ABSTRACT
Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.
ABSTRACT
Procedural modeling has produced amazing results, yet fundamental issues such as controllability and limited user guidance persist. We introduce a novel procedural model called PICO (Procedural Iterative Constrained Optimizer) and PICO-Graph that is the underlying procedural model designed with optimization in mind. The key novelty of PICO is that it enables the exploration of generative designs by combining both user and environmental constraints into a single framework by using optimization without the need to write procedural rules. The PICO-Graph procedural model consists of a set of geometry generating operations and a set of axioms connected in a directed cyclic graph. The forward generation is initiated by a set of axioms that use the connections to send coordinate systems and geometric objects through the PICO-Graph, which in turn generates more objects. This allows for fast generation of complex and varied geometries. Moreover, we combine PICO-Graph with efficient optimization that allows for quick exploration of the generated models and the generation of variants. The user defines the rules, the axioms, and the set of constraints; for example, whether an existing object should be supported by the generated model, whether symmetries exist, whether the object should spin, etc. PICO then generates a class of geometric models and optimizes them so that they fulfill the constraints. The generation and the optimization in our implementation provides interactive user control during model execution providing continuous feedback. For example, the user can sketch the constraints and guide the geometry to meet these specified goals. We show PICO on a variety of examples such as the generation of procedural chairs with multiple supports, generation of support structures for 3D printing, generation of spinning objects, or generation of procedural terrains matching a given input. Our framework could be used as a component in a larger design workflow; its strongest application is in the early rapid ideation and prototyping phases.
ABSTRACT
Changes in canopy architecture traits have been shown to contribute to yield increases. Optimizing both light interception and light interception efficiency of agricultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identification logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving algorithm to allow for fully automatic reconstruction of hundreds of plants. It was employed to generate 3D reconstructions of individual plants within a sorghum association population at the late vegetative stage of development. Light interception parameters estimated from these reconstructions enabled the identification of known and previously unreported loci controlling light interception efficiency in sorghum. The approach is generalizable and scalable, and it enables 3D reconstructions from existing plant high throughput phenotyping datasets. We also propose a set of best practices to increase 3D reconstructions' accuracy.
