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1.
Hortic Res ; 8(1): 212, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34593775

RESUMO

Many studies showed that few degrees above tomato optimum growth temperature threshold can lead to serious loss in production. Therefore, the development of innovative strategies to obtain tomato cultivars with improved yield under high temperature conditions is a main goal both for basic genetic studies and breeding activities. In this paper, a F4 segregating population was phenotypically evaluated for quantitative and qualitative traits under heat stress conditions. Moreover, a genotyping by sequencing (GBS) approach has been employed for building up genomic selection (GS) models both for yield and soluble solid content (SCC). Several parameters, including training population size, composition and marker quality were tested to predict genotype performance under heat stress conditions. A good prediction accuracy for the two analyzed traits (0.729 for yield production and 0.715 for SCC) was obtained. The predicted models improved the genetic gain of selection in the next breeding cycles, suggesting that GS approach is a promising strategy to accelerate breeding for heat tolerance in tomato. Finally, the annotation of SNPs located in gene body regions combined with QTL analysis allowed the identification of five candidates putatively involved in high temperatures response, and the building up of a GS model based on calibrated panel of SNP markers.

2.
BMC Plant Biol ; 21(1): 358, 2021 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-34348650

RESUMO

BACKGROUND: The South America pinworm, Tuta absoluta, is a destructive pest of tomato that causes important losses worldwide. Breeding of resistant/tolerant tomato cultivars could be an effective strategy for T. absoluta management but, despite the economic importance of tomato, very limited information is available about its response to this treat. To elucidate the defense mechanisms to herbivore feeding a comparative analysis was performed between a tolerant and susceptible cultivated tomato at both morphological and transcriptome level to highlight constitutive leaf barriers, molecular and biochemical mechanisms to counter the effect of T. absoluta attack. RESULTS: The tolerant genotype showed an enhanced constitutive barrier possibly as result of the higher density of trichomes and increased inducible reactions upon mild infestation thanks to the activation/repression of key transcription factors regulating genes involved in cuticle formation and cell wall strength as well as of antinutritive enzymes, and genes involved in the production of chemical toxins and bioactive secondary metabolites. CONCLUSIONS: Overall, our findings suggest that tomato resilience to the South America pinworm is achieved by a combined strategy between constitutive and induced defense system. A well-orchestrated modulation of plant transcription regulation could ensure a trade-off between defense needs and fitness costs. Our finding can be further exploited for developing T. absoluta tolerant cultivars, acting as important component of integrated pest management strategy for more sustainable production.


Assuntos
Regulação da Expressão Gênica de Plantas , Lycopersicon esculentum/genética , Doenças das Plantas/genética , Folhas de Planta/genética , Transcriptoma , Animais , Perfilação da Expressão Gênica/métodos , Ontologia Genética , Interações Hospedeiro-Parasita , Larva/fisiologia , Lycopersicon esculentum/metabolismo , Lycopersicon esculentum/parasitologia , Mariposas/fisiologia , Doenças das Plantas/parasitologia , Folhas de Planta/metabolismo , Folhas de Planta/parasitologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA-Seq/métodos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Tricomas/genética , Tricomas/metabolismo , Tricomas/parasitologia
3.
Genes (Basel) ; 12(2)2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-33514027

RESUMO

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.


Assuntos
Genes de Plantas , Lycopersicon esculentum/genética , Melhoramento Vegetal , Resistência à Doença/genética , Evolução Molecular , Genoma de Planta , Estudo de Associação Genômica Ampla , Humanos , Família Multigênica , Doenças das Plantas/genética , Doenças das Plantas/microbiologia
4.
Plants (Basel) ; 9(9)2020 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-32962095

RESUMO

Genomic selection (GS) is a predictive approach that was built up to increase the rate of genetic gain per unit of time and reduce the generation interval by utilizing genome-wide markers in breeding programs. It has emerged as a valuable method for improving complex traits that are controlled by many genes with small effects. GS enables the prediction of the breeding value of candidate genotypes for selection. In this work, we address important issues related to GS and its implementation in the plant context with special emphasis on tomato breeding. Genomic constraints and critical parameters affecting the accuracy of prediction such as the number of markers, statistical model, phenotyping and complexity of trait, training population size and composition should be carefully evaluated. The comparison of GS approaches for facilitating the selection of tomato superior genotypes during breeding programs is also discussed. GS applied to tomato breeding has already been shown to be feasible. We illustrated how GS can improve the rate of gain in elite line selection, and descendent and backcross schemes. The GS schemes have begun to be delineated and computer science can provide support for future selection strategies. A new promising breeding framework is beginning to emerge for optimizing tomato improvement procedures.

