Genomic variation within the maize stiff‐stalk heterotic germplasm pool

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

Genetic mapping of flowering time and plant height in a maize Stiff Stalk MAGIC population

“…Each parental assembly had different numbers of total haplotypes aligning to B73, from 51,070 haplotypes for PHJ40 to 66,890 for B84. PHJ40 is known to be more structurally diverse from the other founders (Bornowski et al 2021), and the next lowest number of aligned haplotypes was 62,144 for LH145. After collapsing haplotypes into consensus sequences, the average number of haplotypes per PHG reference range was reduced from 5.7 to 3.3 (Figure 3A).…”

“…Further, the genome assemblies of the six parents with annotation from a five-tissue transcriptome atlas (Li et al 2021; Bornowski et al 2021) are available for study, which increases the variety of opportunities for maize researchers. This population could be used to assay the effect of the alleles present within the population on combining ability, adaptation, genotype by environment interaction, stability, and provide a new paradigm for studying traditional and genomic selection.…”

“…Inbred PHJ40 is an early flowering flint and Stiff Stalk line developed in Ontario, Canada, with previously demonstrated admixture with B37 (White et al, 2020). All inbred lines except B73 previously underwent whole genome, reference guided assembly, which revealed extensive genetic and genomic diversity between the five lines and B73 (Bornowski et al 2021). S1).…”

“…The B73 RefGen_v5 annotation of genes (Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.gff3, available at maizegdb.org) was used to make the initial reference ranges, which were supplied to the “CreateValidIntervalsFilePlugin” to collapse any overlapping ranges and format for input into PHG. B73 RefGen_v5 was loaded as the reference assembly using the “MakeInitialPHGDBPipelinePlugin”, followed by the other five parental de novo genome assemblies using the “AssemblyHaplotypesMultiThreadPlugin” (Bornowski et al 2021). The “AssemblyHaplotypesMultiThreadPlugin” uses mummer4 to align each assembly to the reference by chromosome in parallel (Marçais et al 2018).…”

“…This research utilized six Stiff Stalk inbreds - B73, B84, NKH8431, LH145, PHB47, and PHJ40 – that represent key founders in commercial breeding programs. Recent work reported the genome sequences of these inbreds (excluding B73) and found extensive genomic variation between B73 and the other five parents along with conservation of base BSSS haplotypes within each inbred (Bornowski et al 2021).…”