Selection of generally applicable SSR markers for evaluation of genetic diversity and identity in Lilium

• Seventy standardized set of SSRs were selected to facilitate characterization and highly efficient breeding practices.
• 430 polymorphic alleles were found when amplified the 70 SSR loci in 69 lily accessions.
• Genetic differentiation of Lilium brownii var. giganteum and Lilium pumilum was first discussed at the molecular level.
• Putative male donors were identified for five F1 hybrids.

There are approximately 100 species and 10,000 cultivars of Lilium and in general their phylogeny is understood. Difficulties remain, however, in understanding the breeding relationships of cultivars and commercial hybrids. One solution to this problem is to identify a selection of validated and transferable SSR markers for use in genotyping. Although over 100 Lilium SSRs have been developed, they have not been validated for use with broad populations. Here, were-evaluated 112 SSRs with 69 lily accessions from different sources, and selected 70 SSRs as easy to score, transferable and polymorphic in all accessions tested. Based on the marker data from 70 SSRs, two main clusters were established for 69 accessions using TREECON, one includes Asiatic hybrids, Longiflorum × Asiatic hybrids and Asiatic local landraces (Lilium brownii, L. brownii var. giganteum, Lilium pumilum, Lilium davidii var. unicolor and Lilium lancifolium), the other is composed primarily of Oriental hybrids and Oriental × Trumpet hybrids, which is in agreement with previous studies and the breeding pedigree. The utility of the 70 SSR markers for establishing parentage and taxon identity of landraces was validated. Our study offers valuable information and validated markers for Lilium systematic classification and the establishment of identity.