5.
Genome Biol Evol ; 11(12): 3466-3477, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31730154

RESUMO

Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multitaxa reconstruction of NB-domain associations allowed us to identify the first NB-LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from Toll/interleukin receptor-NB-LRR members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis support the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell-surface LRR receptors.


Assuntos
Transferência Genética Horizontal , Proteínas NLR/genética , Proteínas de Plantas/genética , Domínios Proteicos/genética , Clorófitas/classificação , Clorófitas/genética , Resistência à Doença/genética , Evolução Molecular , Genoma de Planta/genética , Genômica , Proteínas NLR/metabolismo , Motivos de Nucleotídeos , Óperon , Filogenia , Imunidade Vegetal , Proteínas de Plantas/metabolismo , Plantas/classificação , Plantas/genética
6.
Plant Physiol Biochem ; 143: 50-60, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31479882

RESUMO

The huge amounts of biomass residues, remaining in the field after tomato fruits harvesting, can be utilized to produce bioenergy. A multiple level approach aimed to characterize two Solanum pennellii introgression lines (ILs), with contrasting phenotypes for plant architecture and biomass was carried out. The study of gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation enabled the discovery of key genes and cell processes involved biomass accumulation and composition. Enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplasts and mitochondria energy fluxes. Microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and processability.


Assuntos
Parede Celular/metabolismo , Lycopersicon esculentum/metabolismo , Biomassa , Parede Celular/fisiologia , Lycopersicon esculentum/fisiologia , Folhas de Planta/metabolismo , Folhas de Planta/fisiologia , Locos de Características Quantitativas/genética
7.
Sci Rep ; 9(1): 11769, 2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409808

RESUMO

With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.


Assuntos
Cromossomos de Plantas , Evolução Molecular , Genoma de Planta , Solanum melongena/genética , Etilenos/metabolismo , Redes Reguladoras de Genes , MicroRNAs/genética , Solanum melongena/metabolismo
8.
BMC Plant Biol ; 19(1): 150, 2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30995906

RESUMO

BACKGROUND: Powdery mildew (PM) is a widespread fungal disease of plants in temperate climates, causing significant economic losses in agricultural settings. Specific homologs of the MLO gene family are PM susceptibility factors, as their loss-of function results in durable PM resistance (mlo resistance) in several plant species. The role of MLO susceptibility genes in plant-pathogen interactions is still elusive, however it is known that they are strongly upregulated following PM infection. RESULTS: In this study, we investigated the structure of 414 Putative Promoter Regions (PPRs) of MLO genes and highlighted motif and regulatory element patterns related to genomic relationships among species and phylogenetic distance among homologs. A TC box-like motif and a thymine-rich motif were found to be overrepresented in MLO genes transcriptionally upregulated upon infection with PM fungi. As proof of concept, we showed that the expression of a melon (Cucumis melo L.) gene enriched for the motifs above mentioned was strongly upregulated upon infection with the PM fungus Podosphaera xanthii. CONCLUSION: While identifying a candidate MLO susceptibility gene in melon, this study provides insight on the transcriptional control of MLO genes and indicates diagnostic features useful to identify MLO susceptibility genes across species affected by the PM disease.


Assuntos
Sequência Conservada/genética , Evolução Molecular , Genes de Plantas , Regiões Promotoras Genéticas , Ascomicetos/fisiologia , Sequência de Bases , Biologia Computacional , Cucurbitaceae/genética , Cucurbitaceae/microbiologia , Regulação da Expressão Gênica de Plantas , Motivos de Nucleotídeos/genética , Filogenia , Doenças das Plantas/microbiologia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transcrição Genética , Regulação para Cima/genética
9.
BMC Plant Biol ; 17(1): 66, 2017 03 28.
Artigo em Inglês | MEDLINE | ID: mdl-28347287

