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Home › Publications › Genomic variation within the maize stiff-stalk heterotic germplasm pool

2021 Publications

Genomic variation within the maize stiff-stalk heterotic germplasm pool

Published in:

Plant Genome ( 2021)

Author(s):

Bornowski, N., Michel, K. J., Hamilton, J. P., Ou, S., Seetharam, A. S., Jenkins, J., Grimwood, J., Plott, C., Shu, S., Talag, J., Kennedy, M., Hundley, H., Singan, V. R., Barry, K., Daum, C., Yoshinaga, Y., Schmutz, J., Hirsch, C. N., Hufford, M. B., de Leon, N., Kaeppler, S. M., Buell, C. R.

DOI:

10.1002/tpg2.20114

Abstract:

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.

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