RESUMO
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.
RESUMO
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.
Assuntos
Grão Comestível , Triticum , Animais , Brasil , Variação Genética/genética , Humanos , Melhoramento Vegetal , Triticum/genéticaRESUMO
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.
Assuntos
Gossypium/genética , Regiões 5' não Traduzidas , Arabidopsis/genética , Caulimovirus/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Genes Reporter , Engenharia Genética , Gossypium/anatomia & histologia , Gossypium/crescimento & desenvolvimento , Plantas Geneticamente Modificadas , Regiões Promotoras GenéticasRESUMO
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.
Assuntos
Ferro/toxicidade , Oryza/efeitos dos fármacos , Reação em Cadeia da Polimerase em Tempo Real/métodos , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Gliceraldeído-3-Fosfato Desidrogenases/genética , Gliceraldeído-3-Fosfato Desidrogenases/metabolismo , Oryza/genética , Fator 1 de Elongação de Peptídeos/genética , Fator 1 de Elongação de Peptídeos/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/genética , Brotos de Planta/efeitos dos fármacos , Brotos de Planta/genética , RNA de Plantas/isolamento & purificação , RNA de Plantas/metabolismo , Reação em Cadeia da Polimerase em Tempo Real/normas , Padrões de Referência , Plântula/efeitos dos fármacos , Plântula/genética , Transcrição Gênica/efeitos dos fármacosRESUMO
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.
RESUMO
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.
Assuntos
Oryza/genética , Proteínas de Plantas/biossíntese , Estresse Fisiológico/genética , Transcriptoma/genética , Temperatura Baixa , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Ferro/toxicidade , Oryza/crescimento & desenvolvimento , Proteínas de Plantas/genética , Cloreto de Sódio/toxicidade , Transcriptoma/efeitos dos fármacosRESUMO
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.
Assuntos
Temperatura Baixa , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Giberelinas/farmacologia , Reguladores de Crescimento de Plantas/farmacologia , Prunus persica/genética , Frutas/genética , Frutas/metabolismo , Prunus persica/metabolismoRESUMO
Iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. Comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. A phylogenetic analysis of five metal homeostasis gene families (NAS, NRAMP, YSL, FRO, and IRT) selected in monocots, dicots, gymnosperms, and bryophytes was performed. The homologous genes were found using known iron homeostasis gene sequences of Oryza sativa, Arabidopsis thaliana, and Physcomitrella patens as queries. The phylogeny was constructed using bioinfomatics tools. A total of 243 gene sequences for 30 plant species were found. The evolutionary fingerprint analysis suggested a purifying selective pressure of iron homeostasis genes for most of the plant gene homologues. The NAS and YSL genes appear to accumulate more negative selection sites, suggesting a strong selective pressure on these two gene families. The divergence time analysis indicates IRT as the most ancient gene family and FRO as the most recent. NRAMP and YSL genes appear to share a close relationship in the evolution of iron homeostasis gene families.
Assuntos
Embriófitas/genética , Genes de Plantas , Ferro/metabolismo , Família Multigênica , Filogenia , Seleção Genética , Impressões Digitais de DNA , Homeostase/genéticaRESUMO
BACKGROUND: The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes. RESULTS: In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools. CONCLUSIONS: The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.
Assuntos
Biologia Computacional/métodos , Repetições Minissatélites/genética , Plantas/genética , Arabidopsis/genética , Composição de Bases/genética , Bryopsida/genética , Chlamydomonas reinhardtii/genética , Códon/genética , Bases de Dados de Ácidos Nucleicos , Dimerização , Etiquetas de Sequências Expressas , Loci Gênicos/genética , Marcadores Genéticos , Genoma de Planta/genética , Anotação de Sequência Molecular , Nucleotídeos/genética , Fases de Leitura Aberta/genética , Oryza/genética , Sequências Reguladoras de Ácido Nucleico/genética , Seleção Genética , Especificidade da EspécieRESUMO
BACKGROUND: The orderly progression through mitosis is regulated by the Anaphase-Promoting Complex (APC), a large multiprotein E3 ubiquitin ligase that targets key cell-cycle regulators for destruction by the 26 S proteasome. The APC is composed of at least 11 subunits and associates with additional regulatory activators during mitosis and interphase cycles. Despite extensive research on APC and activator functions in the cell cycle, only a few components have been functionally characterized in plants. RESULTS: Here, we describe an in-depth search for APC subunits and activator genes in the Arabidopsis, rice and poplar genomes. Also, searches in other genomes that are not completely sequenced were performed. Phylogenetic analyses indicate that some APC subunits and activator genes have experienced gene duplication events in plants, in contrast to animals. Expression patterns of paralog subunits and activators in rice could indicate that this duplication, rather than complete redundancy, could reflect initial specialization steps. The absence of subunit APC7 from the genome of some green algae species and as well as from early metazoan lineages, could mean that APC7 is not required for APC function in unicellular organisms and it may be a result of duplication of another tetratricopeptide (TPR) subunit. Analyses of TPR evolution suggest that duplications of subunits started from the central domains. CONCLUSIONS: The increased complexity of the APC gene structure, tied to the diversification of expression paths, suggests that land plants developed sophisticated mechanisms of APC regulation to cope with the sedentary life style and its associated environmental exposures.