RESUMO

BACKGROUND: The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. We used a systems biology approach to elucidate the complex interacting mechanisms regulating the plasticity of sensorial traits. To investigate environmentally challenged transcriptomic and metabolomic remodeling and evaluate the organoleptic consequences of such variations we grown three tomato varieties, Heinz 1706, whose genome was sequenced as reference and two "local" ones, San Marzano and Vesuviano in two different locations of Campania region (Italy). RESULTS: Responses to environment were more pronounced in the two "local" genotypes, rather than in the Heinz 1706. The overall genetic composition of each genotype, acting in trans, modulated the specific response to environment. Duplicated genes and transcription factors, establishing different number of network connections by gaining or losing links, play a dominant role in shaping organoleptic profile. The fundamental role of cell wall metabolism in tuning all the quality attributes, including the sensorial perception, was also highlighted. CONCLUSIONS: Although similar fruit-related quality processes are activated in the same environment, different tomato genotypes follow distinct transcriptomic, metabolomic and sensorial trajectories depending on their own genetic makeup.


Assuntos
Frutas/genética , Frutas/metabolismo , Lycopersicon esculentum/genética , Lycopersicon esculentum/metabolismo , Parede Celular/genética , Parede Celular/metabolismo , Qualidade dos Alimentos , Frutas/fisiologia , Dosagem de Genes , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Genótipo , Itália , Metaboloma , Biologia de Sistemas/métodos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcriptoma
10.
BMC Plant Biol ; 16: 53, 2016 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-26920134

RESUMO

BACKGROUND: Fusarium oxysporum f.sp. radicis-lycopersici (FORL) is one of the most destructive necrotrophic pathogens affecting tomato crops, causing considerable field and greenhouse yield losses. Despite such major economic impact, little is known about the molecular mechanisms regulating Fusarium oxysporum f.sp. radicis-lycopersici resistance in tomato. RESULTS: A transcriptomic experiment was carried out in order to investigate the main mechanisms of FORL response in resistant and susceptible isogenic tomato lines. Microarray analysis at 15 DPI (days post inoculum) revealed a distinct gene expression pattern between the two genotypes in the inoculated vs non-inoculated conditions. A model of plant response both for compatible and incompatible reactions was proposed. In particular, in the incompatible interaction an activation of defense genes related to secondary metabolite production and tryptophan metabolism was observed. Moreover, maintenance of the cell osmotic potential after the FORL challenging was mediated by a dehydration-induced protein. As for the compatible interaction, activation of an oxidative burst mediated by peroxidases and a cytochrome monooxygenase induced cell degeneration and necrosis. CONCLUSIONS: Our work allowed comprehensive understanding of the molecular basis of the tomato-FORL interaction. The result obtained emphasizes a different transcriptional reaction between the resistant and the susceptible genotype to the FORL challenge. Our findings could lead to the improvement in disease control strategies.


Assuntos
Fusarium/fisiologia , Lycopersicon esculentum/genética , Lycopersicon esculentum/microbiologia , Doenças das Plantas/genética , Perfilação da Expressão Gênica , Genoma de Planta , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Transcriptoma
11.
BMC Genomics ; 16: 1112, 2015 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-26715041

RESUMO

BACKGROUND: The powdery mildew disease affects thousands of plant species and arguably represents the major fungal threat for many Cucurbitaceae crops, including melon (Cucumis melo L.), watermelon (Citrullus lanatus L.) and zucchini (Cucurbita pepo L.). Several studies revealed that specific members of the Mildew Locus O (MLO) gene family act as powdery mildew susceptibility factors. Indeed, their inactivation, as the result of gene knock-out or knock-down, is associated with a peculiar form of resistance, referred to as mlo resistance. RESULTS: We exploited recently available genomic information to provide a comprehensive overview of the MLO gene family in Cucurbitaceae. We report the identification of 16 MLO homologs in C. melo, 14 in C. lanatus and 18 in C. pepo genomes. Bioinformatic treatment of data allowed phylogenetic inference and the prediction of several ortholog pairs and groups. Comparison with functionally characterized MLO genes and, in C. lanatus, gene expression analysis, resulted in the detection of candidate powdery mildew susceptibility factors. We identified a series of conserved amino acid residues and motifs that are likely to play a major role for the function of MLO proteins. Finally, we performed a codon-based evolutionary analysis indicating a general high level of purifying selection in the three Cucurbitaceae MLO gene families, and the occurrence of regions under diversifying selection in candidate susceptibility factors. CONCLUSIONS: Results of this study may help to address further biological questions concerning the evolution and function of MLO genes. Moreover, data reported here could be conveniently used by breeding research, aiming to select powdery mildew resistant cultivars in Cucurbitaceae.


