Genomic signatures of artificial selection during early domestication of a wood crop

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.

Methods
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.

为探究一个世纪的人工选择如何改变巨桉（E. grandis）的基因组，我们利用EUChip60K芯片对来自南非三个先进育种项目的1080份个体样本开展单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因分型，并针对其野生祖先种群分析了群体结构与全基因组分化模式。

方法
从1080株田间种植的巨桉个体的叶片或木质部组织中提取基因组DNA。采用EUChip60K SNP芯片对每份样本进行单核苷酸多态性基因分型（Silva-Junior等，2015）。参照Silva-Junior等（2015）的研究方案，使用GenomeStudio（Illumina）重新定义基因型类别，并保留可唯一比对至v.2版巨桉参考基因组序列的单核苷酸多态性位点。