Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice

Abstract

BackgroundIron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe2+) in the soil solution. Although the first interface of the element is in the roots, the consequences of an excessive uptake can be observed in several rice tissues. In an original attempt to find both genes and transposable elements involved in the response to an iron toxicity stress, we used a microarray approach to study the transcriptional responses of rice leaves of cv. Nipponbare (Oryza sativa L. ssp. japonica) to iron excess in nutrient solution.ResultsA large number of genes were significantly up- or down-regulated in leaves under the treatment. We analyzed the gene ontology and metabolic pathways of genes involved in the response to this stress and the cis-regulatory elements (CREs) present in the promoter region of up-regulated genes. The majority of genes act in the pathways of lipid metabolic process, carbohydrate metabolism, biosynthesis of secondary metabolites and plant hormones. We also found genes involved in iron acquisition and mobilization, transport of cations and regulatory mechanisms for iron responses, and in oxidative stress and reactive oxygen species detoxification. Promoter regions of 27% of genes up-regulated present at least one significant occurrence of an ABA-responsive CRE. Furthermore, and for the first time, we were able to show that iron stress triggers the up-regulation of many LTR-retrotransposons. We have established a complete inventory of transposable elements transcriptionally activated under iron excess and the CREs which are present in their LTRs.ConclusionThe short-term response of Nipponbare seedlings to iron excess, includes activation of genes involved in iron homeostasis, in particular transporters, transcription factors and ROS detoxification in the leaves, but also many transposable elements. Our data led to the identification of CREs which are associated with both genes and LTR-retrotransposons up-regulated under iron excess. Our results strengthen the idea that LTR-retrotransposons participate in the transcriptional response to stress and could thus confer an adaptive advantage for the plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0045-6) contains supplementary material, which is available to authorized users.

Genetic variability of Colobanthus quitensis from King George Island (Antarctica)

“…However, it was proved for many plant species that the tendency of TE to insert into repetitive DNA mitigates their deleterious potential (SanMiguel et al 1996;Kalendar et al 1999;Suoniemi et al 1997;Ramsay et al 1999). Furthermore, it was observed that a rapid mutational process in plants caused by TE during environmental stress, could be adventitious for the particular group of organisms, by rapidly increasing genotypic variability, which may be associated with adaptation for abiotic stress (Wessler 1996;Kalendar et al 2000;Finatto et al 2015). The development of iPBS technique allowed for tracking genomic changes induced by TE in species for which genomic information is limited: Prunus arme− niaca (Baránek et al 2012), Malus x domestica (Kuras et al 2013), Cicer species (Andeden et al 2013), Psidium guajava (Mehmood et al 2013), Myrica rubra (Chen and Liu 2014).…”

Research Article Iron excess in rice: from phenotypic changes to functional genomics of WRKY transcription factors.

“…This is the third report linking WRKYs with iron excess response (Ricachenevsky et al, 2010;Finatto et al, 2015). The first shows that OsWRKY80, which is also involved in rice drought response and senescence, increases its transcriptional expression (3-fold) after 6 DUS at 500 ppm (Ricachenevsky et al, 2010).…”

“…The first shows that OsWRKY80, which is also involved in rice drought response and senescence, increases its transcriptional expression (3-fold) after 6 DUS at 500 ppm (Ricachenevsky et al, 2010). The second is a microarray analysis showing that 19 WRKYs are up-regulated when rice is under iron excess (7 mM for 18 DUS), suggesting that this family can perform an important role in iron homeostasis (Finatto et al, 2015).…”

“…The RT-qPCR experiment was performed according to MIQE guidelines (Bustin et al, 2009), using oligonucleotide pairs for four WRKY up-regulated genes in rice shoots exposed to iron toxicity using a microarray approach (Finatto et al, 2015) (Table S1). Oligonucleotides were designed from sequences deposited in The Rice Annotation Project Data Base (RAP-DB), using Primer Express ® (Applied Biosystems TM , Foster City, CA, USA) ( Table S2).…”

“…Table S1. Differential expression in leaves of 18-day-old rice seedlings after 4 days under iron excess (Finatto et al, 2015). Table S2.…”