Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

• Published in: Database : the journal of biological databases and curation 2017, Vol.2017
• Main Authors: Sen, Taner Z., Braun, Bremen L., Schott, David A., Portwood, II, John L., Schaeffer, Mary L., Harper, Lisa C., Gardiner, Jack M., Cannon, Ethalinda K., Andorf, Carson M.
• Format: Article
• Language: English
• Subjects: Databases, Genetic; Datasets; Genetic Variation; Genomes; Genomics; Genotyping; Germplasm; Haplotypes; Inbreeding; Molecular Sequence Annotation - methods; Molecular Sequence Annotation - standards; Original; Pedigree; Plant protection; Researchers; Seed banks; Single-nucleotide polymorphism; User-Computer Interface; Visualization; Web Browser; Zea mays - genetics
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bax031

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: (i) displaying single nucleotide polymorphisms in a given region for a given list of lines, (ii) showing haplotypes for a given list of lines and (iii) 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: (i) 3000 publicly available maize inbred lines used in Romay et al. (Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol, 2013;14:R55) and (ii) 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: (i) presenting immediate progenies of currently available stocks at the MaizeGDB Stock pages, (ii) displaying the most recent ex-PVP lines described in the Germplasm Resources Information Network (GRIN) on the MaizeGDB Stock pages, (iii) developing network views of pedigree relationships and (iv) visualizing genotypes from SNP-based diversity datasets. These 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. Database URL: https://www.maizegdb.org