MaizeGDB 2018: the maize multi-genome genetics and genomics database

Abstract

Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at https://www.maizegdb.org.

Figure 1.

This chart tracks the number of records in MaizeGDB’s database for the listed data types since 2003. Initially there were a comparable number of records for Loci, References, Stock, and Variation data types until July of 2010, when hundreds of thousands of Variation records from the first maize HapMap (43) were added to the database. Gene model records were not introduced until the release of the first maize reference assembly, B73 RefGen_v1 in late 2009, and then began to rise sharply in late 2016 with the release of each new maize genome assembly (see Figure 2). The number of Phenotype records has not changed significantly from 1,016 in 2003 to 1,136 in August of 2018.

Figure 2.

This chart tracks the number of genome assemblies in MaizeGDB’s database since 2003. The first genome integrated into MaizeGDB was the B73 BAC-based assembly in November 2008, and until late 2016 additional genomes only included improved versions of B73. Following the release of B73 RefGen_v4, several assemblies of different maize lines have been sequenced de novo and incorporated into MaizeGDB. We anticipate this number to increase substantially as the cost of sequencing continues to fall, especially with the upcoming release of the 25 NAM founder lines. By 2020 we expect to be hosting ∼40 genomes.

Figure 3.

This image is a composite of the five new tools at MaizeGDB. Section (A) shows a MaizeMine results page for a particular gene model, which includes information on transcripts/proteins, expression, function, pathways, homology, and publications. Section (B) shows two images from qTeller. The top image show the expression values of a particular gene model across all of the tissues in the database. The bottom image shows a scatterplot of FPKM values between two gene models. Section (C) shows the results of a SNPversity query, which indicate the major/minor allele for a given inbred line at the top of the table and whether each SNP is located within a gene model's exon, intron or intergenic region. Section (D) shows the MaizeDIG interface, which allows curators to tag phenotypes in the image and link them to particular genes. The box outline in the middle of the image shows an example of what a tagged phenotype looks like. Section (E) shows the results of a query in the Pedigree Viewer of all stocks that were developed in Illinois.