Application of SSR markers for the breeding of bunching onion (Allium fistulosum)
2010
Tsukazaki, H., National Inst. of Vegetable and Tea Science, Tsu (Japan)
Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. However, despite its economic importance, its genetic characteristics are poorly studied. To establish a genetic basis for molecular breeding of bunching onion, I isolated 1796 simple sequence repeat (SSR) clones by large-scale sequencing of SSR-enriched genomic DNA libraries. Of these, 1331 (74.1%) contained (GT)sub(n) repeats (n 5) and 314 (17.5%) contained (GA)sub(n) repeats. The average numbers of SSRs among the respective clones were 10.5 and 10.4. Five inbred lines contained an average of 3.2 alleles at 100 SSR loci, with a mean polymorphism information content (PIC) of 0.55. These results indicate that bunching onion SSRs are very rich sources of highly informative genetic markers. I constructed a linkage map of bunching onion (2n=16) using an Fsub(2) population of 225 plants. The map, covering 2069 cM, consists of 17 linkage groups with 213 bunching onion SSR markers and 42 bulb onion (A. cepa L.) SSR, insertion-deletion (InDel), cleaved amplified polymorphic sequence (CAPS) or derived CAPS (dCAPS) markers. This is the first linkage map based mainly on SSR markers in Allium. Using 103 anchor markers (81 bunching onion SSRs, 11 bulb onion SSRs, and 11 bulb onion non-SSR markers: 1 InDel, 9 CAPSs, 1 dCAPS), I assigned markers to A. cepa or A. fistulosum chromosomes via the use of several kinds of Allium alien addition lines, and connected 16 of the 17 linkage groups to the 8 basic chromosomes of A. cepa.
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