Wheat blast: The last enemy of hunger fighters.

Effective strategies for disease control are crucial for sustaining world food production and ensuring food security for the population. Wheat blast, a disease caused by the pathogen Magnaporthe oryzae pathotype Triticum, has been a concern for cereal producers and researchers due to its aggressiveness and rapid expansion. To solve this problem, the development of resistant varieties with durable resistance is an effective, economical and sustainable way to control the disease. Conventional breeding can be aided by several molecular tools to facilitate the mining of many sources of resistance, such as R genes and QTLs. The identification of new sources of resistance, whether in the wheat crop or in other cereals are an opportunity for efficient wheat breeding through the application of different techniques. Since this disease is still poorly studied in wheat, knowledge of the rice Magnaporthe pathotype may be adapted to control wheat blast. Thus, genetic mapping, molecular markers, transgenic approaches, and genomic editing are valuable technologies to fight wheat blast. This review aimed to compile the biotechnological alternatives available to accelerate the development of improved cultivars for resistance to wheat blast.

The Genetic Control of SEEDSTICK and LEUNIG-HOMOLOG in Seed and Fruit Development: New Insights into Cell Wall Control.

Although much is known about seed and fruit development at the molecular level, many gaps remain in our understanding of how cell wall modifications can impact developmental processes in plants, as well as how biomechanical alterations influence seed and fruit growth. Mutants of Arabidopsis thaliana constitute an excellent tool to study the function of gene families devoted to cell wall biogenesis. We have characterized a collection of lines carrying mutations in representative cell wall-related genes for seed and fruit size developmental defects, as well as altered germination rates. We have linked these studies to cell wall composition and structure. Interestingly, we have found that disruption of genes involved in pectin maturation and hemicellulose deposition strongly influence germination dynamics. Finally, we focused on two transcriptional regulators, SEEDSTICK (STK) and LEUNIG-HOMOLOG (LUH), which positively regulate seed growth. Herein, we demonstrate that these factors regulate specific aspects of cell wall properties such as pectin distribution. We propose a model wherein changes in seed coat structure due to alterations in the xyloglucan-cellulose matrix deposition and pectin maturation are critical for organ growth and germination. The results demonstrate the importance of cell wall properties and remodeling of polysaccharides as major factors responsible for seed development.

Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza.

Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar's genetics, but the way in which their genes express different phenotypes is not well understood. Further analysis of variation of grain quality genes using new information obtained from the wild relatives of rice should provide important insights into the evolution and potential use of these genetic resources. All analyses were conducted using bioinformatics approaches. The analysis of the protein sequences of grain quality genes across the Oryza suggest that the deletion/mutation of amino acids in active sites result in variations that can negatively affect specific steps of starch biosynthesis in the endosperm. On the other hand, the complete deletion of some genes in the wild species may not affect the amylose content. Here we present new insights for Starch Synthesis-Related Genes (SSRGs) evolution from starch-specific rice phenotypes.

Brazilian Genetic Diversity for Desirable and Undesirable Elements in the Wheat Grain.

Micronutrient deficiency affects billions of people, especially in countries where the diet is low in diversity with inadequate consumption of fruits, vegetables, and animal-source foods, and higher consumption of staple food, i.e., cereals, that have low concentrations of micronutrients. Genetic biofortification is a strategy to mitigate this problem and ensure nutritional security. Wheat is a target of genetic biofortification since it contributes significantly to the caloric requirement. The biofortification process involves a screening related to the presence of genetic variability for grain mineral content. Also, the accumulation of toxic elements must be considered to ensure food safety, because if ingested above the allowed concentrations, it represents health risks. In this sense, this study aimed to quantify the micronutrients iron, zinc, copper, selenium, and manganese and toxic elements arsenic and cadmium in a Brazilian wheat panel grown in Southern Brazil. The presence of genetic variability for the accumulation of micronutrients in the grain was detected; however, we observed that only the copper and manganese accumulation meet the human daily requirements. Iron, zinc, and selenium were detected in insufficient concentration to meet the daily demand. Arsenic and cadmium accumulation were not detected in wheat grain. The wheat genotypes grown in Brazil displayed a similar profile to that found in other countries which may be due to common high-yield breeding goals and the narrowing of the genetic variability, observed worldwide. Thus, the wheat genetic biofortification success in Brazil depends on the introduction of foreign genotypes, landraces, and wild relatives.

