Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum)

Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. To establish a genetic basis for molecular breeding of bunching onion, we isolated 1,796 simple sequence repeat (SSR) clones by large-scale sequencing of SSR-enriched genomic DNA libraries. Of these, 1,331 (74.1%) contained (GT) (n) repeats (n > 5), while 314 (17.5%) were (GA) (n) -containing clones. The average number of SSR repeats was 10.5 and 10.4 in the (GT) (n) - and (GA) (n) -containing clones, respectively. In a sample of five bunching onion inbred lines, an average of 3.2 alleles were detected in the 100 SSR loci investigated, with the polymorphic information content averaging 0.55. These results indicate that bunching onion SSRs are very rich sources of highly informative genetic markers.