We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Central America (1), natural genetic variations in flowering time enabled early Native Americans to select maize adapted to a range of latitudes and lengths of growing seasons, including the very short summer season typical of the eastern Canadian region of Quebec. Under such conditions, early flowering allows seed to mature before the onset of frost. Flowering time is also a key trait of improved drought tolerance. Indeed, it has been shown that a single day of drought during flowering can decrease yield by as much as 8% (2). One way to address such losses is to develop and grow cultivars characterized by a short cycle and able to flower before predictable drought episodes.The genetic variability available for maize breeding is essentially quantitative; i.e., it involves allelic variation at different quantitative trait loci (QTLs), which are influenced by environmental effects. Although a large body of mapping information on QTLs is available for flowering time (3), relatively little is known about the molecular basis of QTLs, with only one gene, Dwarf8, correlated thus far with quantitative effects (4, 5). Furthermore, a few mutants for flowering time have been described (6, 7), two of which, id1 (8) and dlf1 (9), have been cloned. Our results (i) show that the allelic variation responsible for the major flowering-time QTL, Vegetative to generative transition 1 (Vgt1) (10, 11) on chromosome 8, is confined to an Ϸ2-kb intergenic region upstream of an Ap2-like flowering-time gene, (ii) identify maize-sorghum-rice evolutionarily conserved noncoding sequences (CNSs) within Vgt1, and (iii) support a cisacting transcription-regulatory role for Vgt1. ResultsPositional Cloning of Vgt1. Previous work (12) mapped Vgt1 to a 1.3-cM region (Fig. 1A) on bin 8.05, based on a mapping population derived from the cross N28 ϫ C22-4. The strain C22-4 is nearly isogenic to N28 and carries the early Vgt1 allele in an Ϸ7-cM introgression originating from the early maize variety Gaspé Flint. By using standard positional cloning, Vgt1 was confined to an Ϸ2-kb region (Fig. 1 B-D). Sequence annotation of the original BAC clone and the corresponding sequences derived from N28 and Gaspé Flint genetic backgrounds showed that Vgt1 is apparently noncoding and is located Ϸ70 kb (61-76 kb, depending on the genetic background) upstream of an Ap2-like gene identified here as ZmRap2.7. This gene is orthologous to Rap2.7 (also known as TOE1), a transcription factor that regulates flowering time in Arabidopsis (13,14). No other genes were annotated between Vgt1 and ZmRap2.7. Pseudogenes due to transduplication events mediated by nonautonomous helitron elements (15) were observed in N28 and other genetic backgrounds but not in Gaspé Flint (data not shown). Within the Vgt1 region, the contrasting QTL alleles showed 29 SNPs and insertion/deletion-type polymorphisms (Indels) and one 143-bp insertion into the Gaspé Flint allele of a Mite transposon belonging to the Tourist (16) family [ Fig. 4 Lower and supporting information (SI) Fig. 5].Association M...

We report a whole-genome comparison of gene content in allelic BAC contigs from two maize inbred lines. Genic content polymorphisms involve as many as 10,000 sequences and are mainly generated by DNA insertions. The termini of eight of the nine genic insertions that we analyzed shared the structural hallmarks of helitron rolling-circle transposons. DNA segments defined by helitron termini contained multiple gene-derived fragments and had a structure typical of nonautonomous helitron-like transposons. Closely related insertions were found in multiple genomic locations. Some of these produced transcripts containing segments of different genes, supporting the idea that these transposition events have a role in exon shuffling and the evolution of new proteins. We identified putative autonomous helitron elements and found evidence for their transcription. Helitrons in maize seem to continually produce new nonautonomous elements responsible for the duplicative insertion of gene segments into new locations and for the unprecedented genic diversity. The maize genome is in constant flux, as transposable elements continue to change both the genic and nongenic fractions of the genome, profoundly affecting genetic diversity.