2012 Annual Report 1a.Objectives (from AD-416): The objectives of this cooperative research project are to enhance our knowledge regarding grass development including, development in response to biotic and abiotic stress through the use of genetic and genomic tools in sorghum and other cereal grasses. 1b.Approach (from AD-416): In order to identify candidate genes, sample materials will be collected from different sorghum tissues and treatments and used for the generation and sequencing of expression libraries; and QPCR analysis. 3.Progress Report: Research focused on transcript and epigenetic profiling in the reference genome sorghum BTx623 to characterize functional sequence in sorghum, to support structural and functional annotations, and to characterize gene networks. The transcript profiling across several tissues and inclusion of phylogenetic analyses suggests that almost 800 genes are missing from the community annotations and that over 400 gene models are fragmented. Our annotations based on RNA-Seq data include gene models for 30% of the missing genes and resolve 50% of split genes. In addition, we have identified a novel transcriptionally active region. Finally, sampling the methylome by shallow sequencing of bisulfite-treated DNA allowed us to identify methylation patterns that are strongly associated with transcribed loci. A second activity during the past year was to begin characterization of the sorghum secondary cell wall biosynthesis gene regulatory network in high biomass energy sorghum. This work included characterization of plant growth in the field throughout the spring and summer of 2012. Molecular phenotyping for transcript profiling from the stems of one energy sorghum genotype (R07018) and one grain sorghum genotype (BTx623) at day 45 during the phase of linear stem elongation and the identification of ~2.7M SNPs between R07018 and BTx623.