Abstract
The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.
Highlights
The comparative analysis of the gene and repeat content together with the analysis of whole-genome alignments (WGAs) and SNPs confirms the European flints as highly differentiated germplasm of cultivated maize at a whole-genome scale
Cross-consolidation of gene models revealed a moderate number of nonsyntenic genes, suggesting that genic presence–absence variations (PAVs) are less pronounced in maize than previously reported
Significant lower support by expression and homology indicates that less conserved orthologous clusters are likely enriched for nonfunctional and poor gene models
Summary
A genetic map generated from an F2 mapping population of an EP1 × PH207 cross demonstrated a high consensus between genetic and physical map corroborating quality and contiguity of the maize assemblies (Extended Data Fig. 2). Complete BUSCO24 genes totaled >95%, strongly supporting high coverage of the gene space while only ~1.5% and 0.8–2.4% of the BUSCO Liliopsidae set were absent or fragmented in each of the four assemblies on average, respectively (Supplementary Table 2). For the remaining five lines, the number and age distribution of fl-LTRs confirm the high quality of the respective assemblies (Extended Data Fig. 5). While the percentage of shared elements among the different lines shows a marked decrease, the Articles a
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