Regulatory variation controlling architectural pleiotropy in maize

Abstract

AbstractAn early event in plant organogenesis is establishment of a boundary between the 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 identify developmental regulators and their sub-networks at the nexus of these two traits, we used 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 identified new transcription factors that contribute to small trait effects in canopy architecture, likely through redundancy and dose-dependency with interconnected gene family members. We also showed that structural variation in the promoter of one factor contributes tocis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific gene networks to pinpoint small effect genetic loci and theircis-regulatory components, which can be used to fine-tune plant architecture for crop improvement.