Development of novel EST-SSR markers derived from Japanese pear (Pyrus pyrifolia)

We developed 73 novel expressed sequence tag (EST) -simple sequence repeat (SSR) markers based on ESTs derived from 11 different cDNA libraries of the Japanese pear (Pyrus pyrifolia Nakai) cultivar 'Housui', comprising 30, 36, two, one, and four SSRs with repeat motifs of di-, tri-, tetra-, penta-, and hexanucleotides, respectively. Forty-eight EST sequences showed significant homology to Arabidopsis thaliana genes. The linkage groups and positions of 57 loci generated from 53 SSR markers covering all 17 linkage groups, were identified. These EST-SSRs will be useful for high-throughput genotyping of marker-assisted selection. The numbers of alleles and the observed and expected heterozygosities at single-locus EST-SSR markers in ten Japanese and ten European pears suggest high polymorphism and heterozygosity of the EST-SSRs. Di-nucleotide EST-SSRs showed two to three times the polymorphism and heterozygosity of trinucleotide EST-SSRs. Some of the EST-SSRs proved transferable to other species in the Rosaceae, paving the way for the development of markers for the same phenotypic traits among species of the Rosaceae.