Assuntos
Evolução Molecular , Proteínas de Plantas/genética , Plantas/genética , Complexos Ubiquitina-Proteína Ligase/genética , Sequência de Aminoácidos , Ciclossomo-Complexo Promotor de Anáfase , Arabidopsis/genética , Sequência de Bases , Clorófitas/enzimologia , Clorófitas/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Regulação da Expressão Gênica de Plantas , Variação Genética , Genoma de Planta/genética , Dados de Sequência Molecular , Oryza/genética , Filogenia , Proteínas de Plantas/classificação , Plantas/enzimologia , Populus/genética , Subunidades Proteicas/classificação , Subunidades Proteicas/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Rodófitas/enzimologia , Rodófitas/genética , Especificidade da Espécie , Sintenia , Complexos Ubiquitina-Proteína Ligase/classificaçãoRESUMO
Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size and tandem repeat fractions in expressed regions. The conservation of motifs among species and its implication on genome evolution and dynamics are discussed.
RESUMO
The present research was aimed at verifing the effect of different periods of ultraviolet light on the development of the symbiont fungus of leaf cutting ants belonging to the species Acromyrmex ambiguus, Acromyrmex crassispinus and Acromyrmex lundi, through the AFLP technique. The fungus were inoculated in Pagnocca"s medium and maintained in climatized cameras at 25 + 1C and 24 hours of darkness, for a period of 15 days. After that, they were exposed to ultraviolet light for 0, 5, 10, 15, 20, 25, and 30 minutes. At 45 days after the treatment, the extraction and standardization of DNA was performed. PCR reactions were tested using 24 AFLP primer combinations, from which four were selected because they presented larger polymorfism and consistence. The molecular data were transformed in binary mattrix and analyzed by the statistical program NTSYS v. 2.1. The four combinations of primers generated 152 polymorfic bands. The fungus populations from different Acromyrmex species presented a medium genetic similarity of the 37%, and the mutations induced by the ultraviolet light allowed to obtain more dissimilar isolates.(AU)
O presente trabalho teve por objetivo verificar o efeito de diferentes períodos de luz ultravioleta sobre a similaridade genética do fungo simbionte de formigas cortadeiras pertencentes às espécies Acromyrmex ambiguus, Acromyrmex crassispinus e Acromyrmex lundi, através da técnica AFLP. Os fungos foram inoculados em meio de cultura Pagnocca e mantidos em câmaras climatizadas à temperatura de 25 + 1C e escotofase de 24h, por um período de 15 dias. Posteriormente, foram expostos à luz ultravioleta por períodos de: 0, 5, 10, 15, 20, 25 e 30 minutos. Aos 45 dias após o tratamento, foi realizada a extração do DNA e padronização, realizando-se as reações de PCR por meio de 24 combinações de primers AFLP, das quais quatro foram selecionadas por apresentarem maior polimorfismo e consistência. Os dados moleculares foram transformados em matriz binária e analisados pelo programa estatístico NTSYS v. 2.1. As quatro combinações de primers utilizadas geraram 152 bandas polimórficas. As populações de fungos originárias de diferentes espécies de Acromyrmex apresentaram uma similaridade genética média de 37%, sendo que a indução de mutação através da luz ultravioleta permitiu obter isolados mais dissimilares.(AU)