Identification and Characterization of InDel and Microsatellite Loci by Garlic Genome Comparison

Garlic (Allium sativum L.), mainly propagated by asexual bulb, is consumed as vegetable or food condiment over the world. Garilc is considered as native to central Asia region, and its wild progenitor is thought to be A. longicuspis. Until now, genetic architecture of this species has not been well studied in that the genetic characterization methods are not sufficient. In this view, we sequenced the genome of four garlic accessions (3 cultivates and 1 wild type) using GS FLX pyrosequencer for development of promising molecular markers. Total 130.4Mb genomic DNA sequences were acquired and assembled into contigs. The number of contigs was 16,415 with mean depth of 11.6 while 190,310 singletons. Based on the assembled contigs over 500bp, we compared DNA sequence differences among three cultivars, and found 45 distinctive InDel and microsatellite regions. 30 distinguishable InDel and microsatellites between A. sativum and A. longicuspis were also acquired by sequence comparison of these two species. Further, putative microsatellite loci in the genomic DNA sequence were surveyed by ARGOS software. Based on our results, development of new molecular markers on distinctive and putative polymorphic loci might be valuable for evaluating and improving Allium species.