Systemic transcriptomic profiling of drought-responsive genes and their targeting for enhancing tomato drought tolerance

Environmental stresses can greatly reduce crop productivity and largely affect quality. Due to global warming and climate change, abiotic stresses are predicted to become more frequent. In this scenario, to meet a growing global demand for food, breeding crops for enhanced tolerance to harsh environments is promising. The cultivated tomato (Solanum lycopersicum L.) is one of the most important vegetable crops in the world and the genome of its wild relatives Solanum pimpinellifolium, Solanum lycopersicoides and Solanum pennellii have been sequenced and their effective tolerance to extreme environments well documented. However, knowledge about tomato genetic diversity is limited and its phenotypic significance dramatically unpredictable to make its exploitation proficient. The aim of this study was to identify tomato genetic resources for drought tolerance, add insights into the genetic control of the tolerance and develop knowledge-based breeding approach targeting candidate genes. A reference nonredundant core collection of 75 tomato genotypes was selected from a larger collection of worldwide accessions genotyped by SSR markers. The core collection was screened for drought tolerance by applying two levels of soil water potential that is 10-20 kPa in the control treatment and 100-120 kPa for the drought treatment, respectively. The most contrasting phenotypes were selected based on the stability of leaf photo-assimilation rate, stomatal conductance, leaf chlorophyll content, ROS accumulation and drop in fruit yield. To deepen our understanding of the regulatory mechanisms that control photo-assimilation, photoassimilate allocation and fruit yield and quality under limited levels of available water, leaves, stems and fruit at different ripening stages were collected for RNA-seq analysis. Our results highlighted specific transcriptomic response to drought in a more tolerant (Red Setter) and a more sensitive (Severianin) tomato genotype. Several candidate transcripts for controlling water use efficiency and source-to-sink strength in response to drought were selected within photosynthesis, redox potential, carbohydrate metabolism, phytohormone responses, cell wall organization, and solute transport. Among others, the role of glutathione S- transferases genes will be validated for their role in drought tolerance by CRISPR/Cas approach. Segregant populations are currently being develop within tolerant selected genotypes and advanced breeding lines for further biotechnology-assisted breeding schemes.