Railson Schreinert dos Santos

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.

Destanização e conservação de frutos de jambolão

Alternative methods were investigated for the reduction of astringency (detannization) and conservation of Jambolan fruit (Syzygium cumini, L.). In the first experiment, fruits were harvested at an intermediate ripening stage, maintained at room temperature and subjected to the following treatments: control (normal atmosphere), 98kPa CO2, 20kPa CO2, 98kPa N2, ethylene (100ppm), 1-MCP (1ppm) followed by treatment with ethylene (100ppm) and 3,85mL absolute ethanol L-1. Acetaldehyde, soluble tannin, fruit firmness and astringency were evaluated. In the second experiment, fruits were harvested ripe and stored under passive modified atmosphere at room temperature (PMART, 23±1°C) and passive modified atmosphere under cold storage (PMACS, 4±1°C) for 5, 10 and 15 days. Fruits treated with N2, ethylene and ethanol showed the best detannization results, with increased acetaldehyde content, reduction of soluble tannins and astringency. However ethylene and ethanol treatments induced excessive softening of the fruit. Storage under PMAR kept the purple-blue color of fruits and, besides preventing fungal incidence, it aided the maintenance of the total phenolic content, ascorbic acid and antioxidant activity of fruits.

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.

Effects of hypoxia storage on gene transcript accumulation during tomato fruit ripening

Tomato (Solanum lycopersicum L.) is a climacteric fruit, i.e., during ripening an increase in ethylene synthesis and high rate of respiration are observed. Low oxygen levels might inhibit or block ethylene biosynthesis and therefore retard the ripening process. Despite commercial applications of low oxygen treatments, the precise mode of action of low oxygen in fruit tissues and ripening is not well understood. In order to delineate the molecular responses to low oxygen stress in fruits, hypoxia-responsive tomato genes encoding heat shock factors, heat shock proteins, and enzymes involved in fermentation and ethylene synthesis pathways were analyzed. In this study, tomato fruit stored under hypoxia conditions showed that HSP17.7 and HSP21 genes were highly induced by low oxygen level, indicating their primary role in maintaining cellular homeostasis after this stress.

Rice genotypes for drought tolerance: morphological and transcriptional evaluation of auxin-related genes

Drought stress affects crop quality and productivity. The challenge of increasing food availability for a growing worldwide demand relies on the development of tolerant cultivars that will need to be adapted to arid and semi-arid areas. In order to help the understanding of rice response to stress, the phenotypic response of 6 Brazilian rice cultivars and 2 different crosses between them were characterized under drought conditions. Since gene regulation is an important part of root morphological responses to stressful conditions, 4 genes related to auxin response and root modifications (OsGNOM1 CRL4, OsIAA1, OsCAND1 and OsRAA1) were evaluated. The expression of these genes was analyzed in stressed rice using public available microarray data and then through real-time quantitative polymerase chain reaction (RT-qPCR), in the 6 phenotypically evaluated Brazilian genotypes under standard conditions (absence of stress). Our results show that all genotypes lengthened its roots in response to drought, specially the 2 hybrids. The expression of these genes is modified in response to stress, and OsRAA1 has a very special behavior, constituting a target for future studies. Further steps include the study of polymorphisms in these genotypes in order to understand if differences in these genes or in regulatory regions can be associated with differences in root system architecture and/or stress tolerance.

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.

Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity

Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here.

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.