Patterns of Variation in Wild and Domesticated Apple

Our understanding of the genetics of plant domestication have historically been based on studies conducted in annual plants, but current techniques now allow for a focus on the domestication genetics of perennial plants. These comparisons have revealed that patterns and consequences of domestication differ substantially across the perennial/annual divide. Here, we explore the domestication genetics of apple (Malus x domestica) as compared to its wild relatives (Malus sieversii) by examining patterns of nucleotide diversity in a set of candidate domestication and randomly selected ‘background’ genes from across the genome. Genes were targeted using a sequence capture by hybridization method followed by paired-end Illumina sequencing; 49 candidate domestication genes and 68 background genes were included in the sequence-capture approach. Reads were mapped to the Malus x domestica reference genome and also assembled using a reference-free approach, followed by comparisons of nucleotide diversity across species and gene classes.