Location: Corn Insects and Crop Genetics Research
2021 Annual Report
Accomplishments
1. The Maize Genetics and Genomics Database (MaizeGDB) provided pan-genomic resources for a set of 44 maize genome assemblies. Research on crops is increasingly relying on a complete set of genes across a species (i.e. pan-genome). Pan-genomes are especially valuable in plants with high genomic diversity (e.g. maize) that can be exploited for crop improvement. ARS researchers at Ames, Iowa, have introduced a pan-genomic approach to hosting a genomic database, leveraging the large number of diverse maize genomes available and their associated datasets to efficiently connect plant genomes with traitsw of interest and their inheritance and control. Over the past several years, MaizeGDB has transitioned from a single reference genome to a multi-genomics resource. MaizeGDB now hosts data and tools integrated across 44 diverse maize genome assemblies. Recent improvements at MaizeGDB include an improved method for gene annotation (published in BMC Bioinformatics), a tool to visualize structural variation across genomes, methods to connect functional annotations across genomes, and an updated resource to compare and visualize gene atlases. This new pan-genomic approach is a potential framework for other crop databases and a resource to facilitate improved crop performance by helping researchers understand the relationship between the genes in a plant and the traits observed in farmers’ fields.
Review Publications
Shamimuzzaman, M., Gardiner, J.M., Walsh, A.T., Triant, D.A., Le Tourneau, J.J., Tayal, A., Unni, D.R., Nguyen, H.H., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Elsik, C.G. 2020. MaizeMine: A data mining warehouse for the maize genetics and genomics database (MaizeGDB). Frontiers in Plant Science. 11. Article 592730. https://doi.org/10.3389/fpls.2020.592730.
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC Bioinformatics. 22. Article 205. https://doi.org/10.1186/s12859-021-04120-9.
Marcon, C.; Altrogge, L.; Win Y.N.; Stöcker, T.; Gardiner, J.M.; Portwood, J.L. 2nd; Opitz, N.; Kortz, A.; Baldauf, J.A.; Hunter, C.T.; McCarty, D.R.; Koch, K.E.*; Schoof, H.; Hochholdinger, F. 2020 BonnMu: A sequence-indexed resource of transposon-Induced maize mutations for functional genomics studies. Plant Physiology 184(2):620-631. https://doi.org/10.1104/pp.20.00478
Wilkey, A., Brown, A.V., Cannon, S.B., Cannon, E.K. 2020. GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data. Biomed Central (BMC) Genomics. 21. Article 822. https://doi.org/10.1186/s12864-020-07217-2.
