Genotyping-by-Sequencing (GBS) for Population Genomics of Aspen (Populus tremuloides)

Aspen (Populus tremuloides) is the most widely distributed tree species in North America, and is important ecologically and economically. We explored range-wide genomic variation using Genotyping-by-Sequencing (GBS), an emerging complexity-reduction technique useful in organisms lacking a reference genome. Adapters are designed to capture genomic fragments digested by restriction enzymes, and incorporate barcodes for multiplexing, and primers for Illumina sequencing. We multiplexed 88 samples per lane, recording approximately 1.9 million reads per individual, with an average read length 97 bp. Quality assessment of the reads resulted in 93% of reads being retained for SNP discovery. We detected over 160,000 SNPs with an average of 28% of individuals covered per SNP. The average individual was represented by 44,550 SNPs, and over 6,000 SNPs were represented by 90% of individuals sampled. We explored the distribution of SNP loci across the genome using the closely related species P. trichocarpa, for which a complete genome sequence is available. Mapping of the aspen GBS reads on the P. trichocarpa genome assembly revealed that 63% of all reads (not SNPs) mapped to the nuclear genome, the remaining to organellar and oligodimer contamination. Reads mapped to an average depth of 8X, and covered approximately 4% of the nuclear genome of P. trichocarpa, distributed evenly across chromosomes. We examine the feasibility of GBS for population genetic studies and compare results to those from microsatellite markers. We also explore cost effectiveness of the GBS approach.