Comparison of AFLPs, RAPD Markers, and Isozymes for Diversity Assessment of Garlic and Detection of Putative Duplicates in Germplasm Collections

Garlic (Allium sativum L.) is an asexually propagated crop that displays much morphological diversity. Studies which have assessed garlic diversity with isozymes and randomly amplified polymorphic DNA (RAPD) markers generally agreed with the morphological observations but sometimes failed to discriminate clones. To discriminate among closely related garlic clones in more detail, we introduced amplified fragment-length polymorphism (AFLPs) to evaluate the genetic diversity and phenetic relatedness of 45 garlic clones and three A. longicuspis clones and we compared AFLP results with RAPD markers and isozymes. Three AFLP primer combinations generated a total of 183 polymorphic fragments. Although similarities between the clusters were low (≥0.30), some clones within the clusters were very similar (>0.95) with AFLP analysis. Sixteen clones represented only six different banding patterns, within which they shared 100% polymorphic AFLPs and RAPD markers, and likely are duplicates. In agreement with the results of other investigators, A. longicuspis and A. sativum clones were clustered together with no clear separation, suggesting these species are not genetically or specifically distinct. The topology of AFLP, RAPD, and isozyme dendrograms were similar, but RAPD and isozyme dendrograms reflected less and much less polymorphism, respectively. Comparison of unweighted pair group method with arithmetic averaging (UPGMA) dendrograms of AFLP, RAPD, and isozyme cluster analyses using the Mantel test indicated a correlation of 0.96, 0.55, and 0.57 between AFLP and RAPD, AFLP and isozyme, and RAPD and isozyme, respectively. Polymorphic AFLPs are abundant in garlic and demonstrated genetic diversity among closely related clones which could not be differentiated with RAPD markers and isozymes. Therefore, AFLP is an additional tool for fingerprinting and detailed assessment of genetic relationships in garlic. longicuspis clones were discriminated morphologically from A. sativum clones by generally having exerted and purple anthers, higher flowering rate and seed production, and smaller bulbils in inflorescence (Etoh and Simon, 2002). The species have the same karyotype and A. sativum and A. longicuspis clones have been crossed successfully (Etoh, 1984; Pooler and Simon, 1994). Garlic has been propagated by vegetative means for centuries and the presence of many closely related or duplicated garlic clones is likely in germplasm collections. Large numbers of molecular markers are needed to discriminate closely related clones or to identify duplicates. One particularly useful tool to achieve this goal is amplified fragment-length polymorphism (AFLP), which could produce high multiplex informative mark- ers in a single reaction and, therefore, could generate sufficient markers to assess genetic diversity among garlic clones. AFLP is a PCR-based DNA fingerprinting technique (Vos et al., 1995) and like randomly amplified polymorphic DNA (RAPD), it generates primarily dominant markers. Neither AFLP nor RAPD require any probe or sequence information (Barker et al., 1999) and they can be applied to any species after some minor modifications. Isozymes, RAPD, and AFLP have been used extensively for determining genetic diversity and relatedness