiological and biochemical effects on oil palm have been extensively studied, the molecular mechanisms underlying drought stress tolerance remain unclear. Under water deficit conditions, this study investigates two commercial E. guineensis cultivars, IRHO 7001 and IRHO 2501. Water deficit adversely affected the physiology of both cultivars, with IRHO 2501 being more severely impacted. After several days of water deficit, there was a 40% reduction in photosynthetic rate (A) for IRHO 7001 and a 58% decrease in IRHO 2501. Further into the drought conditions, there was a 75% reduction in A for IRHO 7001 and a 91% drop in IRHO 2501. Both cultivars reacted to the drought stress conditions by closing stomata and reducing the transpiration rate. Despite these differences, no significant variations were observed between the cultivars in stomatal conductance, transpiration, or instantaneous leaf-level water use efficiency. This indicates that IRHO 7001 is more tolerant to drought stress than IRHO 2501. A differential gene expression and network analysis was conducted to elucidate the differential responses of the cultivars. The DESeq2 algorithm identified 502 differentially expressed genes (DEGs). The gene coexpression network for IRHO 7001 comprised 274 DEGs and 46 predicted HUB genes, whereas IRHO 2501's network included 249 DEGs and 3 HUB genes. RT-qPCR validation of 15 DEGs confirmed the RNA-Seq data. The transcriptomic profiles and gene coexpression network analysis revealed a set of DEGs and HUB genes associated with regulatory and transcriptional functions. Notably, the zinc finger protein ZAT11 and linoleate 13S-lipoxygenase 2-1 (LOX2.1) were overexpressed in IRHO 2501 but under-expressed in IRHO 7001. Additionally, phytohormone crosstalk was identified as a central component in the response and adaptation of oil palm to drought stress.

Molecular network of the oil palm root response to aluminum stress.

BACKGROUND: The solubilization of aluminum ions (Al3+) that results from soil acidity (pH < 5.5) is a limiting factor in oil palm yield. Al can be uptaken by the plant roots affecting DNA replication and cell division and triggering root morphological alterations, nutrient and water deprivation. In different oil palm-producing countries, oil palm is planted in acidic soils, representing a challenge for achieving high productivity. Several studies have reported the morphological, physiological, and biochemical oil palm mechanisms in response to Al-stress. However, the molecular mechanisms are just partially understood. RESULTS: Differential gene expression and network analysis of four contrasting oil palm genotypes (IRHO 7001, CTR 3-0-12, CR 10-0-2, and CD 19 - 12) exposed to Al-stress helped to identify a set of genes and modules involved in oil palm early response to the metal. Networks including the ABA-independent transcription factors DREB1F and NAC and the calcium sensor Calmodulin-like (CML) that could induce the expression of internal detoxifying enzymes GRXC1, PER15, ROMT, ZSS1, BBI, and HS1 against Al-stress were identified. Also, some gene networks pinpoint the role of secondary metabolites like polyphenols, sesquiterpenoids, and antimicrobial components in reducing oxidative stress in oil palm seedlings. STOP1 expression could be the first step of the induction of common Al-response genes as an external detoxification mechanism mediated by ABA-dependent pathways. CONCLUSIONS: Twelve hub genes were validated in this study, supporting the reliability of the experimental design and network analysis. Differential expression analysis and systems biology approaches provide a better understanding of the molecular network mechanisms of the response to aluminum stress in oil palm roots. These findings settled a basis for further functional characterization of candidate genes associated with Al-stress in oil palm.

The Dynamic Interaction between Oil Palm and Phytophthora palmivora in Bud Rot Disease: Insights from Transcriptomic Analysis and Network Modelling.

Bud Rot, caused by Phytophthora palmivora, is considered one of the main diseases affecting African oil palm (Elaeis guineensis). In this study, we investigated the in vitro molecular dynamics of the pathogen-host interaction by analyzing gene expression profiles from oil palm genotypes that were either susceptible or resistant to the disease. We observed distinct interactions of P. palmivora with resistant and susceptible oil palms through co-expression network analysis. When interacting with susceptible genotypes, P. palmivora exhibited upregulation of carbohydrate and sulfate transport genes. These genes demonstrated co-expression with apoplastic and cytoplasmic effectors, including cell wall degrading enzymes, elicitins, and RxLR motif effectors. The pathogen manipulated susceptible oil palm materials, exacerbating the response and compromising the phenylpropanoid pathway, ultimately leading to susceptibility. In contrast, resistant materials exhibited control over their response through putative Heat Shock Proteins (HSP) that maintained homeostasis between primary metabolism and biotic defense. Co-expressed genes related to flavonoids, WRKY transcripts, lectin-type receptors, and LRR receptors may play important roles in pathogen control. Overall, the study provides new knowledge of the molecular mechanisms underlying the interaction between E. guineensis and P. palmivora, which can contribute to controlling Bud Rot in oil palms and gives new insights into the interactions of P. palmivora with their hosts.

Simultaneous transcriptome analysis of oil palm clones and Phytophthora palmivora reveals oil palm defense strategies.

Phytophthora palmivora is an oomycete that causes oil palm bud rot disease. To understand the molecular mechanisms of this disease, palm clones with contrasting responses (Ortet 34, resistant and Ortet 57, susceptible) were inoculated with P. palmivora, and RNAseq gene expression analysis was performed. The transcriptome was obtained by sequencing using Illumina HiSeq2500 technology during the asymptomatic phase (24, 72 and 120 hours postinfection, hpi). A simultaneous analysis of differentially expressed gene (DEG) profiles in palm and P. palmivora was carried out. Additionally, Gene Ontology (GO) and gene network analysis revealed differences in the transcriptional profile of the two ortets, where a high specificity of the pathogen to colonize the susceptible ortet was found. The transcriptional analysis provided an overview of the genes involved in the recognition and signaling of this pathosystem, where different transcription factors, phytohormones, proteins associated with cell wall hardening and nitrogen metabolism contribute to the resistance of oil palm to P. palmivora. This research provides a description of the molecular response of oil palm to P. palmivora, thus becoming an important source of molecular markers for the study of genotypes resistant to bud rot disease.