Insights obtained using different modules of the cotton uceA1.7 promoter.

MAIN CONCLUSION: The structure of the cotton uceA1.7 promoter and its modules was analyzed; the potential of their key sequences has been confirmed in different tissues, proving to be a good candidate for the development of new biotechnological tools. Transcriptional promoters are among the primary genetic engineering elements used to control genes of interest (GOIs) associated with agronomic traits. Cotton uceA1.7 was previously characterized as a constitutive promoter with activity higher than that of the constitutive promoter from the Cauliflower mosaic virus (CaMV) 35S gene in various plant tissues. In this study, we generated Arabidopsis thaliana homozygous events stably overexpressing the gfp reporter gene driven by different modules of the uceA1.7 promoter. The expression level of the reporter gene in different plant tissues and the transcriptional stability of these modules was determined compared to its full-length promoter and the 35S promoter. The full-length uceA1.7 promoter exhibited higher activity in different plant tissues compared to the 35S promoter. Two modules of the promoter produced a low and unstable transcription level compared to the other promoters. The other two modules rich in cis-regulatory elements showed similar activity levels to full-length uceA1.7 and 35S promoters but were less stable. This result suggests the location of a minimal portion of the promoter that is required to initiate transcription properly (the core promoter). Additionally, the full-length uceA1.7 promoter containing the 5'-untranslated region (UTR) is essential for higher transcriptional stability in various plant tissues. These findings confirm the potential use of the full-length uceA1.7 promoter for the development of new biotechnological tools (NBTs) to achieve higher expression levels of GOIs in, for example, the root or flower bud for the efficient control of phytonematodes and pest-insects, respectively, in important crops.

Expression levels of the agr locus and prfA gene during biofilm formation by Listeria monocytogenes on stainless steel and polystyrene during 8 to 48 h of incubation 10 to 37 °C.

The objective of this study was to compare the gene expression levels of the agr locus and prfA gene during adhesion and biofilm formation by four L. monocytogenes isolates (2 biofilm-forming and 2 non-forming) on stainless steel and polystyrene surfaces at different temperatures (10 °C, 20 °C and 37 °C), and times (8 h, 12 h, 24 h and 48 h). The agrA and prfA genes were expressed at higher levels than the agrBCD genes. The levels of agr locus expression were higher in the biofilm-forming strains, and the greatest difference between biofilm-forming and non-forming isolates was observed for the agrB, agrC and agrD genes. However, no difference in the expression of the prfA gene was seen among the isolates, independent of the biofilm-forming ability. Maximum expression of the agr locus and prfA gene was observed at 37 °C, whereas expression was lowest at 10 °C. The agr locus, and particularly the agrB, agrC and agrD genes, is important in the initial adhesion phase of biofilm production by L. monocytogenes, with this expression independent of prfA. In addition, the agr locus and prfA gene expression levels were strongly influenced by time and temperature.

Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases.

