Switchgrass (Panicum virgatum L.) is a perennial grass which has high biomass production potential. To enable genomic selection (GS) and genome wide association study (GWAS) of switchgrass, germplasm resources, including both bi-parental linkage populations and association populations, were developed. Unlike traditional genotyping methods, genotyping by sequencing (GBS) is a high-throughput, low-cost way to explore the genetic diversity in populations. About 1000 individuals were genotyped using GBS. Using a creative SNP calling method designed for species without reference genomes, more than one million high density SNP markers were generated. These markers provide unparalleled insights into diversity, population structure, phylogeny, phylogeography, polyploidy and evolutionary dynamics. 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.