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.