To determine how a century of artificial selection has changed the genome of E. grandis, we generated SNP genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors.

Genomic DNA was isolated from leaf or xylem tissue of 1080 individual field grown E. grandis trees. Single nucleotide polymorphism (SNP) genotpying was performed for each sample using the EUChip60K SNP chip (Silva-Junior et al., 2015). Genotypic classes were redefined as described by Silva-Junior et al. (2015) using GenomeStudio (Illumina) and SNPs with unique mapping positions to the v.2 reference E. grandis genome sequence was retained.

The genotypes are presented in a single comma separated dataframe with samples in rows (n = 1080), SNP ID in columns (m = 57,567), and alleles separated by an underscore ( "_").  Missing data are indicated as "NA".