Genetic Diversity of Shallot (Allium cepa var. aggregatum) Based on Morphology and Molecular Markers
Shallot (Allium cepa var. aggregatum) in Indonesia are commonly vegetative propagated, but the scattered shallots are so diverse that they are suspected of having high genetic diversity. This study aimed to identify morphological diversity using 21 characters of shallot and molecular diversity using RAPD markers. The results showed that morphological characters divided 40 shallot genotypes into two main groups at a dissimilarity coefficient of 0.59 i.e group A (38 genotypes) and group B (2 genotypes), while morphological analysis based on 14 morphological characters of bulbs showed two main groups at 0.50 dissimilarity coefficient i.e group A and group B, consisted of 36 and 4 genotypes, respectively. Based on molecular markers, there were two main groups at 0.41 dissimilarity coefficient i.e. group A (3 genotypes) and group B (37 genotypes). RAPD markers generated 229 DNA polymorphic band with a total of 100%, and the informative primers were SBN2, OPE11, and SBN9. The clustering of 40 genotypes in this study did not relate to geographic origin. The genotypes of BM12, BM19, BM78, and BM01 have long leaf size, largest size and bulb diameter, and having dark of skin base color dry bulb intensity. BM63 and BM24 have erect foliage attitude, medium leaf length, medium size and bulb diameter. These potential genotypes can be developed to improve shallot varieties in Indonesia.
Keywords: dissimilarity coefficient, genotype, informative primers, RAPD