Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp

This paper deals with the diversity assessment of tropical Indian onion and cross amplification of genomic and EST-SSR markers in distantly related native wild species. Out of 60 SSRs, 10% genomic SSRs were able to amplify as compared to EST-SSR where 53.3% primers were able to reveal amplicons. Clustering revealed five groups and indigenous short day onion formed separate cluster from the exotic short day and long day onions. A. roylei accessions exhibited a dissimilarity index of 35.5% between themselves whereas ‘Pran’ and A. × proliferum grouped together at a genetic distance of 0.4. A . fistulosum accessions formed a tight cluster and distantly related wild species A. carolinianum , A . chinense and A. hookeri formed neutral nodes. Present results are important to aid in analyzing the diversity present in short day onion and its utilization in breeding programs. Further, this is the first time that three accessions of A. roylei Stearn were used and rare alleles amplified in wild species will aid in detecting population structure and molecular marker aided selection for interspecific hybrid development.