Background: Many commercial banana varieties lack sources of resistance to pests and diseases, as a consequence of sterility and narrow genetic background. Fertile wild relatives, by contrast, possess greater variability and represent potential sources of disease resistance genes (R-genes). The largest known family of plant R-genes encode proteins with nucleotide-binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. Conserved motifs in such genes in diverse plant species offer a means for isolation of candidate genes in banana which may be involved in plant defence.

Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.

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Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where it meets its natural condition of high rainfall throughout the year. The palm oil industry faces criticism due to a series of practices that was considered not environmentally sustainable, and it finds itself under pressure to adopt new and innovative procedures to reverse this negative public perception. Cultivating this oilseed crop outside the rainforest zone is only possible using artificial irrigation. Close to 30% of the world’s irrigated agricultural lands also face problems due to salinity stress. Consequently, the research community must consider drought and salinity together when studying to empower breeding programs in order to develop superior genotypes adapted to those potential new areas for oil palm cultivation. Multi-Omics Integration (MOI) offers a new window of opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity tolerance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA), and MOI study on the leaves of young oil palm plants submitted to very high salinity stress. Taken together, a total of 1239 proteins were positively regulated, and 1660 were negatively regulated in transcriptomics and proteomics analyses. Meanwhile, the metabolomics analysis revealed 37 metabolites that were upregulated and 92 that were downregulated. After performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE proteins, and 19 DE metabolites underwent MOI analysis, revealing several pathways affected by this stress, with at least one DE molecule in all three omics platforms used. The Cysteine and methionine metabolism (map00270) and Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each one with 20 DE molecules.

BackgroundPhotosynthesis can be roughly separated into biochemical and photochemical processes. Both are affected by drought and can be assessed by non-invasive standard methods. Gas exchange, which mainly assesses the first process, has well-defined protocols. It is considered a standard method for evaluation of plant responses to drought. Under such stress, assessment of photochemical apparatus by chlorophyll fluorescence needs improvement to become faster and reproducible, especially in growing plants under field conditions. For this, we developed a protocol based on chlorophyll fluorescence imaging, using a rapid light curve approach.ResultsAlmost all parameters obtained by rapid light curves have shown statistical differences between control and drought stressed maize plants. However, most of them were affected by induction processes, relaxation rate, and/or differences in chlorophyll content; while they all were influenced by actinic light intensity on each light step of light curve. Only the normalized parameters related to photochemical and non-photochemical quenching were strongly correlated with data obtained by gas exchange, but only from the light step in which the linear electron flow reached saturation.ConclusionsThe procedure developed in this study for discrimination of plant responses to water deficit stress proved to be as fast, efficient and reliable as the standard technique of gas exchange in order to discriminate the responses of maize genotypes to drought. However, unlike that, there is no need to perform daily and time consuming calibration routines. Moreover, plant acclimation to the dark is not required. The protocol can be applied to plants growing in both controlled conditions and full sunlight in the field. In addition, it generates parameters in a fast and accurate measurement process, which enables evaluating several plants in a short period of time.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-017-0209-z) contains supplementary material, which is available to authorized users.

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We have designed an in vitro experimental setup to study the role of sucrose in sugar-mediated acclimation of banana meristems using established highly proliferating meristem cultures. It is a first step toward the systems biology of a meristem and the understanding of how it can survive severe abiotic stress. Using the 2D-DIGE proteomic approach and a meristem-specific EST library, we describe the long-term acclimation response of banana meristems (after 2, 4, 8, and 14 days) and analyze the role of sucrose in this acclimation by setting up a control, a sorbitol, and a sucrose acclimation treatment over time. Sucrose synthase is the dominant enzyme for sucrose breakdown in meristem tissue, which is most likely related to its lower energy consumption. Metabolizing sucrose is of paramount importance to survive, but the uptake of sugar and its metabolism also drive respiration, which may result in limited oxygen levels. According to our data, a successful acclimation is correlated to an initial efficient uptake of sucrose and subsequently a reduced breakdown of sucrose and an induction of fermentation likely by a lack of oxygen.

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