Development of Novel SSR (Simple Sequence Repeat) Markers and Construction of Genetic Map in Apple for Korean Apple Genome Project

Apple (Malus x domestica Borkh.) is one of the most important fruit crops in Korea. A new apple genome project has been started since 2012 for a nine -year schedule (supported by Biogreen 21 program of Rural Development Administration, Korea). This project aims integrate genomic information to develop a practical platform and to increase the efficiency of apple breeding program in Korea. As a starting point of this genome project, identification of genetic relationship among Korean apples and selection of standard SSRs were conducted to apply cultivar identification, core collection management, and reference map construction. First of all 51 SSRs primers were screened and selected which were reported in HiDRAS (High-quality Disease Resistant Apples for a Sustainable Agriculture). Then 6,165 SSRs markers were developed from ‘Golden Delicious’ full sequencing database by bioinformatics techniques. Finally we selected 213 reliable SSRs primers that amplify all alleles from 7 apple cultivars ('Hongro', 'Alps otome', 'Hwahong', ‘M.asiatica’, 'Liberty', 'Chukwang', ‘Golden Delicious’). Which are used for the construction of genetic map. Those 264 markers show a high level of genetic polymorphism, with on average 8.2 alleles per locus and an average heterozygosity was 0.80. Total of 264 standard SSRs distributed through the 17 chromosomes.  An apple genetic linkage map has been constructed on the basis of a segregating population of the cross between the cultivars ‘Hongro’and ’Alps otome’. A total of 264 SSRs markers were used for map constructed with JoinMap 3.0 and spanning 1,114.5 cM.