Genetic fingerprinting of onion (Allium cepa L.) varieties using simple sequence repeat markers

Thirty bulb onion microsatellites were screened for PCR amplification in 20 varieties of bulb onions including 3 shallot and 3 leek varieties. The study tried to establish the DNA profiles of onion varieties grown in the Philippines using microsatellites or simple sequence repeat markers (SSRs), and identify SSR marker applicable for variety identification. All of the screened primers generated a total of 88 alleles with an average of 2.93 alleles per locus. Ten of these primers showed high degree of polymorphism. The number of alleles observed per polymorphic locus ranged 2-6. The PIC value ranged 0.40-0.83. Resulting banding patterns for all of the markers used ranged 2-8 with molecular sizes ranging 75 to 650 bp. Among the polymorphic markers, AMS02 which amplified the highest number of alleles (6), also generated the highest number of banding pattern and exhibited more unique bands at some particular loci that can be used as marker for variety identification. This marker can identify 'Red Hawk', 'Super Creole', 'Superex' and 'ON-10-364'. Marker AMS23 also amplified distinct band for variety 'ON-10-364'. Amplification of the marker AMS05 and AMS15 revealed a distinct band pattern in the genotypes 'Red Express' and 'Yellow Granex', respectively. Primer AMS21 produced specific bands for the variety 'Yellow Granex' and 'Red Hunter'. 'Batanes Jumbo' and 'Red Hunter' can be identified by using the marker AMS08. Profiles of the bands from all the polymorphic markers were used to group the varieties analyzed using UPGMA-SAHN cluster analysis. Cluster analysis showed that onion varieties cluster into two groups at 0.90 similarity level which separated the red onions from white, shallot and leek types. This study provides genetic information that can delineate onion cultivars. Results proved the usefulness of microsatellites in establishing the DNA fingerprints of onion varieties that can be used as reference for future genetic studies such as construction of genetic maps. Identified polymorphic SSR markers also revealed their potential use of rapid identification of onion genotypes.