Genotyping By Sequencing of a Collection of Miscanthus spp. Accessions

A genotyping by sequencing (GBS) experiment to genotype our living Miscanthus spp. collection was initiated. This collection includes ~170 accessions of M. sinensis, M. sachariflorus, M .x giganteus and ~100 hybrids. In addition we analyzed DNAs of several closely related species. Our procedure follows with modifications the protocol from Elshire et al. 2011 (PLoS ONE 6(5): e19379. doi:10.1371). Illumina HiSeq2000 next generation sequencing was applied to generate large numbers of SNPs from sequencing genomic DNA. The SNPs are used as molecular markers to determine the genetic distances between the accessions. To reduce the complexity of the results, the genomic DNA was fragmented by the restriction enzyme PstI. We used a set of 96 adapters with different barcodes and sequenced in parallel 96 samples. The quality of each library was checked on the Agilent Bioanalyzer. The pooled libraries were sequenced on the Illumina HiSeq 2000 platform and 139 million reads were obtained on 1 lane.