BACKGROUND: SUMOylation is an essential eukaryotic post-translation modification that, in plants, regulates numerous cellular processes, ranging from seed development to stress response. Using rice as a model crop plant, we searched for potential regulatory points that may influence the activity of the rice SUMOylation machinery genes. RESULTS: We analyzed the presence of putative cis-acting regulatory elements (CREs) within the promoter regions of the rice SUMOylation machinery genes and found CREs related to different cellular processes, including hormone signaling. We confirmed that the transcript levels of genes involved in target-SUMOylation, containing ABA- and GA-related CREs, are responsive to treatments with these hormones. Transcriptional analysis in Nipponbare (spp. japonica) and LC-93-4 (spp. indica), showed that the transcript levels of all studied genes are maintained in the two subspecies, under normal growth. OsSUMO3 is an exceptional case since it is expressed at low levels or is not detectable at all in LC-93-4 roots and shoots, respectively. We revealed post-transcriptional regulation by alternative splicing (AS) for all genes studied, except for SUMO coding genes, OsSIZ2, OsOTS3, and OsELS2. Some AS forms have the potential to alter protein domains and catalytic centers. We also performed the molecular and phenotypic characterization of T-DNA insertion lines of some of the genes under study. Knockouts of OsFUG1 and OsELS1 showed increased SUMOylation levels and non-overlapping phenotypes. The fug1 line showed a dwarf phenotype, and significant defects in fertility, seed weight, and panicle architecture, while the els1 line showed early flowering and decreased plant height. We suggest that OsELS1 is an ortholog of AtEsd4, which was also supported by our phylogenetic analysis. CONCLUSIONS: Overall, we provide a comprehensive analysis of the rice SUMOylation machinery and discuss possible effects of the regulation of these genes at the transcriptional and post-transcriptional level. We also contribute to the characterization of two rice SUMO proteases, OsELS1 and OsFUG1.

Can WRKY transcription factors help plants to overcome environmental challenges?

WRKY transcription factors (TFs) are responsible for the regulation of genes responsive to many plant growth and developmental cues, as well as to biotic and abiotic stresses. The modulation of gene expression by WRKY proteins primarily occurs by DNA binding at specific cis-regulatory elements, the W-box elements, which are short sequences located in the promoter region of certain genes. In addition, their action can occur through interaction with other TFs and the cellular transcription machinery. The current genome sequences available reveal a relatively large number of WRKY genes, reaching hundreds of copies. Recently, functional genomics studies in model plants have enabled the identification of function and mechanism of action of several WRKY TFs in plants. This review addresses the more recent studies in plants regarding the function of WRKY TFs in both model and crop plants for coping with environmental challenges, including a wide variety of abiotic and biotic stresses.

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.

Dealing with iron metabolism in rice: from breeding for stress tolerance to biofortification.

Iron is a well-known metal. Used by humankind since ancient times in many different ways, this element is present in all living organisms, where, unfortunately, it represents a two-way problem. Being an essential block in the composition of different proteins and metabolic pathways, iron is a vital component for animals and plants. That is why iron deficiency has a severe impact on the lives of different organisms, including humans, becoming a major concern, especially in developing countries where access to adequate nutrition is still difficult. On the other hand, this metal is also capable of causing damage when present in excess, becoming toxic to cells and affecting the whole organism. Because of its importance, iron absorption, transport and storage mechanisms have been extensively investigated in order to design alternatives that may solve this problem. As the understanding of the strategies that plants use to control iron homeostasis is an important step in the generation of improved plants that meet both human agricultural and nutritional needs, here we discuss some of the most important points about this topic.

Evolutionary analysis of the SUB1 locus across the Oryza genomes.

BACKGROUND: Tolerance 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. FINDINGS: Chromosomal 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. CONCLUSION: We 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.

Dealing with iron metabolism in rice: from breeding for stress tolerance to biofortification

Abstract Iron is a well-known metal. Used by humankind since ancient times in many different ways, this element is present in all living organisms, where, unfortunately, it represents a two-way problem. Being an essential block in the composition of different proteins and metabolic pathways, iron is a vital component for animals and plants. That is why iron deficiency has a severe impact on the lives of different organisms, including humans, becoming a major concern, especially in developing countries where access to adequate nutrition is still difficult. On the other hand, this metal is also capable of causing damage when present in excess, becoming toxic to cells and affecting the whole organism. Because of its importance, iron absorption, transport and storage mechanisms have been extensively investigated in order to design alternatives that may solve this problem. As the understanding of the strategies that plants use to control iron homeostasis is an important step in the generation of improved plants that meet both human agricultural and nutritional needs, here we discuss some of the most important points about this topic.

