DNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia)

We performed random shotgun sequencing to obtain genome sequences from Japanese pear 'Housui' (Pyrus pyrifolia) for use in developing molecular markers. Nearly 2.7 million single-read sequences were obtained, with an average read length of 374 bases. More than 990 Mb of nucleotide sequence were recovered, which is equivalent to twice the size of the Japanese pear genome. We designed 237 simple sequence repeat (SSR) markers with motifs of 4, 5, or 10-14 nucleotides based on more than 50,000 SSR sequences. Out of these 237 markers, 128 loci could be added to at least one of three genetic linkage maps: European pears (P. communis) ‘Bartlett’ and 'La France', and Japanese pear ‘Housui’. 86 of the 144 tested expressed sequence tag (EST)-SSR markers from apple (Malus × domestica) were mapped in one or more of the pear cultivars. The new genetic linkage map of 'Bartlett' consisted of 485 loci from SSR and single-nucleotide polymorphism markers, covering 17 linkage groups with a total length of 965 cM. The linkage map of 'La France' contained 370 loci in 17 linkage groups, with a total length of 1160 cM, and that of ‘Housui’ contained 415 loci in 20 linkage groups, with a total length of 1177 cM. The information obtained from this study will help us develop genome-wide markers and perform marker-assisted selection in pear breeding programs.