Flowering time is a fundamental trait of maize adaptation to different agricultural environments. Although a large body of information is available on the map position of quantitative trait loci for flowering time, little is known about the molecular basis of quantitative trait loci. Through positional cloning and association mapping, we resolved the major flowering-time quantitative trait locus, Vegetative to generative transition 1 ( Vgt1 ), to an ≈2-kb noncoding region positioned 70 kb upstream of an Ap2 -like transcription factor that we have shown to be involved in flowering-time control. Vgt1 functions as a cis-acting regulatory element as indicated by the correlation of the Vgt1 alleles with the transcript expression levels of the downstream gene. Additionally, within Vgt1 , we identified evolutionarily conserved noncoding sequences across the maize–sorghum–rice lineages. Our results support the notion that changes in distant cis-acting regulatory regions are a key component of plant genetic adaptation throughout breeding and evolution.

Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.

One of the major quantitative trait loci for flowering time in maize, the Vegetative to generative transition 1 (Vgt1) locus, corresponds to an upstream (70 kb) noncoding regulatory element of ZmRap2.7, a repressor of flowering. At Vgt1, a miniature transposon (MITE) insertion into a conserved noncoding sequence was previously found to be highly associated with early flowering in independent studies. Because cytosine methylation is known to be associated with transposons and to influence gene expression, we aimed to investigate how DNA methylation patterns in wild-type and mutant Vgt1 correlate with ZmRap2.7 expression. The methylation state at Vgt1 was assayed in leaf samples of maize inbred and F₁ hybrid samples, and at the syntenic region in sorghum. The Vgt1-linked conserved noncoding sequence was very scarcely methylated both in maize and sorghum. However, in the early maize Vgt1 allele, the region immediately flanking the highly methylated MITE insertion was significantly more methylated and showed features of methylation spreading. Allele-specific expression assays revealed that the presence of the MITE and its heavy methylation appear to be linked to altered ZmRap2.7 transcription. Although not providing proof of causative connection, our results associate transposon-linked differential methylation with allelic state and gene expression at a major flowering time quantitative trait locus in maize.