Plant evolution and crop domestication is founded on genetic complexity that goes well beyond single gene mutations with dramatic phenotypic effects. To study the mechanisms and principles underlying quantitative trait variation, we are using genome editing to investigate the genetic and functional architecture of cis-regulatory regions from key developmental genes. We have found that the mutagenesis of promoters can reveal hidden dosage-sensitivity of genes, and a range of transcriptional alleles and can be created to “tune” quantitative variation. Open chromatin and evolutionary conserved sequences in these promoters can predict functionally important cis-regulatory regions, but tissue-specific regulatory elements exist and can be resolved empirically. This work raises the question of whether rules for predicable quantitative phenotypic outcomes will emerge from genome editing to enable more efficient use of this technology for basic biology and crop improvement.