Regulatory gene architecture and its relation to plant fitness

We assessed transcriptome variation in populations of 216 accessions of rice, Oryza sativa, which represented all major varietal groups including indica and japonica. During the 2016 Philippines dry season populations of accessions were planted in triplicate (with two accessions planted in triplicate three times as replicated checks) in identical alpha-lattice layouts of 660 plots in two fields: a continuously wet paddy, and a field where plants were exposed to intermittent drought in the vegetative and reproductive stages. We measured transcript levels in leaf blades at 33 days after seedling transplant, and 17 days after withholding water in the dry field, using a liquid automation-based 3’ mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library.