Switchgrass (Panicum virgatum L.)  and reed canarygrass (Phalaris arundinacea L.) are perennial grasses which have high biomass production potential. To enable genomic selection and genome wide association analysis of these species, germplasm resources, including both bi-parental linkage populations and association populations, have been developed. Unlike traditional genotyping methods, genotyping by sequencing (GBS) is a high-throughput, low-cost way to explore the genetic diversity in populations. About 2000 individual plants are being genotyped using GBS. As many as 100,000 high density SNP markers have been generated. These markers will provide unparalleled insights into genomic variation, polyploidy, diversity and population structure. This same germplasm has been simultaneously phenotyped for multiple morphological and developmental traits, allowing genomic selection and genome wide association study to be brought into practice.