Genome-wide identification and analysis of candidate genes for disease resistance in tomato

Tomato (Solanum lycopersicum L.) has served as an important model system for studying the genetics and molecular basis of resistance mecha- nisms in plants. An unprecedented challenge is now to capitalize on the genetic and genomic achievements obtained in this species. In this study, we show that information on the tomato genome can be used predictively to link resistance function with specific sequences. An integrated genomic approach for identifying new resistance (R) gene candidates was developed. An R gene functional map was created by co-localization of candidate pathogen recognition genes and anchoring molecular markers associated with resistance phenotypes. In-depth characterization of the identified pathogen recognition genes was performed. Finally, in order to highlight expressed pathogen recognition genes and to provide a first step in validation, the tomato transcriptome was explored and basic molecular analyses were conducted. Such methodology can help to better direct positional cloning, reducing the amount of effort required to identify a functional gene. The resulting candidate loci selected are available for exploiting their specific function

Structural and Functional Genomics of Tomato

Tomato (Solanum lycopersicum L.) is the most intensively investigated Solanaceous species both in genetic and genomics studies. It is a diploid species with a haploid set of 12 chromosomes and a small genome (950 Mb). Based on the detailed knowledge on tomato structural genomics, the sequencing of the euchromatic regions started in the year 2005 as a common effort of different countries. The manuscript focuses on markers used for tomato, on mapping efforts mainly based on exploitation of natural biodiversity, and it gives an updated report on the international sequencing activities. The principal tools developed to explore the function of tomato genes are also summarized, including mutagenesis, genetic transformation, and transcriptome analysis. The current progress in bioinformatic strategies available to manage the overwhelming amount of data generated from different tomato “omics” approaches is reported, and emphasis is given to the effort of producing a computational workbench for the analysis of the organization, as well as the functionality and evolution of the Solanaceae family

PRGdb 2.0 : towards a community-based database model for the analysis of R-genes in plants

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

Resistance traits and AFLP characterization of diploid primitive tuber-bearing potatoes.

ISSN: 0925-986

Fine mapping of two major QTLs conferring resistance to powdery mildew in tomato

Tomato (Solanum lycopersicum) is the most cultivated crop in the Solanaceae family and is a host for Oidium neolycopersici, the cause agent of powdery mildew disease. In wild species of tomato, genes (Ol-1–Ol-6) for monogenic resistance have been identified. Moreover, three quantitative resistance loci (QRLs), namely Ol-qtl1, Ol-qtl2 and Ol-qtl3, have been mapped in Solanum neorickii G1.1601. In this work, we developed several advanced backcross populations in order to fine-map these Ol-qtls. Resistant lines harboring individual Ol-qtl were produced and used in recombinant screening. Ten recombinants were identified in chromosomal regions carrying Ol-qtl1s. The recombinant individuals were used to produce recombinant families (RFs). By screening these RFs with molecular markers and testing them with O. neolycopersici, we could localize Ol-qtl1 in a region of about 2.3 Mbp on the long arm of chromosome 6 and Ol-qtl2 in a region of 2.5 Mbp on the short arm of chromosome 12. On the other hand, the presence of Ol-qtl3 locus was not confirmed in this study. The fine-mapping results further demonstrated the co-localization between Ol-qtls and genes for monogenic resistance; the Ol-qtl1 interval contains the Ol-1 gene and the Ol-qtl2 interval harbors the Lv gene that confers monogenic resistance to Leveillula taurica, another species of tomato powdery mildew

Alien Domains Shaped the Modular Structure of Plant NLR Proteins

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

Fusarium oxysporum f.sp. radicis-lycopersici induces distinct transcriptome reprogramming in resistant and susceptible isogenic tomato lines

8openInternationalItalian coauthor/editorBackground: 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 dehydrationinduced 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.openManzo, D.; Ferriello, F.; Puopolo, G.; Zoina, A.; D’Esposito, D.; Tardella, L.; Ferrarini, A.; Ercolano, M.R.Manzo, D.; Ferriello, F.; Puopolo, G.; Zoina, A.; D’Esposito, D.; Tardella, L.; Ferrarini, A.; Ercolano, M.R

PRGdb: a bioinformatics platform for plant resistance gene analysis

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

Valorising faba bean residual biomass : Effect of farming system and planting time on the potential for biofuel production

Research was carried out in southern Italy with the aim to assess the quality of faba bean residual biomass and its potential for biorefinery application. Faba bean is a sustainable crop, due to its ability to fix atmospheric nitrogen, and a large amount of biomass remains after harvest which can be valorised for energy production. Greenhouse and early planting are known to affect pod yield and, in this respect, even the residual biomass quality needs to be assessed. For this purpose, the effects of five planting times (i.e. the dates of transplants ranging from 27 September to 22 November at two-week interval, earlier and later than the common planting date of 25 October in Naples province) on pods yield, residual biomass, and saccharification potential were evaluated in faba bean grown in open field and in greenhouse. The third planting time resulted in the highest fruit and residual biomass yield under greenhouse, whereas the fourth was the best in open field. Harvest index was best affected by the third and fourth planting times in open field. Greenhouse grown biomass showed higher values of lignin, hemicellulose and pectin, compared to open field, whereas the opposite trend was recorded with cellulose. Lignin content showed a gradual decrease from the first to the last planting time (17.7%–13.7% biomass fraction respectively), as well as pectin (from 14.1 to 11.5% biomass fraction); conversely, cellulose increased from the first to the last planting time (from 41.1 to 48.7% biomass fraction). Glucose was the most represented monosaccharide (46.7 mol%), followed by xylose (27.4 mol%) and galactose (9.9 mol%). Overall, the potential of faba bean residual biomass for energy production was best affected by open field growing, the latest planting time and alkali pre-treatment, the latter giving the highest value of saccharification (60.7 g kg−1 h−1 compared to 27.6 relevant to hot water pre-treatment)