Abstract
Cultivated tomato (Solanum lycopersicum L.) is susceptible to abiotic stresses, including drought and chilling stress, while its wild relative (Solanum habrochaites) exhibits tolerance to many abiotic stresses. Chilling roots to 6°C induces rapid-onset water stress by impeding water movement from roots to shoots. Wild S. habrochaites responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato fails to close stomata and wilts. This phenotypic response (shoot turgor maintenance under root chilling) is controlled by a major QTL stm9 on chromosome 9 from S. habrochaites that was previously high-resolution mapped to a 0.32 cM region, but its effects on transcriptional regulation were unknown. Here we used paired near isogenic lines (NILs) differing only for the presence or absence of the S. habrochaites introgression containing stm9 in an otherwise S. lycopersicum background to investigate global transcriptional regulation in response to rapid-onset water stress induced by root chilling. NIL175 contains the S. habrochaites introgression and exhibits tolerance to root chilling stress, while NIL163 does not contain the introgression and is susceptible. RNA from roots of the two NILs was obtained at five time points during exposure to root chilling and mRNA-Seq performed. Differential expression analysis and hierarchical clustering of transcript levels were used to determine patterns of and changes in mRNA levels. Our results show that the transcriptional response of roots exposed to chilling stress is complex, with both overlapping and unique responses in tolerant and susceptible lines. In general, susceptible NIL 163 had a more complex transcriptional response to root chilling, while NIL175 exhibited a more targeted response to the imposed stress. Our evidence suggests that both the tolerant and susceptible NILs may be primed for response to root-chilling, with many of these response genes located on chromosome 9. Furthermore, serine/threonine kinase activity likely has an important role in the root chilling response of tolerant NIL175.
Highlights
Plant exposure to abiotic stresses may limit plant growth and development, and in crop plants may affect yield
We looked at genome-wide patterns of transcriptional regulation in a set of paired near isogenic lines (NILs) that differed in their tolerance to rapid-onset water stress induced by root chilling
We observed overlap between root chilling-tolerant NIL175 and chilling susceptible NIL163 for significantly enriched Gene ontology (GO) terms related to cell communication, transcription factor activity, various metabolic processes, response to light, and response to oxygen-containing compounds
Summary
Plant exposure to abiotic stresses may limit plant growth and development, and in crop plants may affect yield. Abiotic stresses such as drought, salinity, and temperature extremes may lead to turgor loss, disorganization of membranes, loss of protein activity, increased levels of reactive oxygen species (ROS) and subsequent oxidative damage (Krasensky and Jonak, 2012). Seedlings exposed to cold soils during the spring may experience root chilling stress leading to wilting and injury due to decreased water and nutrient uptake that affects plant growth and yield (Nobel, 1983, 1999; Allen and Ort, 2001)
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