GRAINGENES: VISUALIZATION, TOOLS, AND RESOURCES FOR WHEAT Abstract uri icon

abstract

  • GrainGenes (https://wheat.pw.usda.gov; https://graingenes.org) is the centralized, curated USDA-ARS database for wheat, barley, oat, and rye, ensuring long-term data sustainability for small grains researchers. GrainGenes hosts a JBrowse genome browser instance for the IWGSC RefSeq v1.0 assembly, which is populated with multiple diversity tracks generated by the Akhunov (Kansas State Univ.) and Dubcovsky (UC Davis) Labs. Svevo GrainGenes contributes to the JBrowse genome browser development and is developing a BLAST plug-in that can perform sequence similarity searches from the genome browser tracks. This plug-in will be available for implementation by other JBrowse users. Large curated mapping projects available via the comparative mapping tool CMap were added to GrainGenes including the Spring Wheat Nested Association Mapping (NAM) population based on 2,100 recombinant inbred lines from 28 families used to construct 588 chromosome-specific genetic maps. The genome assembly for the most recent tetraploid genome, Svevo, is shown in the GrainGenes genome browser with links to QTLs to the GrainGenes pages. GrainGenes is an active participant of the Wheat Information System (WheatIS) under the Wheat Initiative: for facilitated data discovery, GrainGenes indexed maps, QTL, germplasm, and genes from the Wheat Gene Catalogue into WheatIS.

publication date

  • July 2019