GabiPD: the GABI primary database--a plant integrative 'omics' database

Riaño-Pachón, Diego Mauricio; Nagel, Axel; Neigenfind, Jost; Wagner, Robert E.; Basekow, Rico; Weber, Elke; Mueller‐Roeber, Bernd; Diehl, Svenja; Kersten, Birgit

doi:10.1093/nar/gkn611

Cited by 39 publications

(15 citation statements)

References 19 publications

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“…The 42,688 SNPs were distributed in 9,855 genes and showed significantly different allele frequencies between resistant and susceptible genotype pools. Candidate genes were selected using the following criteria in order of relevance: the level of significance for the differential expression between resistance and susceptible pools, using the p -value for differential frequency of the SNP allele, the number of differential SNPs per gene and the gene’s position on the Solanaceae function map for pathogen resistance in the GABI (Genome Analysis of the Plant Biological System) Primary Database 2 ( Meyer et al, 2005 ; Riaño-Pachón et al, 2009 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja

et al. 2017

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The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein ( StTL15A ) and a stem 28 kDa glycoprotein ( StGP28 ). Key message : A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight.

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Section: Methodsmentioning

confidence: 99%

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja

et al. 2017

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“…This information is being dynamically drawn from GabiPD (22). Such information will help users to establish links between specific phosphorylation sites or kinase substrates and phosphorylating kinases.…”

Section: New and Improved Features Of The Databasementioning

confidence: 99%

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

Durek

Schmidt

Heazlewood

et al. 2009

Nucleic Acids Research

342

329

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The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows ‘on-the-fly’ prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences.

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“…Nine tomato markers previously identified as carrying highly divergent alleles within Solanum lycopersicum . a (Additional file 2: Figure S1). b Genetic linkage map positions from [45] or [46]. …”

Section: Resultsmentioning

confidence: 99%

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

Labate¹,

Robertson²

2012

BMC Plant Biol

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BackgroundMany highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions.ResultsEach marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles.ConclusionOf the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.

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GabiPD: the GABI primary database--a plant integrative 'omics' database

Cited by 39 publications

References 19 publications

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

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