Skip to main content
ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #381179

Research Project: MaizeGDB: Enabling Access to Basic, Translational, and Applied Research Information

Location: Corn Insects and Crop Genetics Research

Title: De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

item HUFFORD, MATTHEW - Iowa State University
item SEETHARAM, ARUN - Iowa State University
item Woodhouse, Margaret
item CHOUGIE, KAPEEL - Cold Spring Harbor Laboratory
item OU, SHUJUN - Iowa State University
item LIU, JIANING - University Of Georgia
item RICCI, WILLIAM - University Of Georgia
item GUO, TINGTING - Iowa State University
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item QIU, YINGJIE - University Of Minnesota
item Portwood, John
item Cannon, Ethalinda
item Andorf, Carson
item Ware, Doreen
item DAWE, KELLY - University Of Georgia

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 1/14/2021
Publication Date: 1/16/2021
Citation: Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougie, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R., et all. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv.

Interpretive Summary: We report the genome sequencing and assembly of 26 maize (corn) cultivars that represent the diversity of domesticated maize. These 26 cultivars have used by corn researchers for years to study corn development, disease resistance, and other crop improvement-related features. The high-quality genome assemblies of these cultivars, along with their gene and functional information derived from this study, will allow researchers to better understand the structural and functional diversity of the maize genome across the species, leading to future crop improvement.

Technical Abstract: We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.