Development of a Saturated Linkage Map in Prunus salicina L. Using Genotyping by Sequencing (GBS)

Japanese plum (Prunus salicina L.), is an important temperate fruit crop with a diploid genome (2n = 2x = 16). For years, many efforts have been made to construct linkage maps in cultivated Prunusspecies such as peach, cherries, almond, apricot, but almost all of these maps were constructed using low-throughput molecular markers. Currently, robust genotyping methods such as GBS have been developed, which have provided a high marker density. GBS uses restriction enzymes to reduce the genome complexity followed by multiplex sequencing to produce high-quality polymorphism data in a form of SNPs at a relatively low cost per sample. This information is extremely relevant for molecular breeding in order to develop rapid and highly saturated genetic maps, which can accelerate the breeding cycle in woody perennial plants as Japanese plum.

In this work, we used a GBS approach to produce a highly saturated map in a biparental segregant population of Japanese plum. We analyzed 57,536 SNPs in two parental lines (cv. Angeleno x cv. Aurora) plus 68 offspring. In addition, we used the sequenced peach genome as a reference where we were able to identify 36 scaffold. The first eight scaffold were associated with linkage groups identified for peach; the number of observed SNP ranged between 11,978 SNPs (Scaffold 1) and 5,711 SNPs (Scaffold 5). We discuss the Japanese plum genetic map and its relationship with the peach genome.