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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #382114

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

Location: Corn Insects and Crop Genetics Research

Title: Sequence, assembly and annotation of maize inbred B104

item MANCHANDA, NANCY - Iowa State University
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item FENGLER, KEVIN - Corteva Agriscience
item SEETHARAM, ARUN - Iowa State University
item LIACA, VICTOR - Corteva Agriscience
item ZASTROW-HAYES, GINA - Corteva Agriscience
item WEI, SHARON - Cold Spring Harbor Laboratory
item BRAUN, IAN - Iowa State University
item Lopez, Miriam
item PLOYARAM, WIRIYANAT - Iowa State University
item ZARECOR, SCOTT - Iowa State University
item LU, ZEFU - University Of Georgia
item WALLEY, JUSTIN - Iowa State University
item YANDEAU-NELSON, MARNA - Iowa State University
item WANG, KAN - Iowa State University
item ADAMS, DEAN - Iowa State University
item Ware, Doreen
item SCHMITZ, BOB - University Of Georgia
item Woodhouse, Margaret
item Lauter, Nicholas
item Andorf, Carson
item LAWRENCE-DILL, CAROLYN - Iowa State University
item HUFFORD, MATTHEW - Iowa State University

Submitted to: Maize Annual Meetings
Publication Type: Abstract Only
Publication Acceptance Date: 3/6/2021
Publication Date: 3/8/2021
Citation: Manchanda, N., Chougule, K., Olson, A., Fengler, K., Seetharam, A., Liaca, V., Zastrow-Hayes, G., Wei, S., Braun, I., Lopez, M.D., Ployaram, W., Zarecor, S., Lu, Z., Walley, J., Yandeau-Nelson, M., Wang, K., Adams, D., Ware, D., Schmitz, B., Woodhouse, M.H., Lauter, N.C., Andorf, C.M., Lawrence-Dill, C., Hufford, M. 2021. Sequence, assembly and annotation of maize inbred B104. Maize Annual Meetings. 76.

Interpretive Summary:

Technical Abstract: B104 is a highly transformable maize inbred line which shows high sequence similarity with the reference maize line B73. B73 and B104 inbred lines share the same background; they were developed as part of the Iowa Stiff Stalk Synthetic breeding program. To understand the dynamics and tempo of maize genome evolution within a modern maize breeding program and enhance our knowledge of maize transformation, we have generated a high-quality genome assembly of B104. The new assembly was generated using high-depth PacBio data and a Bionano optical map and is significantly more contiguous and complete (32 scaffolds and 98Mb N50) than the previous draft assembly based on short-read data. RNA-seq from multiple tissues was used to annotate the assembly using an evidence-driven and ab-initio approach. Transposable Elements (TEs) were annotated in the B104 genome using a pipeline that combines homology based-annotations with the structure-based annotations to provide a complete summary of the transposons. We characterized both large-scale (>1Mb) and small- to medium- scale (50bp - 1Mb) structural variations using read and genome alignment based approaches. To characterize the differences in the contributions of stiffstalk founder lines to B73 and B104 and explore how this governs patterns of structural variation, transposon, and methylation variation, we painted the genomes with the founder haplotypes and identified regions of shared and distinct founder ancestry. We explored the gene content variation between B73 and B104, based on the complete set of structural annotations from B104, B73 and 25 NAM founder lines and identified the number of core (50%), dispensable (44.6%) and private genes (5%) in B104. We further identified genes which are differentially expressed (1.3%) between B73 and B104 across the 10 tissues. We present a summary of structural variations including genic presence/absence, variation in gene expression and TE families across regions of shared and different founder ancestry.