Global Expression In Sorghum Brown Midrib Mutants; a Tool to Improve Biomass for Biofuels.

brown midrib (bmr) mutants are being investigated for their ability to increase the conversion efficiency of sorghum biomass for lignocellulosic bioenergy.  brown midrib 6 and 12 (bmr6 and 12) are impaired in the last two steps of monolignol biosynthesis resulting in reduced lignin content and altered lignin composition.  Bmr6 and Bmr12 encode a cinnamyl alcohol dehydrogenase (CAD) and a caffeic acid-O-methyltransferase (COMT), respectively.  To comprehensively characterize the effects of bmr6 and bmr12 on sorghum gene expression in developing stalks, nearly 200 million reads were sequenced using the Illumina next-gen sequencing platform representing the transcriptome of bmr and wild-type stalks.  Expression profiles were generated from wild-type and near-isogenic lines containing bmr6, bmr12 or both bmr mutants in three different sorghum varieties. Single Nucleotide Polymorphisms (SNPs) in expressed transcripts were discovered between and amongst the three sorghum varieties profiled (Atlas, R Tx430 and B Wheatland) compared to JGI sequenced reference genome R Tx623.  These SNPs can used be as genetic markers for mapping and sorghum breeding and a subset are relevant to breeding sorghum for bioenergy uses.  Differentially expressed genes were identified in bmr mutants relative to wild-type, which may connect specific gene product functions in cell wall formation, lignification or bioenergy availability.  Roughly triple the number of genes were differentially expressed in bmr6 stalks relative to wild-type as compared to bmr12 relative to wild-type.  Together these data demonstrate that bmr6 and bmr12 each had distinct impacts upon gene expression, which may have specific implications on plant physiology.