We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species.

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

Switchgrass (Panicum virgatum L.), is a warm season C 4 perennial grass, native to North American tall grass prairies. The high biomass production potential of switchgrass with low inputs makes it an excellent choice as a sustainable bioenergy crop. The objective of this study was to determine the genetic variability within and among 31 switchgrass populations obtained from Germplasm Resources Information Network (GRIN). Six plants from each population (186 genotypes) were characterized with 24 conserved grass expressed sequence tag-simple sequence repeats (EST-SSR) and 39 switchgrass EST-SSR markers. The partitioning of variance components based on the analysis of molecular variance (AMOVA) revealed that the variability within population was significantly higher (80%) than among populations (20%). Pair-wise genetic distance estimates based on SSR data revealed dissimilarity coefficients for genotypes ranging from 0.45 to 0.81. The uplands and lowlands were generally grouped in distinct sub-clusters. The genotypes were grouped into the different adaptive zones based on the geographical locations of the collections. Ploidy estimation showed that 20 of the accessions were tetraploid, four of them were octoploids and the remaining seven had mixed ploidy levels. Flow cytometry analysis of genotypes within cultivars collected from commercial seed sources did not always support the ploidy mixtures that were found in GRIN collections. Three genotypes of two accessions that clustered differently from other genotypes of the same accessions also had different ploidy levels.