Genetic diversity in indonesian shallot (Allium cepa var. ascalonicum) and Allium x wakegi revealed by RAPD markers and origin of A. x wakegi identified by RFLP analyses of amplified chloroplast genes

RAPD and PCR-RFLP analyses were conducted to establish the phylogenetic relationships among collected accessions of shallot and Allium x wakegi, and to assess the origin of A. x wakegi. Twenty out of 100 primers were amplified with 112 scorable bands for cluster analysis. Two main cluster groups consisting of one group for shallot and another group for A. x wakegi were clearly separated. The sub-groups of clusters reflected the phenotype differentiation in shallots and regional specificity in some A. x wakegi accessions. The present results were also in agreement with previous systematics by isozymes of which the highest genetic variation of A. x wakegi in Indonesia was found in West Java suggesting the possibility that this place might be one of the germplasm centers. From RFLP analysis of amplified matK gene of cpDNA it was demonstrated that A. x wakegi originated from shallot as a maternal plant x Welsh onion as a paternal plant as well as from reciprocal crosses.