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:10.1038/npre.2008.2210.1

Cited by 7 publications

(8 citation statements)

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“…We discarded contigs from the Sce_Assembly03 sequence set that showed E-values larger than E-20 and the proposed best hits representing at least 10% of the full contig size. The established EST resource Sce_Assembly03 is available from the GABI primary database [30], http://www.gabipd.org.…”

Section: Methodsmentioning

confidence: 99%

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

et al. 2011

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BackgroundThe improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology.ResultsMore than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool.ConclusionsThe established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.

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Section: Methodsmentioning

confidence: 99%

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

et al. 2011

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“…Subsequently, the genomes of many economically important crops such as rice and maize have been sequenced and increasing amount of information on genomics is becoming available in databases such as, e.g. GABI DB (Riano-Pachon et al 2009) or the TAIR DB (Huala et al 2001). High-definition genotyping can now be performed with thousands of plants in robotised platforms, which allows for an increasing speed of genotype selection in breeding programs (Langridge and Fleury 2011).…”

Section: Phenotyping Machinesmentioning

confidence: 99%

Phenotyping plants: genes, phenes and machines

Pieruschka

Poorter

2012

Functional Plant Biol.

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Abstract.No matter how fascinating the discoveries in the field of molecular biology are, in the end it is the phenotype that matters. In this paper we pay attention to various aspects of plant phenotyping. The challenges to unravel the relationship between genotype and phenotype are discussed, as well as the case where 'plants do not have a phenotype'. More emphasis has to be placed on automation to match the increased output in the molecular sciences with analysis of relevant traits under laboratory, greenhouse and field conditions. Currently, non-destructive measurements with cameras are becoming widely used to assess plant structural properties, but a wider range of non-invasive approaches and evaluation tools has to be developed to combine physiologically meaningful data with structural information of plants. Another field requiring major progress is the handling and processing of data. A better e-infrastructure will enable easier establishment of links between phenotypic traits and genetic data. In the final part of this paper we briefly introduce the range of contributions that form the core of a special issue of this journal on plant phenotyping.

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“…Additionally, the utilisation of model plants, and in particular A. thaliana, has opened up for comparative investigations, not least since Arabidopsis is a close relative to Brassica species, and thus, facilitated and pushed efforts toward molecular breeding (Snowdon and Friedt, 2004) and state-ofthe-art metabolomics-assisted breeding (Fernie and Schauer, 2008). Recent approaches for potential genotype selection and cultivar development in the Brassicaceae (Snowdon, 2007;Duran et al, 2009;Nicolas et al, 2009;Riaño-Pachón et al, 2009) …”

Section: Plant Breeding Towards Insect Resistance In Brassica Cropsmentioning

confidence: 99%

Defence mechanisms of Brassicaceae: implications for plant-insect interactions and potential for integrated pest management. A review

Ahuja

Rohloff

Bones

2010

Agron. Sustain. Dev.

205

165

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-Brassica crops are grown worldwide for oil, food and feed purposes, and constitute a significant economic value due to their nutritional, medicinal, bioindustrial, biocontrol and crop rotation properties. Insect pests cause enormous yield and economic losses in Brassica crop production every year, and are a threat to global agriculture. In order to overcome these insect pests, Brassica species themselves use multiple defence mechanisms, which can be constitutive, inducible, induced, direct or indirect depending upon the insect or the degree of insect attack. Firstly, we give an overview of different Brassica species with the main focus on cultivated brassicas. Secondly, we describe insect pests that attack brassicas. Thirdly, we address multiple defence mechanisms, with the main focus on phytoalexins, sulphur, glucosinolates, the glucosinolate-myrosinase system and their breakdown products. In order to develop pest control strategies, it is important to study the chemical ecology, and insect behaviour. We review studies on oviposition regulation, multitrophic interactions involving feeding and host selection behaviour of parasitoids and predators of herbivores on brassicas. Regarding oviposition and trophic interactions, we outline insect oviposition behaviour, the importance of chemical stimulation, oviposition-deterring pheromones, glucosinolates, isothiocyanates, nitriles, and phytoalexins and their importance towards pest management. Finally, we review brassicas as cover and trap crops, and as biocontrol, biofumigant and biocidal agents against insects and pathogens. Again, we emphasise glucosinolates, their breakdown products, and plant volatile compounds as key components in these processes, which have been considered beneficial in the past and hold great prospects for the future with respect to an integrated pest management.Brassicas / insect pests / chemical ecology / trophic levels / glucosinolates / isothiocyanates / defence mechanisms / biocontrol / trap crops / integrated pest management

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GabiPD: The GABI Primary Database - a plant integrative ‘omics’ database

Cited by 7 publications

References 1 publication

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

Phenotyping plants: genes, phenes and machines

Defence mechanisms of Brassicaceae: implications for plant-insect interactions and potential for integrated pest management. A review

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