Genomic variation within the maize Stiff Stalk heterotic germplasm pool

The Stiff Stalk heterotic group 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 ex-Plant Variety Protection lines LH145 representing B14, NKH8431
of mixed descent, PHB47 representing B37, and PHJ40 which is a Pioneer
Hi-Bred early Stiff Stalk type. Sequence was generated using long-read
sequencing achieving highly contiguous assemblies of 2.13 to 2.18 Gbp with
N50 scaffold lengths greater than 200 Mbp. Inbred-specific gene
annotations were generated using a core five-tissue gene expression atlas
and transposable element annotation was conducted using de novo and
homology-directed methodologies. In comparison to the reference inbred
B73, synteny analyses revealed extensive collinearity across the five
Stiff Stalk genomes, although unique components of the maize pan-genome
were detected. Comparison of this set of Stiff Stalk genome sequences with
the original Stiff Stalk 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 pan-genome.