Amplified fragment length polymorphism (AFLP) is a molecular marker technique based on DNA and is extremely useful in detection of high polymorphism between closely related genotypes like Korean wheat cultivars. Six sequence characterized amplified regions (SCARs) have been developed from inter simple sequence repeat (ISSR) analysis which enabled the identification and differentiation of 13 Korean wheat cultivars from the other cultivars. We used six combinations of primer sets in our AFLP analysis for developing additional cultivar-specific markers in Korean wheat. Fifty-eight of the AFLP bands were isolated from EA-ACG/MA-CAC, EA-AGC/MA-CTG and EA-AGG/MA-CTA primer combinations. Of which 40 bands were selected to design SCAR primer pairs for Korean wheat cultivar identification. Three of 58 amplified primer pairs, KWSM006, KWSM007 and JkSP, enabled wheat cultivar identification. Consequently, 23 of 32 Korean wheat cultivars were classified by eight SCAR marker sets.

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Inter simple sequence repeat (ISSR) is a technique that leads to the development of novel specific molecular markers and relationship analysis between species. In this study, 54 ISSRs were used to develop cultivar-specific DNA sequence characterized amplified regions (SCARs) for Korean wheat cultivars (Triticum aestivum). Using nine of 54 UBC ISSR primers, 16 cultivar-specific fragments were detected among 32 wheat cultivars. Of the 16 primers, 10 successfully amplified targets in 32 cultivars and six novel cultivar-specific markers were finally selected. A total of 13 Korean wheat cultivars (Ol, Dahong, Namhae, Jinpum, Anbaek, Jopoom, Jokyung, Sinmichal 1, Jeokjoong, Dajung, Goso and Joah) were classified by newly developed six SCAR markers. Cultivar-specific markers can be used not only for cultivar fingerprinting but also for marker-assisted selection in wheat breeding program.

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