Genotyping By Sequencing (GBS) in Numerous Species: Lessons from the Bench

Genotyping-by-sequencing (GBS) uses restriction enzymes and multiplexed next-generation sequencing to obtain large numbers of genome-wide SNPs in a cost efficient manner. Over the past two years, the Cornell Institute of Genomic Diversity (IGD) has used GBS to genotype more than 100,000 samples from over 100 different genera of plants, animals and fungi for scientists worldwide.  By far, our most frequently asked question is, “How many SNPs will I get?” The answer is complicated as it depends on factors related to genome size and structure, diversity (extant in the species and within the sample), and whether or not a reference sequence is available for SNP calling. We will discuss these issues and share general patterns we have observed.