Project description:Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level.

Project description:TIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in the defense responses to biotic and abiotic stresses. Here we identified the TIFY genes (designated as PvTIFY) from the legume common bean (Phaseolus vulgaris) and functionally characterized PvTIFY10C as a transcriptional regulator. Twenty-three genes from the PvTIFY gene family were identified through whole genome sequence analysis. Most of these were induced upon methyl-JA elicitation. We selected PvTIFY10C as a representative JA-responsive PvTIFY gene for further functional analysis. Transcriptome analysis via microarray hybridization using the designed Bean Custom Array 90K was performed in transgenic roots of composite plants with modulated -RNAi-silencing or over-expression- PvTIFY10C gene expression. Data were interpreted using Mapman adapted to common bean. Microarray differential gene expression data were validated by real-time qRT-PCR expression analysis. Comparative global gene expression analysis revealed opposite regulatory changes in processes such as RNA and protein regulation, stress response and metabolism in silenced vs. over-expressing roots. These data point to transcript reprogramming -mainly repression- orchestrated by PvTIFY10C. In addition we found that several PvTIFY genes as well as genes from the JA biosynthetic pathway responded to P-deficiency. Relevant P-responsive genes that participate in carbon metabolic pathways, cell wall synthesis, lipid metabolism, transport, DNA, RNA and protein regulation, signaling, were oppositely-regulated in control vs. PvTIFY10C silenced roots. These data indicate that PvTIFY10C regulates, directly or indirectly, gene expression of some P-responsive genes something that could be mediated by JA-signaling.

Project description:TIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in the defense responses to biotic and abiotic stresses. Here we identified the TIFY genes (designated as PvTIFY) from the legume common bean (Phaseolus vulgaris) and functionally characterized PvTIFY10C as a transcriptional regulator. Twenty-three genes from the PvTIFY gene family were identified through whole genome sequence analysis. Most of these were induced upon methyl-JA elicitation. We selected PvTIFY10C as a representative JA-responsive PvTIFY gene for further functional analysis. Transcriptome analysis via microarray hybridization using the designed Bean Custom Array 90K was performed in transgenic roots of composite plants with modulated -RNAi-silencing or over-expression- PvTIFY10C gene expression. Data were interpreted using Mapman adapted to common bean. Microarray differential gene expression data were validated by real-time qRT-PCR expression analysis. Comparative global gene expression analysis revealed opposite regulatory changes in processes such as RNA and protein regulation, stress response and metabolism in silenced vs. over-expressing roots. These data point to transcript reprogramming -mainly repression- orchestrated by PvTIFY10C. In addition we found that several PvTIFY genes as well as genes from the JA biosynthetic pathway responded to P-deficiency. Relevant P-responsive genes that participate in carbon metabolic pathways, cell wall synthesis, lipid metabolism, transport, DNA, RNA and protein regulation, signaling, were oppositely-regulated in control vs. PvTIFY10C silenced roots. These data indicate that PvTIFY10C regulates, directly or indirectly, gene expression of some P-responsive genes something that could be mediated by JA-signaling. Our work contributed to the functional characterization of PvTIFY transcriptional regulators in common bean, an agronomically important legume. Members from the large PvTIFY gene family are important global transcriptional regulators that could participate as repressors of the JA signaling pathway. In addition we propose that the JA-signaling pathway that involves PvTIFY genes might play a role in regulating the plant response / adaptation to P-starvation.

Project description:BackgroundTIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in defense responses to biotic and abiotic stresses. Here, we identified the TIFY genes (designated PvTIFY) from the legume common bean (Phaseolus vulgaris) and functionally characterized PvTIFY10C as a transcriptional regulator.ResultsNineteen genes from the PvTIFY gene family were identified through whole-genome sequence analysis. Most of these were induced upon methyl-JA elicitation. We selected PvTIFY10C as a representative JA-responsive PvTIFY gene for further functional analysis. Transcriptome analysis via microarray hybridization using the newly designed Bean Custom Array 90 K was performed on transgenic roots of composite plants with modulated (RNAi-silencing or over-expression) PvTIFY10C gene expression. Data were interpreted using Gene Ontology and MapMan adapted to common bean. Microarray differential gene expression data were validated by real-time qRT-PCR expression analysis. Comparative global gene expression analysis revealed opposite regulatory changes in processes such as RNA and protein regulation, stress responses and metabolism in PvTIFY10C silenced vs. over-expressing roots. These data point to transcript reprogramming (mainly repression) orchestrated by PvTIFY10C. In addition, we found that several PvTIFY genes, as well as genes from the JA biosynthetic pathway, responded to P-deficiency. Relevant P-responsive genes that participate in carbon metabolic pathways, cell wall synthesis, lipid metabolism, transport, DNA, RNA and protein regulation, and signaling were oppositely-regulated in control vs. PvTIFY10C-silenced roots of composite plants under P-stress. These data indicate that PvTIFY10C regulates, directly or indirectly, the expression of some P-responsive genes; this process could be mediated by JA-signaling.ConclusionOur work contributes to the functional characterization of PvTIFY transcriptional regulators in common bean, an agronomically important legume. Members from the large PvTIFY gene family are important global transcriptional regulators that could participate as repressors in the JA signaling pathway. In addition, we propose that the JA-signaling pathway involving PvTIFY genes might play a role in regulating the plant response/adaptation to P-starvation.

