Genomic variation within the maize stiff-stalk heterotic germplasm pool

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

doi:10.1002/tpg2.20114

Genomic variation within the maize stiff-stalk heterotic germplasm pool

Journal Article · Sun Jul 18 00:00:00 EDT 2021 · The Plant Genome

DOI:https://doi.org/10.1002/tpg2.20114· OSTI ID:1813409

Bornowski, Nolan ^[1]; Michel, Kathryn J. ^[2]; Hamilton, John P. ^[1]; Ou, Shujun ^[3]; ^[3]; Jenkins, Jerry ^[4]; Grimwood, Jane ^[4]; Plott, Chris ^[4]; Shu, Shengqiang ^[5]; Talag, Jayson ^[6]; Kennedy, Megan ^[5]; Hundley, Hope ^[5]; Singan, Vasanth R. ^[5]; Barry, Kerrie ^[5]; Daum, Chris ^[5]; Yoshinaga, Yuko ^[5]; Schmutz, Jeremy ^[7]; ^[8]; Hufford, Matthew B. ^[3]; Leon, Natalia ^[2] more »

Michigan State Univ., East Lansing, MI (United States)
Univ. of Wisconsin, Madison, WI (United States)
Iowa State Univ., Ames, IA (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Arizona, Tucson, AZ (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Minnesota, St. Paul, MN (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); USDA

Grant/Contract Number:: AC02-05CH11231; FC02-07ER64494

OSTI ID:: 1813409

Journal Information:: The Plant Genome, Journal Name: The Plant Genome Journal Issue: 3 Vol. 14; ISSN 1940-3372

Publisher:: Alliance of Crop, Soil, and Environmental Science SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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