Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

Author
item Sen, Taner
item Braun, Bremen
item Schott, David
item Portwood, John
item Schaeffer, Mary
item Harper, Elisabeth
item Cannon, Ethalinda
item Andorf, Carson

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2017
Publication Date: 4/17/2017
Citation: Sen, T.Z., Braun, B., Schott, D., Portwood Ii, J.L., Schaeffer, M.L., Harper, E.C., Cannon, E.K., Andorf, C.M. 2017. Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bax031.

Interpretive Summary: In order to prioritize tool development and data curation efforts, the Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing genetic relatedness and diversity. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in the summer of 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered two priorities for visualization as displaying single nucleotide polymorphisms (SNPs) in given chromosome regions in certain maize lines and pedigree relationships. The survey also identified two maize populations that would be most useful to display. In response to this strong stakeholder input, MaizeGDB staff are currently working to improve its interface and web-based tools. The survey results can also guide other biological databases in their efforts to serve user preferences in their communities for similar types of data.

Technical Abstract: The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data, and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in Summer 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered their top priorities for visualization as: 1) displaying single nucleotide polymorphisms (SNPs) in a given region for a given list of lines, 2) showing haplotypes for a given list of lines, and 3) presenting pedigree relationships visually. The survey also asked which populations would be most useful to display. The following two populations were on top of the list: 1) 3000 publicly available maize inbred lines used in Romay et al. (Genome Biol, 14:R55, 2013), and 2) maize lines with expired Plant Variety Protection Act (ex-PVP) certificates. Driven by this strong stakeholder input, MaizeGDB staff are currently working in four areas to improve its interface and web-based tools: 1) presenting immediate progenies of currently available stocks at the MaizeGDB Stock pages, 2) displaying the most recent ex-PVP lines described in the Germplasm Resources Information Network (GRIN) on the MaizeGDB Stock pages, 3) developing network views of pedigree relationships, and 4) visualizing genotypes from SNP-based diversity datasets. The survey results can help other biological databases to direct their efforts according to user preferences as they serve similar types of data sets for their communities.

Last Modified: 08/21/2017
Footer Content Back to Top of Page