Comparative transcriptomics of rice plants under cold, iron, and salt stresses.

Abiotic stresses such as salinity, iron toxicity, and low temperatures are the main limiting factors of rice (Oryza sativa L.) yield. The elucidation of the genes involved in responses to these stresses is extremely important to understand the mechanisms that confer tolerance, as well as for the development of cultivars adapted to these conditions. In this study, the RNA-seq technique was used to compare the transcriptional profile of rice leaves (cv. BRS Querência) in stage V3, exposed to cold, iron, and salt stresses for 24 h. A range of 41 to 51 million reads was aligned, in which a total range of 88.47 to 89.21 % was mapped in the reference genome. For cold stress, 7905 differentially expressed genes (DEGs) were observed, 2092 for salt and 681 for iron stress; 370 of these were common to the three DEG stresses. Functional annotation by software MapMan demonstrated that cold stress usually promoted the greatest changes in the overall metabolism, and an enrichment analysis of overrepresented gene ontology (GO) terms showed that most of them are contained in plastids, ribosome, and chloroplasts. Saline stress induced a more complex interaction network of upregulated overrepresented GO terms with a relatively low number of genes compared with cold stress. Our study demonstrated a high number of differentially expressed genes under cold stress and a greater relationship between salt and iron stress levels. The physiological process most affected at the molecular level by the three stresses seems to be photosynthesis.

Global agricultural intensification during climate change: a role for genomics.

Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.

Transcriptional regulatory networks controlling woolliness in peach in response to preharvest gibberellin application and cold storage.

BACKGROUND: Postharvest fruit conservation relies on low temperatures and manipulations of hormone metabolism to maintain sensory properties. Peaches are susceptible to chilling injuries, such as 'woolliness' that is caused by juice loss leading to a 'wooly' fruit texture. Application of gibberellic acid at the initial stages of pit hardening impairs woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcriptional profiling to investigate the effects of gibberellic acid application and cold storage on harvested peaches. RESULTS: Approximately half of the investigated genes exhibited significant differential expression in response to the treatments. Cellular and developmental process gene ontologies were overrepresented among the differentially regulated genes, whereas sequences in cell death and immune response categories were underrepresented. Gene set enrichment demonstrated a predominant role of cold storage in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone responses exhibited a more complex transcriptional response, indicating an extensive network of crosstalk between hormone signaling and low temperatures. Time course transcriptional analyses demonstrate the large contribution of gene expression regulation on the biochemical changes leading to woolliness in peach. CONCLUSION: Overall, our results provide insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach and suggest that hormone mediated reprogramming previous to pit hardening affects the onset of chilling injuries.

Stay-green: a potentiality in plant breeding / Stay-green: uma potencialidade no melhoramento genético de plantas

Looking at the new demands of the global agricultural scenario, the search for more productive, efficient and stress adapted genotypes has attracted attention of plant breeders regarding plants with improved physiological characteristics. Therefore, the stay-green trait has taken proeminence as an important strategy to overcome the current yield plateaus allied with yield adaptability and stability. This review has aimed to bring light the main aspects of the stay-green character, showing their employment potential of plant breeding.

Observando as novas demandas do cenário agrícola mundial, a busca por genótipos mais produtivos, eficientes e adaptados a estresses tem chamado a atenção de melhoristas de plantas na análise de plantas com melhores características fisiológicas. Nesse contexto, o caráter stay-green vem tomando destaque, como uma importante estratégia em superar os atuais tetos de produtividade, aliados à adaptabilidade e estabilidade. Esta revisão tem com objetivo trazer à luz os principais aspectos relacionados ao caráter stay-green, mostrando suas potencialidades de emprego no melhoramento genético de plantas.

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects.

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

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

BACKGROUND: Iron 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 (Fe(2+)) 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. RESULTS: A 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. CONCLUSION: The 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.

The roots of future rice harvests.

Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.