15-01: Crown and rhizome transcriptomes from upland and lowland tetraploid switchgrasses

We first used the Roche 454-FLX pyrosequencing platform to obtain approximately 1 million reads consisting of 216 million bases to build a crown and rhizome transcriptome of an upland tetraploid switchgrass cultivar, cv Summer.  These reads were assembled into 27,687 contigs and 43,094 singletons, and resulted in the identification of 30,177 new sequences that were not in the databases.  We next combined this 454 assembly with datasets obtained from the Illumina platform to build a hybrid transcriptome.  RNA seq analysis of mRNA obtained from two contrasting switchgrass populations, namely cv Summer, an upland tetraploid cultivar with good winter hardiness, and cv Kanlow, a lowland tetraploid cultivar with limited adaptation to the central great plains was performed.  Gene set enrichment analysis revealed that 41 gene sets were over-represented in Kanlow and 9 gene sets were over-represented in Summer. Further analysis of these gene sets suggest that metabolism in the below ground parts were slowing in Summer plants.  In contrast, the crowns and rhizomes of Kanlow plants appeared to be metabolically highly active and potentially accumulating new tissues.  Results from these next-generation sequencing studies will be discussed relative to C and N nutrient recycling data obtained for Kanlow and Summer plants over a growing season.  Combining these and related datasets obtained from different populations of switchgrass can be expected to provide significant insights into how developmental changes in the shoots affects the metabolism of below-ground tissues.