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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #411374
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: Unlocking genomic diversity: harnessing the power of FAIR principles in gramene

Author
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item NAAMATI, GUY - Embl-Ebi
item DYER, SARAH - Embl-Ebi
item Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/12/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Gramene knowledgebase (https://www.gramene.org) embraces the FAIR guiding principles for research data stewardship (findability, accessibility, interoperability, and reusability). The resource currently hosts 150 plant reference genomes and four crop-focused pan-genome websites (sorghumbase.org, maize-pangenome.gramene.org, oryza.gramene.org, and vitis.gramene.org) with over 100 additional crop-specific genomes. These sites leverage the same comparative genomics infrastructure and are interconnected through shared anchor genomes. Alongside pan-genome reference assemblies, SNPs and indels are available for more than 17 species. SNPs can be easily viewed and filtered based on their predicted functional effect (missense, stop-gained, etc.) and impact (SIFT scores). Moreover, they are downloadable as images and tables. The genetic variation databases are developed in collaboration with the community, EMBL-EBI Ensembl Plants, and for some species, the data has been imported from the European Variation Archive (EVA). Ongoing efforts aim to standardize germplasm identifiers, biosamples metadata, as well as to increase our variation collection with additional SNP and indels sets, neutron mutagenized variation and EMS-induced variants, and phenotypic associations (GWAs). We will present new efforts to support adoption of reference SNP cluster identifiers (rsIDs), assigned by EVA, as unique labels used by researchers and databases working with human data to unequivocally identify a particular SNP. These rsIDs will provide improved standards for linking sequence to function and interoperability for agricultural resources. Gramene is funded by USDA ARS 8062-21000-041-00D, and Ensembl Plants by Wellcome Trust Grant 222155/Z/20/Z, BBSRC/NSF grant BB/T015608/1, and the European Molecular Biology Laboratory.