RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root

Abstract

Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. this may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RnA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short-(6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short-and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.

Ethylene Differentially Modulates Hypoxia Responses and Tolerance across Solanum Species

“…However, whether ethylene also contributes to metabolic hypoxia acclimation and if this correlates with flooding tolerance in these Solanum species is currently unknown. Several studies showed that genes involved in ethylene signaling and ethanolic fermentation are induced in response to flooding and hypoxia, but not consistently across all plant tissues in these Solanum species [37,40,41,45,46].…”

Identification of nitric oxide (NO)-responsive genes under hypoxia in tomato (Solanum lycopersicum L.) root

“…The current study represents the comparative transcriptome modulation of tomato (cv. Moneymaker) root in response to long-term (48 h) hypoxia 53 and SNP-application. Long-term hypoxia, but not SNP-treatment, resulted in significantly (P < 0.05) lower root fresh weight and chlorophyll content (SPAD values) ( Fig.…”

“…Plant age and growth condition was the same for both hypoxia and SNP studies. The hypoxia treatment has been previously described in details 53 . Tomato plants (Solanum lycopersicum L. cv.…”

“…The number of 1144 genes were differentially regulated (Padj < 0.05) in response to 48 h SNP-treatment (792 down-and 352 up-regulated genes). After comparison with 1421 differentially regulated genes (897 up-and 524 down-regulated) under 48 h hypoxia (Padj < 0.05) 53 , it was observed that 395 DEGs, were concertedly regulated under both, hypoxia and SNP-treatment ( Fig. 2).…”

“…Accumulation of ROS and reactive nitrogen species (RNS) is associated with low oxygen stress 53,86,87 . NO and its derivatives such as peroxynitrite (OONO -), dinitrogen trioxide (N 2 O 3 ), and nitrous acid (HNO 2 ) have been reported to be involved in the modification of cellular redox statues 88,89 .…”