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Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific  Setaria italica  x  Setaria viridis  recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in  Setaria . In this population, alleles inherited from the weedy  S .  viridis  parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated  S .  italica  parent collectively act to increase plant height later in development.

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria