期刊
PLANT GENOME
卷 14, 期 3, 页码 -出版社
WILEY
DOI: 10.1002/tpg2.20114
关键词
-
资金
- U.S. Department of Energy Great Lakes Bioenergy Research Center (DOE BER Office of Science) [DE-FC02-07ER64494]
- National Science Foundation Plant Genome Research Program [IOS-1546657, IOS-1546727, IOS1546719, IOS-1822330]
- National Institute of Food and Agriculture, United States Department of Agriculture Hatch [1013139, 1022702]
- Office of Science of the US Department of Energy [DE-AC0205CH11231]
High-quality genome assemblies of maize stiff-stalk inbreds were created, revealing extensive collinearity among these inbreds and unique components in the maize pangenome. While representing only a proportion of variation in the original stiff-stalk pool, these inbreds showed significant genetic and genomic variation, supporting the potential for continued breeding success in this pool.
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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