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In the future, it is expected that integrative approaches that combine -omics technologies by using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and crop adaptation to the changing environment. CROPINNO project aims to implement multi-omics tools, with emphasis on epigenomics, for increased climate resilience of sunflower, chosen model crop for the project. In order to determine epigenetic variations in sunflower drought response, effects of drought and plant recovery are analysed at chromatin and transcriptional level. Preliminary drought stress protocols that mimic field progressive stress condition were developed with the aim to characterize sunflower response to the environmental challenges at molecular level using -omics tools, such as RNA-Seq and ChIP-Seq, as well as histone modifications such as H3K4me H3K27me3. Stress experiments are performed to identify both candidate genes and their chromatin state, associated with a variable molecular response among the characterized lines and the molecular signature, in the form of a list of regulatory pathways affected.

Drought as a major abiotic stress induces numerous, complex responses in plant cells. Those include gene expression alteration, accumulation of different metabolites, and synthesis of specific proteins. At molecular level, changes are under the control of complex regulatory pathways that include epigenetic mechanisms responsible for suitable and fast reactions to newly occurring stress conditions. Epigenetic modifications cause gene expression alteration through histone posttranscriptional modifications, DNA methylation, and small RNAs and lncRNAs expression. Some of these epigenetic modifications might pass on to the next generation, thus providing a good basis for a quicker response to drought stress. Revealing the epigenetic memory mechanisms involved in stress response could be of use in breeding programs for a prompt adaptation of plants to stress conditions. In the contest of the Cropinno project, funded under the Europe Horizon Programme, our aim is to develop an exploratory research project dedicated to the implementation of multi-omics tools for increasing the climate resilience of sunflowers.

Drought as a major abiotic stress induces numerous, complex responses in plant cells. Those include gene expression alteration, accumulation of different metabolites, and synthesis of specific proteins. Changes on a molecular level are under the control of complex regulatory pathways that include epigenetic mechanisms responsible for suitable and fast reactions to newly occurring stress conditions. Epigenetic modifications cause gene expression alteration through histone posttranscriptional modifications, DNA methylation, and small RNAs and lncRNAs expression. Some of these epigenetic modifications might pass on to the next generation and thus providing a good basis for a quicker response to drought stress. Revealing the epigenetic mechanisms involved in stress response could be of use in breeding programs for a prompt adaptation of plants to stress conditions. Hence, we have tested 30 sunflower inbred lines created at the Institute of Field and Vegetable Crops (IFVCNS) in in vitro conditions using PEG 6000 for creating a smaller panel of genotypes for analyzing their transcriptome alterations induced by drought.

Drought is the leading cause of agricultural production loss, with 75% of the world's harvested land sustaining yield losses due to this major abiotic stress. According to global climate models, drought conditions are expected to worsen as droughts will grow more severe and prolonged as a result of climate change. Production of sunflower, the fourth most important oil crop, is affected by drought, hence breeding for drought tolerance presents a major task for breeders. So far, the majority studies were oriented toward understanding changes drought causes on morphological, physiological and more recently, on genomic, transcriptomic and proteomic level. Epigenetic mechanisms of drought tolerance in sunflower are still to these days unrevealed. At the Institute of Field and Vegetable Crops several drought tests are being developed for detecting drought tolerant sunflower genotypes from our vast collection. In vitro tests with PEG6000 and rhizothron testing allows detecting genotypes tolerant at early stages of sunflower development, while pot tests in walk-in-chambers enables detection of tolerant sunflower in the flowering stage. We will analyze differentially expressed non-coding sRNAs and lncRNAs and their target genes between the most drought tolerant and least drought tolerant genotype for the identification of epiQTLs that can be used in sunflower breeding programs. Additionally, mild drought stress mimicking field conditions is applied to plants grown in pots at early stage of development, to investigate chromatin dynamics during stress application and after recovery from the stress.

To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.