Variants generated by GBS
In total 95 plants were digested, sequenced, and genotyped using GBS, representing 10 locations (Table 1, Figure 1). After quality filtering a total of 242,207,242 reads were obtained from sequencing on a single lane of Illumina HiSeq 100bp single end reads. The pipeline Universal Network-Enabled Analysis Kit (UNEAK: Citation) as implemented in Iplant was used to derive single nucleotide polymorphisms (SNP). Variant calling resulted in a total of 59,437 raw SNP variants. After filtering for a mean depth of 10, quality score of 30, minor allele frequency (MAF) of 0.05, and 5% missingness, 8,004 bi-allelic SNPs were retained. After removing SNPs with missing data, we retained 2,935 high-quality SNPs among the 95 individuals across the study.