Assuntos
Ascomicetos/classificação , Ascomicetos/fisiologia , Cucurbitaceae/genética , Cucurbitaceae/microbiologia , Filogenia , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
12.
BMC Plant Biol ; 15: 51, 2015 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-25850033

RESUMO

BACKGROUND: ATP-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. They have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about ABC superfamily functions in plants. RESULTS: Recently released plant genome sequences allowed us to identify 803 ABC transporters in four vascular plants (Oryza. sativa, Solanum lycopersicum, Solanum tuberosum and Vitis vinifera) and 76 transporters in the green alga Volvox carteri, by comparing them with those reannotated in Arabidopsis thaliana and the yeast Saccharomyces cerevisiae. Retrieved proteins have been phylogenetically analysed to infer orthologous relationships. Most orthologous relationships in the A, D, E and F subfamilies were found, and interesting expansions within the ABCG subfamily were observed and discussed. A high level of purifying selection is acting in the five ABC subfamilies A, B, C, D and E. However, evolutionary rates of recent duplicate genes could influence vascular plant genome diversification. The transcription profiles of ABC genes within tomato organs revealed a broad functional role for some transporters and a more specific activity for others, suggesting the presence of key ABC regulators in tomato. CONCLUSIONS: The findings achieved in this work could contribute to address several biological questions concerning the evolution of the relationship between genomes of different species. Plant ABC protein inventories obtained could be a valuable tool both for basic and applied studies. Indeed, interpolation of the putative role of gene functions can accelerate the discovering of new ABC superfamily members.


Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Evolução Molecular , Variação Genética , Magnoliopsida/genética , Proteínas de Plantas/genética , Saccharomyces cerevisiae/genética , Volvox/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Perfilação da Expressão Gênica , Lycopersicon esculentum/genética , Lycopersicon esculentum/metabolismo , Magnoliopsida/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , Saccharomyces cerevisiae/metabolismo , Ativação Transcricional , Transcriptoma , Volvox/metabolismo
13.
Plant Cell ; 27(4): 954-68, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25873387

RESUMO

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.


Assuntos
Genoma de Planta/genética , Solanum tuberosum/genética , Solanum/genética , Aclimatação , Evolução Biológica , Filogenia , Solanum/classificação , Solanum tuberosum/classificação
14.
PLoS One ; 9(5): e94963, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24804963

RESUMO

Since gene expression approaches constitute a starting point for investigating plant-pathogen systems, we performed a transcriptional analysis to identify a set of genes of interest in tomato plants infected with F. oxysporum f. sp. lycopersici (Fol) and Tomato Mosaic Virus (ToMV). Differentially expressed tomato genes upon inoculation with Fol and ToMV were identified at two days post-inoculation. A large overlap was found in differentially expressed genes throughout the two incompatible interactions. However, Gene Ontology enrichment analysis evidenced specific categories in both interactions. Response to ToMV seems more multifaceted, since more than 70 specific categories were enriched versus the 30 detected in Fol interaction. In particular, the virus stimulated the production of an invertase enzyme that is able to redirect the flux of carbohydrates, whereas Fol induced a homeostatic response to prevent the fungus from killing cells. Genomic mapping of transcripts suggested that specific genomic regions are involved in resistance response to pathogen. Coordinated machinery could play an important role in prompting the response, since 60% of pathogen receptor genes (NB-ARC-LRR, RLP, RLK) were differentially regulated during both interactions. Assessment of genomic gene expression patterns could help in building up models of mediated resistance responses.


Assuntos
Fusarium/patogenicidade , Lycopersicon esculentum/microbiologia , Doenças das Plantas/microbiologia , Tobamovirus/patogenicidade , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
15.
BMC Genomics ; 15: 138, 2014 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-24548308

RESUMO

BACKGROUND: Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits. RESULTS: Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars. CONCLUSIONS: The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.


