Daniel da Rosa Farias

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

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.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago.Genome assemblies of 13 domesticated and wild rice relatives reveal salient features of genome evolution across the genus Oryza, especially rapid species diversification and turnover of transposons. This study also releases a complete long-read assembly of IR 8 ‘Miracle Rice’.

Ethylene response factors gene regulation and expression profiles under different stresses in rice

Stresses can cause large yield reductions in cultivated plants. The response to these stresses occurs via a plethora of signalling pathways, where a large number of genes is induced or repressed. Among the environmental stress responsive genes, there are the members of the ethylene response factors (ERF) gene family. The mRNA levels of different ERF are regulated by many hormones and molecules produced under different stress conditions. In this study, with the goal of identifying the response of rice ERF genes to environmental stress, it was analysed the transcriptional expression profile of 114 of these genes under stress by anoxia, salt and Magnaporthe grisea. Also, aiming to characterize how the regulation of ERF genes occurs, the amount of known cis regulatory elements in the promoter region of these genes and their association with the expression profiles under the tested conditions were also assessed. The results indicate that some ERF members present the same specific expression profiles under different environmental stresses, while others do not. Within the ERF family, the regulation of gene expression is complex for some genes which have many cis elements in their promoters, but simple for others, demonstrating high levels of divergence among them. The findings demonstrate the importance of the study of each ERF separately, since it is not possible to establish general rules for regulation and probably for the function of these genes.

Evolutionary analysis of the SUB1 locus across the Oryza genomes

BackgroundTolerance to complete submergence is recognized in a limited number of Asian rice (Oryza sativa L.) varieties, most of which contain submergence-inducible SUB1A on the polygenic SUBMERGENCE-1 (SUB1) locus. It has been shown that the SUB1 locus encodes two Ethylene-Responsive Factor (ERF) genes, SUB1B and SUB1C, in all O. sativa varieties. These genes were also found in O rufipogon and O nivara, wild relatives of O. sativa. However, detailed analysis of the polygenic locus in other Oryza species has not yet been made.FindingsChromosomal location, phylogenetic, and gene structure analyses have revealed that the SUB1 locus is conserved in the long arm of chromosome 9 in most Oryza species. We also show that the SUB1A-like gene of O. nivara is on chromosome 1 and that Leersia perrieri, a grass-tolerant to deep-flooding, presents three ERF genes in the SUB1 locus.ConclusionWe provide here a deeper insight into the evolutionary origin and variation of the SUB1 locus and raise the possibility that an association of these genes with flooding tolerance in L. perrieri may exist.

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

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.

Oryza glumaepatula Steud.

Oryza glumaepatula is the only native wild rice from the Americas that has a diploid genome (2n = 24). Thus, this species constitutes a source of genetic variability for the improvement of Oryza sativa cultivated in the New World. Wild rice species are important sources of commercially important characters, such as tolerance to acid soils and drought, yield potential, cytoplasmic male-sterility, heat tolerance, and elongation ability. The transference of alleles associated to target characters from O. glumaepatula into O. sativa could be done via introgression or through the use of genetic engineering. Oryza glumaepatula occurs in Central and South America and Caribe, growing in flooded areas, swamps, rivers, and humid areas with clay soils and that present invasive or colonizing behavior. It presents populations with perennial, annual, or biannual cycle, depending of geographical localization, with bushy growth, fragile stems near the base of plants, which can detach and fluctuate, forming new populations. Flowering occurs between October and November, presenting self- and outcrossing. Recently, O. glumaepatula had its genome sequenced, enabling comparative studies among different Oryza species. These studies suggest the expansion and contraction of gene families, diversity, and variation in the number of noncoding genes and divergence in the sequences among the species are associated with the adaptation of each species to different environmental conditions. These results demonstrate the importance of species from the Oryza genus in the development of new O. sativa cultivars.

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.