Regulatory variation controlling architectural pleiotropy in maize

An early event in plant organogenesis is establishment of a boundary between the stem cell containing meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we use regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses. In addition to defining network plasticity around core pleiotropic loci, we identify new transcription factors that contribute to phenotypic variation in canopy architecture, and structural variation that contributes to cis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific developmental networks to pinpoint pleiotropic loci and their cis-regulatory components, which can be used to fine-tune plant architecture for crop improvement.