Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple

Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and lo wild apples were genotyped using specific-locus ampli- fied fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investi- gate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than culti- vated apples. Linkage disequilibrium （LD） decays were observed quite rapidly in cultivated and wild apples, with an r2-value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribu- tion patterns of LD blocks were detected betweendomesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domes- tication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgres- sion could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.