RNA-Seq FOR SUSTAINABLE SOIL MANAGEMENT IN TOMATO

The soil is the ultimate source of mineral nutrients and sustains several living organisms. In order to contrast soil degradation, it is important to convert conventional agricultural practices to environmentally sustainable management of crops. To this end, the application of biotic or abiotic bio-stimulants could be considered as a good strategy. PGPR (Plant Growth Promoting Rhizobacteria) are included into the biotic bio-stimulant category and can promote plant growth by: i) regulating nutritional and hormonal balance; ii) solubilizing nutrients and inducing resistance against plant pathogens. Humic acids (HA) (abiotic bio-stimulants) are naturally occurring organic compounds that arise from the decomposition of plant, animal, and microbial residues. They are chemically complex with no clearly defined chemical structure and can directly impact on metabolic plant processes, as well as can exert hormone-like effects. Compost tea combines biotic and abiotic bio-stimulants, because it is produced from compost by extraction and fermentation processes, conducted in liquid phase, with or without active aeration. The aim of this work is to develop a strategy of investigation, using RNA-Seq experiments, in order to describe the molecular mechanisms underpinning tomato plant response to bio-stimulation by PGPR, HA and compost-tea. The ultimate goal is the identification of key genes to be used in breeding programmes to develop low-input tomato varieties for sustainable agriculture. In a first phase, preliminary tests were performed in vitro to identify the growth-promoting bacterial strain belonging to Pseudomonas putida species, as well as the optimal concentration of both HA and compost-tea. The results showed, in general, an increase of root development in tomato treated seeds. In a second phase, tomato plants in controlled hydroponics conditions were inoculated with P. putida strain 16, or HA, or sterile/non-sterile compost-tea. Then, plant roots were sampled at 24, 48 and 72 h after bio-stimulation, and the RNA were extracted. Before proceeding with RNA sequencing, we checked if plant-bacteria interaction occurred by evaluating expression levels of candidate genes involved in the interaction using qRT-PCR. In case of P. putida, results confirmed that the interaction took place in the experimental conditions adopted since an increased expression of the genes was observed, in the roots, compared to the untreated control plants. At the moment, a directional single-end sequencing has been performed on an Illumina HiSeq1500 device only for all the sample collected after bio-stimulation with P. putida. Ongoing bioinformatics analysis includes: i) Read quality checking and adapter trimming; ii) read alignments to the tomato reference genome; iii) summarization: aggregation of sequence reads over gene loci as biological units; iv) intra- and inter-sample normalization; v) identification of differentially expressed genes. This work was carried out in the frame of the "GenoPom-pro - Integrating post-genomic platforms to enhance the tomato production chain" project (PON02_00395_3082360) and is supported by the PON R&C 2007-2013 grant funded by the Italian Ministry of Education, University and Research in cooperation with the European Funds for the Regional Development (FESR).