Development of simple sequence repeat (SSR) markers that are polymorphic between cultivars in Brassica rapa subsp. rapa

Abstract

Simple sequence repeats (SSRs) markers were developed through data mining of 3,803 expressed sequence tags (ESTs) previously published. A total of 144 di- to penta-type SSRs were identified and they were screened for polymorphism between two turnip cultivars, ‘Tsuda’ and ‘Yurugi Akamaru’. Out of 90 EST-SSRs for which polymerase chain reaction (PCR) primers were designed, 85 could be successfully amplified, 13 showed polymorphism and eight were regarded as valid markers based on Hardy-Weinberg equilibrium (HWE) in the F₂ population developed from a cross between the two cultivars. Additionally, 1551 SSR markers reported in public database were also subjected to polymorphism survey. Among these SSR markers, 66 showed polymorphism between the two cultivars, while 28 showed HWE with Ho in a range of 0.4 to 0.6. A linkage map was constructed using these eight EST-SST markers and 28 published SSR markers in the F₂ population.

Key words: EST-SSR, linkage map, polymorphism, single sequence repeats, turnip.