Characterization and cross-species transferability of EST-SSRs from de novo transcriptome sequencing of white calla lily (Zantedeschia aethiopica)

A total of 10,089 simple sequence repeat (SSR) loci were identified from 81,072 Illumina-based transcriptomic unigenes of white calla lily (Zantedeschia aethiopica), an evergreen ornamental plant of Zantedeschia section Zantedeschia, cultivated worldwide. Of these SSRs, dinucleotide repeats were the most common type (63.43%), followed by trinucleotide repeats (35.02%). Microsatellite motifs AG/CT and AGG/CCT separately predominated in dimeric and trimeric repeat motifs. PCR primer pairs were successfully designed for 5104 SSR loci with appropriate flanking sequences. To validate the usefulness of SSRs in white calla lily, 153 perfect markers (repeat length ≥20 bp) were selected, of which 120 yielded stable and repeatable products, while the remaining failed to generate any clear DNA products. Twenty-seven SSR markers were then randomly selected to assess genetic diversity in 16 white calla lily accessions and cross-species transferability in 16 colored calla lily cultivars of Zantedeschia section Aestivae. The results showed that the number of alleles and the polymorphism information content (PIC) in white calla lily ranged from two to four and from 0.110 to 0.613, respectively. Moreover, 24 (89%) SSR markers were transferable to the cultivars of colored calla lily, in spite of the reproductive isolation between species of the two sections. These novel SSRs will be useful for further research on germplasm evaluation, comparative genomics, phylogenetic relationships and molecular breeding in the genus Zantedeschia.