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Abstract 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 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 developmental networks to pinpoint pleiotropic loci and theircis-regulatory components, which can be used to fine-tune plant architecture for crop improvement. 

Abstract. This study describes a modeling framework, model evaluation, and source apportionment to understand the causes of Los Angeles (LA) air pollution. A few major updates are applied to the Community Multiscale Air Quality (CMAQ) model with a high spatial resolution (1 km × 1 km). The updates include dynamic traffic emissions based on real-time, on-road information and recent emission factors and secondary organic aerosol (SOA) schemes to represent volatile chemical products (VCPs). Meteorology is well predicted compared to ground-based observations, and the emission rates from multiple sources (i.e., on-road, volatile chemical products, area, point, biogenic, and sea spray) are quantified. Evaluation of the CMAQ model shows that ozone is well predicted despite inaccuracies in nitrogen oxide (NOx) predictions. Particle matter (PM) is underpredicted compared to concurrent measurements made with an aerosol mass spectrometer (AMS) in Pasadena. Inorganic aerosol is well predicted, while SOA is underpredicted. Modeled SOA consists of mostly organic nitrates and products from oxidation of alkane-like intermediate volatility organic compounds (IVOCs) and has missing components that behave like less-oxidized oxygenated organic aerosol (LO-OOA). Source apportionment demonstrates that the urban areas of the LA Basin and vicinity are NOx-saturated (VOC-sensitive), with the largest sensitivity of O3 to changes in VOCs in the urban core. Differing oxidative capacities in different regions impact the nonlinear chemistry leading to PM and SOA formation, which is quantified in this study. 

Abstract Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture, yet little is known about the intersecting pathways and how they are rewired during development. Here, we show that a single mutation in a gene encoding an AP1/FUL-like MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis. Previous reports of AP1/FUL-like genes in cereals have revealed extensive functional redundancy, and in panicoid grasses, no associated inflorescence phenotypes have been described. In S. viridis, perturbation of SvFul2, both through chemical mutagenesis and gene editing, converted a normally determinate inflorescence habit to an indeterminate one, and also repressed determinacy in axillary branch and floral meristems. Our analysis of gene networks connected to disruption of SvFul2 identified regulatory hubs at the intersection of floral transition and inflorescence determinacy, providing insights into the optimization of cereal crop architecture.