GBIS: the information system of the German Genebank

Oppermann, Markus; Weise, Stéphan; Dittmann, Claudia; Knüpffer, H.

doi:10.1093/database/bav021

Cited by 44 publications

(39 citation statements)

References 17 publications

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“…We analyzed genotyping-by-sequencing (GBS) data from a total of 22,626 DNA samples (Supplementary Table 1). The majority of these were derived from single plants of 21,405 accessions of the IPK barley collection 5 . We also included single-plant samples for 297 accessions of the collection of the National Crop Genebank of China at the Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences, 684 barley accessions of the Swiss national genebank of Agroscope and 240 GBS samples from a previous study 2,6 .…”

Section: Resultsmentioning

confidence: 99%

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Genebank genomics highlights the diversity of a global barley collection

et al. 2018

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Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world's major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.

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Section: Resultsmentioning

confidence: 99%

“…Awn roughness was assessed visually and by sliding one's finger along the central part of the awn in the direction from top to bottom. Flowering dates were retrieved from digitized records of genebank propagation cycles 5 . Seed regenerations were performed between 1946 and 2015 in Gatersleben (51° 49′ N 11° 16′ E).…”

Section: Discussionmentioning

confidence: 99%

Genebank genomics highlights the diversity of a global barley collection

et al. 2018

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“…The Wheat@URGI portal is a major node of the WheatIS federation that expose genomic, genetic and phenomic integrated data to the community. The WheatIS data discovery tool allows a one-stop search in GnpIS [4] (including IWGSC browsers, InterMine and GnpIS-coreDB; URGI), EnsemblPlants (EMBL-EBI) [31], CrowsNest [38] (PGSB), CR-EST [39], GBIS [40] and MetaCrop [41] (IPK), The Triticeae Toolbox (Triticeae CAP), CIMMYT DSpace and Dataverse (CIMMYT), Gramene [42] (CSH, OSU, EMBL-EBI), Cropnet (IPGPAS), WheatPan [43] (UWA) and GrainGenes [44] (USDA).…”

Section: Discussionmentioning

confidence: 99%

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Alaux

Rogers²,

Letellier

et al. 2018

Preprint

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26The Wheat@URGI portal (https://wheat-urgi.versailles.inra.fr) has been developed to provide 27 the international community of researchers and breeders with access to the bread wheat 28 reference genome sequence produced by the International Wheat Genome Sequencing 29 Consortium. Genome browsers, BLAST, and InterMine tools have been established for in 30 depth exploration of the genome sequence together with additional linked datasets including 31 physical maps, sequence variations, gene expression, and genetic and phenomic data from 32 other international collaborative projects already stored in the GnpIS information system. The 33 portal provides enhanced search and browser features that will facilitate the deployment of 34 the latest genomics resources in wheat improvement. 35 36 37 Background 38The International Wheat Genome Sequencing Consortium (IWGSC) [1] is an international 39 collaborative group of growers, academic scientists, and public and private breeders that was 40 established to generate a high quality reference genome sequence of the hexaploid bread 41 wheat, and to provide breeders with state-of-the-art tools for wheat improvement. The vision 42 of the consortium is that the high quality, annotated ordered genome sequence integrated 43 with physical maps will serve as a foundation for the accelerated development of improved 44 varieties and will empower all aspects of basic and applied wheat science to address the 45 important challenge of food security. A first analysis of the reference sequence produced by 46 the consortium (IWGSC RefSeq v1.0) was recently published [2]. 47To ensure that wheat breeding and research programs can make the most of this extensive 48 genomic resource, the IWGSC endorsed the establishment of a data repository at URGI (Unité parties in data management as well as analysis and usage of the sequence data. Wheat 54 functional genomics (expression, methylation, etc.), genetic, and phenomic data has increased 55 concurrently, requiring the development of additional tools and resources to integrate 56 different data for biologists and breeders. To manage this escalation of data, URGI have built 57 this data repository for the wheat community with the following specific aims: (i) store 58 resources for which no public archive exists (e.g. physical maps, phenotype information); (ii) 59 enable pre-publication access to specific datasets (e.g. sequence assemblies and annotations, 60 physical maps, markers); and (iii) rapid release of integrated resources upon publication. The 61 repository has been designed in accordance with the "FAIR" principles [3] to ensure that the 62 data are Findable, Accessible, Interoperable and Reusable. To address the challenge of 63 integrating diverse data types from multiple sources, URGI employs solutions that provide 64 enhanced features for data exploration, mining and visualisation using the GnpIS information 65 system [4] combined with a high level of data interoperability. 66Here we describe the data and tools currently available through...

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“…cereale ], S. cereale subsp. vavilovii , further S. cereale subspecies, S. strictum , and S. sylvestre) were selected based on passport information (taxonomic status, country of origin, collection site) available in the genebank information system of the German Federal ex situ Genebank at IPK Gatersleben (GBIS; https://gbis.ipk-gatersleben.de/GBIS_I, Oppermann, Weise, Dittmann, & Knupffer, ). Seeds from the selected accessions were obtained from the IPK genebank.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing

Schreiber

Himmelbach

Börner

et al. 2018

Evolutionary Applications

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Rye ( Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genomewide markers have been published to date. We collected genotyping‐by‐sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale . Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single nucleotide polymorphisms with present genotype calls in 90% of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale . We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale species because of either ongoing gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in‐depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale .

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GBIS: the information system of the German Genebank

Cited by 44 publications

References 17 publications

Genebank genomics highlights the diversity of a global barley collection

Genebank genomics highlights the diversity of a global barley collection

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing

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