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The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia formosa

Brandon Schlautman, Vera Pfeiffer, Juan Zalapa, Johanne Brunet
American Journal of Plant Sciences 2014 v.5 no.15 pp. 2402-2412
Aquilegia, DNA, DNA primers, alleles, databases, expressed sequence tags, forests, gene flow, genetic markers, genetic polymorphism, heterozygosity, loci, microsatellite repeats, Oregon
Numerous microsatellite markers were developed for Aquilegia formosa from sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers designed for 9 SSR containing sequences in the Nucleotide Database, 3,803 sequences in the EST database and 2,226 sequences in the GSS database. For validation purposes, 45 primer-pairs were used to amplify DNA from 16 A. formosa individuals from the H.J. Andrews Experimental Forest in Oregon, a Long Term Ecological Research (LTER) site. Genetic polymorphisms were identified at 30 of the 45 microsatellite loci with an average of 13.2 alleles per locus. A high level of heterozygosity was observed at the majority of these loci. The use of 10 of these polymorphic loci was sufficient to individually separate the 16 individuals using a principal coordinate analysis. This comprehensive collection of primers significantly increases the availability of microsatellite primers for Aquilegia spp. and provides ample material for future studies that require highly variable SSRs such as mapping and association studies and investigation of plant mating system and gene flow.