Transcriptome sequencing of Prunus sp. rootstocks roots to identify candidate genes involved in the response to root asphyxia

Root hypoxia limits stone fruit tree (SFTs) development. To overcome this problem, SFTs are grafted on rootstocks with different degrees of tolerance to root hypoxia. However, the molecular base of such variability is largely unknown. Here we performed a transcriptome analysis of roots from rootstocks with contrasting responses to hypoxia using Illumina deep sequencing. Plants of the genotypes ‘Mariana 2624’ and 'Mazzard F12/1', tolerant and sensitive respectively, were subjected to hypoxic conditions by waterlogging. Transcriptomes from root samples collected from control (without waterlogging) and hypoxia stressed plants (6, 24 and 72h) were compared. The 81% of generated sequences were mapped to the reference genome of P. persica (L.). Analysis of the differentially expressed genes (DEG) revealed that most of the genes were down-regulated in the waterlogging stages. Regarding their identities and mode of regulation (up or down regulated) among DEGs, there was a high number of common DEG between the two genotypes for each sampling time, but also a high number of exclusive DEG was detected per genotype at each time. A few DEG presented opposite modes of regulations between the two genotypes throughout the hypoxia treatment. The most differentially affected functional categories are “oxidation reduction”, “carbohydrate metabolic process” and “oxidoreductase activity” at both genotypes, but only the susceptible genotype showed significant alteration of genes involved in responses to “oxidative stress”, “oxidoreductase activity”, “peroxidase activity” and “antioxidant activity”. This research represents a valuable source of information for further studies to identify the mechanism and genes that define tolerance to hypoxia in Prunus. Acknowledgment: CEAF_R08I1001 – CONICYT, FONDECYT 1121117, FONDECYT11110079 (RA).