Functional Genomics: Transcriptomics

Transcriptomics approaches in the Prunus genus started to be developed since the beginning of the new century. In few years, a set of tools have been developed and used, mainly in peach, apricot and almond. Transcriptomics tools have been primarily used to investigate fruit ripening and post-harvest physiology, but also disease resistance and flower transition. At the beginning of the second decade of the century, more than 100,000 ESTs are available in public databases, the majority of which were obtained from peach fruit. This repertoire has been used for digital expression analyses of transcriptome changes associated with fruit ripening and the appearance of chilling-induced post-harvest fruit disorders. The microarrays developed on peach ESTs have been extensively used mainly to investigate fruit biology but are soon going to be replaced by genome-wide platforms based on the recently released peach genome sequence. Transcriptome profi ling based on second generation DNA sequencing (SGS) technologies are also expected to have a tremendous impact in Prunus genomics. Pilot experiments conducted in several laboratories show that the peach genome sequence may be used for SGS approaches also in other Prunus species. Many molecular markers have been developed from ESTs and used to construct transcriptome maps in order to find the genetic determinants of Mendelian and quantitative traits. Transcriptomics is expected to speed up the fi nding of functional molecular markers to be used in marker-assisted programs for the development of new varieties across Prunus species. The use of information obtained with the new generation sequencing technologies will allow crossing information and looks for differential expression into different varieties within the same specie as well as different ones.