The Quest for More Tolerant Rice: How High Concentrations of Iron Affect Alternative Splicing?

Artur Teixeira De Araujo Junior,Daniel Da Rosa Farias

doi:10.4172/2329-8936.1000122

Abstract

Rice (Oryza sativa L.) is a global staple food crop and an important model organism for plant studies. Recent reports have shown that alternative splicing is affected by many stressful conditions, suggesting its importance for the adaptation to adverse environments. Due to the little information on this subject, this study aimed to explore changes in splicing patterns that occur in response to high iron concentration in nutrient solutions. Here we quantified different kind of junctions and splicing events in the transcriptome of a relatively tolerant rice cultivar BRS Querencia, under iron excess with concentration of 300 mg L-1 Fe+2. Plants kept under standard conditions (control) presented 127,781 different splicing junctions, while stressed plants had 123,682 different junctions. Canonical (98.85% and 98.91%), semi-canonical (0.73% and 0.70%) and non-canonical (0.42% and 0.40%) junctions were found in control and stressed plants, respectively. Intron retention was the most frequent event (44.1% and 47.4%), followed by 3’ splice site (22.6% and 21.9%), exon skipping (18.9% and 17.3%) and alternative 5’ splice site (14.4% and 13.4%) in control and stressed plants, respectively. We also found 25 differentially expressed genes (five up and 20 down regulated) that are related to post-translational modifications. These results represent an important step in the understanding of how plant stress responses occur in an iron tolerant genotype, uncovering novel genes involved in iron stress response.

Highlights

Rice (Oryza sativa L.) is the second most widely grown cereal and one of the most important food sources for human nutrition
The analysis of 5’ and 3’ splice sites in all introns of Arabidopsis and rice indicates that these are very similar to human, with just some subtle differences in the frequencies of specific nucleotides at specific positions
These join together portions of two separate mRNA molecules leading to frame shifting, which is caused by an intron excision, a lower number of non-canonical sites junctions can be a defense strategy against the stress in this cultivar [10]

Summary

Introduction

Rice (Oryza sativa L.) is the second most widely grown cereal and one of the most important food sources for human nutrition. The low oxygen environment favors the reduction of this mineral, resulting in ferrous iron (Fe+2) [5], a quite soluble form present in higher concentrations in the soil solution This excessive iron can be absorbed and transported along the xylem, carried by the transpiration stream, leading to the generation of reactive oxygen species (ROS) in leaves, where the first symptoms are observed. AS is an important post-transcriptional regulatory mechanism that modulates gene expression and, eventually, protein forms and functions [8,9] This process consists in a posttranscriptional modification responsible for increasing the diversity of proteins generating two or more mRNA variants of a single gene causing the inclusion or exclusion of peptide sequences, and modulation of gene expression by producing mRNA variants [14]. Due to the little information available on this subject, in this study, we explore changes in splicing patterns

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