Transcriptome profiling of Prunus persica plants under flooding

Key message Transcriptome of Prunus persica revealed several and specific differences in gene expression when subjected to flooding, which provides valuable information for identifying mechanisms involved in the response under stressful conditions. Soil flooding stress in fruit trees affects growth, vegetative and reproductive development, which is reflected in low productivity, poor fruit quality, and premature decay of trees. Using Illumina Hiseq2500 we performed transcriptome analysis of leaves from ‘Capdeboscq’ ( P. persica ) rootstocks, which are sensitive to hypoxia. Transcriptomes from control and flood-stressed plants (48 h) were compared, using P. persica as reference genome. The flooding conditions changed the transcription profile in ‘Capdeboscq’, and the RNA-seq analysis showed 2971 differentially expressed genes (DEGs), of which 1559 were up-regulated and 1412 were down-regulated. The functional scoring of DEGs was carried out by means of the software MapMan and through the identification of over-represented GOs referring to three ontological classes: biological processes, cell components and molecular function. The major up-regulated processes were those related to the secondary metabolism of lipids, sugars, and tetrapyrrole molecules whereas, for the down-regulated processes, the luminous reactions, photorespiration, metabolism of nitrate and cell wall have stood out. The transcriptome profiling of peach trees supports the development of specific molecular markers for the complete elucidation of molecular mechanisms involved in the response of P. persica under flooding, and this is essential to aid breeding programs in the selection of more tolerant genotypes.