Characterization of Genomic Microsatellites and Development of SSR Markers of Eucommia ulmoides

Based on genome sequencing of Eucommia ulmoides, the perfect SSR (17 nucleotide repeats) and compound SSR sequences were searched from Eucommia genome (26,947/854,758,160 bp) by using MISA. 488,592 SSR loci were found from 25,694 Scaffolds, accounting for 95.3% of the total Scaffolds. The results indicated that every 1 749 bp contained one SSR microsatellite on the average. The SSRs which had mononucleotide repeats were the most of all, accounting for 54.34%, and the dinucleotide repeats accounted for 20.47%. The percentage of compound SSR, trinucleotide repeats, tetranucleotide repeats, pentanucleotide repeats, hexanucleotide repeats, and heptanucleotides repeats were 20.29%, 23.89%, 0.77%, 0.13%, 0.10% and 0.01%, respectively. Meanwhile, the A/T repeats were predominant type among these SSRs. A total of 290 pairs of primer was designed and synthesized. The primers were verified by using 8 Eucommia clones, among which 162 pairs of primers were able to amplify products and 16 pairs of them were polymorphic and stable. 84 alleles were detected in these Eucommia clones, (5.25 alleles per SSR locus in average). The results are applicable for analyzing genetic diversity constructing genetic map, and identifying early sex status by using SSR molecular markers on Eucommia ulmoides.