Microsatellite enrichment in organisms with large genomes (Allium cepa L.)

To exploit the polymorphism of repeat numbers in short tandem repeat (STR) sequences (microsatellites) as molecular markers, STRs must be isolated and PCR primers must be developed in flanking sequences. In species with large genomes such as Allium cepa L. (onion and shallot), an efficient selection procedure for genomic fragments containing STRs is a crucial step. Here we describe a nonradioactive method for microsatellite isolation based on affinity capture of single-stranded restriction fragments annealed to biotinylated microsatellite oligonucleotides (CA)10, (GAA)8 and (AAC)8 followed by adapter-mediated genomic PCR. Cloning of the products in E. coli and plasmid sequencing revealed more than 60% positive clones. Primers were designed in STR-flanking regions, and one or two bands were amplified in 13 diploid onion and five shallot accessions. Allelism of the bands was confirmed by product sequencing.