Comparative analysis of genetic diversity in garlic (Allium sativum L.) using AFLP, RAPD, and isozyme markers and characterization of a cytoplasmic marker associated with the bolting phenotype

Garlic (Allium sativum L.) is an asexually propagated crop with much morphological diversity. We evaluated the genetic diversity and phenetic relatedness of 45 garlic clones and three Allium longicuspis clones using AFLPs, and compared them with RAPDs and isozymes. Although similarities between the clusters were low (≥0.30), some clones within the clusters were very similar (≥0.95) with AFLP analysis. As in earlier studies, 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 was similar and correlations among the dendrograms were significant. However, RAPD and isozyme dendrograms reflected less polymorphism. AFLPs are abundant in garlic and could be used as an additional tool for fingerprinting and detailed assessment of genetic relationships in garlic.; In mapping or genetic diversity studies with RAPD or AFLP markers in plant species, it has been hypothesized that amplicons sharing the same position on a gel have the same DNA sequence identity. To test this hypothesis in garlic, sequence identity of 79 AFLPs representing seven polymorphic AFLP markers from two primer combinations were characterized. 95.5% of co-migrating AFLP fragments sharing the same position on a gel contained homologous sequences. In some cases, closely related clones shared identical bands, while unrelated garlic clones had a different sequence identity although they shared the same position on the gel. Thus, AFLP amplicon sequence identity conservation reflects phylogenetic relationships in garlic.; Organelle genome analysis in garlic revealed PCR differences between bolting and non-bolting garlic clones. Screening of 333 garlic accessions demonstrated that a 1.4 kb marker did not amplify in any of the non-bolting clones while amplification of this marker was observed in bolting clones. This marker was also not amplified in 91% of partially bolting garlic clones. Sequence information of this marker revealed that it included both mitochondrial and chloroplast DNAs. Analysis of DNA flanking both the 5′ and 3′ ends of this marker suggested that approximately a 4.8 kb chloroplast DNA was inserted into the mitochondrial genome of garlic downstream from the mitochondrial cox3 gene.