Location: Corn Insects and Crop Genetics Research
2020 Annual Report
Accomplishments
1. The Maize Genetics and Genomics Database (MaizeGDB) released data and resources for a set of 26 diverse maize genome assemblies. Over the past decade, maize researchers have relied on a single reference genome as the genomic representation of maize. However, maize genetics, genomics, and breeding research depends upon the diversity within maize for basic research and to improve agriculturally important traits, and that diversity is not adequately represented by a single reference genome. To make multi-genomics data and resources available to maize researchers, ARS researchers in Ames, Iowa, worked closely with the University of Georgia, Cold Spring Harbor Laboratory, and Iowa State University to offer 26 high-quality, diverse maize genomes and supporting data sets through MaizeGDB, the genetics and genomics database for the maize research community. These reference genomes are notable for their completeness (low number of gaps), accuracy (low number of errors), and a high percentage of sequences assembled into chromosomes. The methods used to sequence and assemble the genomes are described in two papers from Nature Communications and Genome Biology. This release includes 26 genome pages, over one million gene pages, 206 downloadable data sets, and 134 sets of sequences that can be searched based on homology. In addition, MaizeGDB upgraded to next-generation genome browsers allowing researchers to easily navigate within and across this set of genomes and visualize over 1,000 data sets corresponding to functional regions within the maize genome. The data includes over 200 agriculturally important traits associated with tens of thousands of locations across the 10 maize chromosomes. A tool used to assess the quality of the genomes and annotations is published in the scientific journal BMC Genomics and is available for public use through MaizeGDB. These new resources will lead to improved crop performance by helping researchers better understand the relationship between the genes in a plant and the traits observed in farmers’ fields.
Review Publications
Coffman, S.M., Hufford, M.B., Andorf, C.M., Lubberstedt, T. 2019. Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theoretical and Applied Genetics. 133:547-561. https://doi.org/10.1007/s00122-019-03486-y.
Manchanda, N., Portwood II, J.L., Woodhouse, M.H., Seetharam, A., Lawrence-Dill, C.J., Andorf, C.M., Hufford, M. 2020. GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations. BMC Genomics. 21. https://doi.org/10.1186/s12864-020-6568-2.
Ou, S., Liu, J., Chougule, K., Fungtammasan, A., Seetharam, A., Stein, J., Llaca, V., Manchanda, N., Gilbert, A., Wei, S., Ware, D., Woodhouse, M.H., et all. 2020. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11. https://doi.org/10.1038/s41467-020-16037-7.
Walsh, J.R., Woodhouse, M.R., Andorf, C.M., Sen, T.Z. 2020. Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. Biomed Central (BMC) Plant Biology. 20. https://doi.org/10.1186/s12870-019-2218-8.
Liu, J., Seetharam, A.S., Chougule, K.M., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.H., Manchanda, N., Presting, G.G., Kurdna, D.A., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M.B., Dawe, R.K. 2020. Gapless assembly of maize chromosomes using long-read technologies. Genome Biology. 21. https://doi.org/10.1186/s13059-020-02029-9.
