Genomic variation within the maize stiff-stalk heterotic germplasm pool

Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia de LeonShawn M. Kaeppler, C. Robin Buell

Research output: Contribution to journalArticlepeer-review


The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13–2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

Original languageEnglish (US)
JournalPlant Genome
Early online dateJul 18 2021
StatePublished - Jul 18 2021

Bibliographical note

Funding Information:
This work was funded by the U.S. Department of Energy Great Lakes Bioenergy Research Center (DOE BER Office of Science DE‐FC02‐07ER64494) to CRB, SMK, NdL; the National Science Foundation Plant Genome Research Program IOS‐ 1546657 to CRB, IOS‐1546727 to CNH; and IOS‐ 1546719 and IOS‐ 1822330 to MBH; and the National Institute of Food and Agriculture, United States Department of Agriculture Hatch 1013139 and 1022702 project to SMK. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No DE‐AC02‐05CH11231. We acknowledge the assistance of David Kudrna for contributions to the high molecular weight DNA isolation and the assistance of Brieanne Vaillancourt with sequence data management.

Publisher Copyright:
© 2021 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America

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