Assuntos
Genoma de Planta , Lycopersicon esculentum/genética , Mapeamento Cromossômico , Frutas/metabolismo , Deleção de Genes , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Especificidade da Espécie
16.
Plant Physiol Biochem ; 74: 42-9, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24262994

RESUMO

Fusarium oxysporum f. sp. radicis-lycopersici (FORL) leading to fusarium crown and root rot is considered one of the most destructive tomato soilborne diseases occurring in greenhouse and field crops. In this study, response to FORL infection in tomato roots was investigated by differential proteomics in susceptible (Monalbo) and resistant (Momor) isogenic tomato lines, thus leading to identify 33 proteins whose amount changed depending on the pathogen infection, and/or on the two genotypes. FORL infection induced accumulation of pathogen-related proteins (PR proteins) displaying glucanase and endochitinases activity or involved in redox processes in the Monalbo genotype. Interestingly, the level of the above mentioned PR proteins was not influenced by FORL infection in the resistant tomato line, while other proteins involved in general response mechanisms to biotic and/or abiotic stresses showed significant quantitative differences. In particular, the increased level of proteins participating to arginine metabolism and glutathione S-transferase (GST; EC 2.5.1.18) as well as that of protein LOC544002 and phosphoprotein ECPP44-like, suggested their key role in pathogen defence.


Assuntos
Fusarium/patogenicidade , Lycopersicon esculentum/microbiologia , Proteínas de Plantas/metabolismo , Raízes de Plantas/microbiologia , Proteômica , Genótipo , Lycopersicon esculentum/genética , Doenças das Plantas
17.
Nucleic Acids Res ; 41(Database issue): D1167-71, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23161682

RESUMO

The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens. Initiated in 2009, the database has grown more than 6-fold to recently include annotation derived from recent plant genome sequencing projects. Release 2.0 currently hosts useful biological information on a set of 112 known and 104 310 putative R-genes present in 233 plant species and conferring resistance to 122 different pathogens. Moreover, the website has been completely redesigned with the implementation of Semantic MediaWiki technologies, which makes our repository freely accessed and easily edited by any scientists. To this purpose, we encourage plant biologist experts to join our annotation effort and share their knowledge on resistance-gene biology with the rest of the scientific community.


Assuntos
Bases de Dados Genéticas , Resistência à Doença/genética , Genes de Plantas , Genoma de Planta , Internet , Modelos Genéticos
18.
BMC Res Notes ; 5: 678, 2012 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-23216678

RESUMO

BACKGROUND: Plant resistance genes, which encode R-proteins, constitute one of the most important and widely investigated gene families. Thanks to the use of both genetic and molecular approaches, more than 100 R genes have been cloned so far. Analysis of resistance proteins and investigation of domain properties may afford insights into their role and function. Moreover, genomic experiments and availability of high-throughput sequence data are very useful for discovering new R genes and establish hypotheses about R-genes architecture. RESULT: We surveyed the PRGdb dataset to provide valuable information about hidden R-protein features. Through an in silico approach 4409 putative R-proteins belonging to 33 plant organisms were analysed for domain associations frequency. The proteins showed common domain associations as well as previously unknown classes. Interestingly, the number of proteins falling into each class was found inversely related to domain arrangement complexity. Out of 31 possible theoretical domain combinations, only 22 were found. Proteins retrieved were filtered to highlight, through the visualization of a Venn diagram, candidate classes able to exert resistance function. Detailed analyses performed on conserved profiles of those strong putative R proteins revealed interesting domain features. Finally, several atypical domain associations were identified. CONCLUSION: The effort made in this study allowed us to approach the R-domains arrangement issue from a different point of view, sorting through the vast diversity of R proteins. Overall, many protein features were revealed and interesting new domain associations were found. In addition, insights on domain associations meaning and R domains modelling were provided.


Assuntos
Proteínas de Plantas/química , Simulação por Computador , Genes de Plantas , Proteínas de Plantas/genética
19.
Int J Mol Sci ; 13(8): 10316-35, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22949863

RESUMO

Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.


Assuntos
Genoma de Planta , Genômica/métodos , Plantas/genética , Poliploidia , Sequenciamento de Nucleotídeos em Larga Escala , Fenótipo
20.
Nucleic Acids Res ; 38(Database issue): D814-21, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19906694

RESUMO

PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Bases de Dados de Ácidos Nucleicos , Perfilação da Expressão Gênica , Genes de Plantas/genética , Genoma de Planta , Doenças das Plantas/genética , Biologia Computacional/tendências , Bases de Dados de Proteínas , Armazenamento e Recuperação da Informação/métodos , Internet , Estresse Oxidativo , Plantas/metabolismo , Estrutura Terciária de Proteína , Software , Interface Usuário-Computador
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