Project description:Background and aimsRoot architecture is a primary determinant of soil resource acquisition. We hypothesized that root architectural phenes will display both positive and negative interactions with each other for soil resource capture because of competition for internal resources and functional trade-offs in soil exploration.MethodsWe employed the functional-structural plant model SimRoot to explore how interactions among architectural phenes in common bean determine the acquisition of phosphate and nitrate, two key soil resources contrasting in mobility. We evaluated the utility of basal root whorl number (BRWN) when basal root growth angle, hypocotyl-borne roots and lateral root branching density (LRBD) were varied, under varying availability of phosphate and nitrate.Key resultsThree basal root whorls were optimal in most phenotypes. This optimum shifted towards greater values when LRBD decreased and to smaller numbers when LRBD increased. The maximum biomass accumulated for a given BRWN phenotype in a given limiting nutrient scenario depended upon root growth angle. Under phosphorus stress shallow phenotypes grew best, whereas under nitrate stress fanned phenotypes grew best. The effect of increased hypocotyl-borne roots depended upon BRWN as well as the limiting nutrient. Greater production of axial roots due to BRWN or hypocotyl-borne roots reduced rooting depth, leading to reduced biomass under nitrate-limiting conditions. Increased BRWN as well as greater LRBD increased root carbon consumption, resulting in reduced shoot biomass.ConclusionsWe conclude that the utility of a root architectural phenotype is determined by whether the constituent phenes are synergistic or antagonistic. Competition for internal resources and trade-offs for external resources result in multiple phenotypes being optimal under a given nutrient regime. We also find that no single phenotype is optimal across contrasting environments. These results have implications for understanding plant evolution and also for the breeding of more stress-tolerant crop phenotypes.

Project description:Common bean (Phaseolus vulgaris L.) is a staple food in Brazil with both nutritional and socioeconomic importance. As an orphan crop, it has not received as much research attention as the commodity crops. Crop losses are strongly related to virus diseases transmitted by the whitefly Bemisia tabaci, one of the most important agricultural pests in the world. The main method of managing whitefly-transmitted viruses has been the application of insecticides to reduce vector populations. Compared to chemical vector control, a more sustainable strategy for managing insect-borne viruses is the development of resistant/tolerant cultivars. RNA interference has been applied to develop plant lines resistant to the whitefly in other species, such as tomato, lettuce and tobacco. Still, no whitefly-resistant plant has been made commercially available to date. Common bean is a recalcitrant species to in vitro regeneration; therefore, stable genetic transformation of this plant has been achieved only at low frequencies (<1%) using particle bombardment. In the present work, two transgenic common bean lines were obtained with an intron-hairpin construct to induce post-transcriptional gene silencing against the B. tabaci vATPase (Bt-vATPase) gene, with stable expression of siRNA. Northern blot analysis revealed the presence of bands of expected size for siRNA in leaf samples of the line Bt-22.5, while in the other line (11.5), the amount of siRNA produced was significantly smaller. Bioassays were conducted with both lines, but only the line Bt-22.5 was associated with significant mortality of adult insects (97% when insects were fed on detached leaves and 59% on the whole plant). The expression of the Bt-vATPase gene was 50% lower (p < 0.05) in insects that fed on the transgenic line Bt-22.5, when compared to non-transgenic controls. The transgenic line did not affect the virus transmission ability of the insects. Moreover, no effect was observed on the reproduction of non-target organisms, such as the black aphid Aphis craccivora, the leafminer Liriomyza sp. and the whitefly parasitoid Encarsia formosa. The results presented here serve as a basis for the development of whitefly-tolerant transgenic elite common bean cultivars, with potential to contribute to the management of the whitefly and virus diseases.

Project description:BACKGROUND:Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. METHODS:An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. RESULTS:Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. CONCLUSIONS:The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.

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Basal root whorl number: a modulator of phosphorus acquisition in common bean (Phaseolus vulgaris).

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Basal root whorl number: a modulator of phosphorus acquisition in common bean (Phaseolus vulgaris).

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