Transcriptomic analysis of barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.): tool for crop improvement.

The thesis is focused on differential transcriptomics analysis of barley (Hordeum vulgare) and wheat (Triticum aestivum), two economically important cereals. It is also described the development of a new bioinformatics software allowing the annotation of novel transcripts and the functional analysis of differentially expressed genes. The theoretical part deals with the description of the main technologies of RNA-sequencing, design of the RNA-sequencing experiment and down-stream bioinformatics analysis. The experimental part is divided into three chapters. The first chapter aimed to understand the differential transcriptomics of transgenic barley lines overexpressing the Arabidopsis cytokinin dehydrogenase 1 gene under the control of the mild root specific promotor of maize -glycosidase. The results showed transgenic lines are more tolerant to drought than the wild-type plants, mainly due to the alteration of their root architecture and a stronger lignification of root tissue. The second chapter is focused on the development of SATrans, new freely available software for the annotation of transcriptome and the functional analysis of differentially expressed genes. The software was developed with Perl and MySQL as programing languages and has been tested on a test data set. It provided a fast and robust functional annotation of novel sequences and performed advanced gene ontology analysis of the differentially expressed genes. The last chapter covered different approaches to analyze RNAseq data generated for four new inbred lines of hexaploid wheat with different root architecture. Three different assembly approaches (ab initio, de novo and combined) were used and evaluated for their ability to provide the best reference wheat transcriptome for downstream analyses. The combined approach, i.e. coupling ab initio and de novo transcriptome assemblies, was evaluated as the best tool to generate a root-specific reference transcriptome. Down-stream bioinformatics analyses were performed in order to highlight the genes whose differential expression might be related to various root architecture observed between for the four-wheat new inbred lines. The data showed that few biological processes were affected, including the transmembrane transport of the phytohormone auxin and the hydrolysis of its conjugates. Nevertheless, our hypothesis will have to be supported by qPCR analysis and strong physiological experiments.