Genetic diversity and DNA fingerprinting of Hemerocallis spp. accessions based on EST-SSR markers

Daylilies (Hemerocallis spp.) are widely cultivated as perennial ornamentals worldwide with important edible, medicinal, and ornamental value. In this study, a total of 9139 SSR loci were detected in the daylily cultivar ‘Autumn Red’ through Single Molecular Real Time sequencing, of which 2604 unigenes contained two or more SSR loci. Tri-nucleotide repeats were predominated (5270, 57.66%) among the SSR loci, followed by di-nucleotide repeats (3253, 35.50%). Forty (44.44%) valid EST-SSR markers were identified from 90 synthesized EST-SSR markers by screening six accessions, including one daylily wild species, one daylily variant, two daylily cultivars and two night lily landraces cultivated in the National Hemerocallis Germplasm Resource Bank of China. Genetic diversity analysis of 104 Hemerocallis accessions was conducted using 30 polymorphic EST-SSR markers and a total of 98 alleles was identified with an average of 3.23, ranging from 2 to 8 alleles per loci. The polymorphism information content (PIC) values ranged from 0.01 to 0.70, with an average of 0.25. Five markers (XC007, XC057, XC058, XC068 and XC072) showed high polymorphism (PIC > 0.5). Cluster analysis showed that daylilies and night lilies were clustered into two phylogenetic groups, which was confirmed by population structure analysis and PCoA analysis. Among them, Cluster I was classified into six subclusters (Group A–F) in the NJ dendrogram. Combined with the analysis of morphological characteristics of accessions, it was found that the genetic distance may be affected by the source of accessions, which needs further research. Finally, DNA fingerprints of 104 Hemerocallis accessions were constructed using seven efficient EST-SSR markers. The EST-SSRs developed in this study provided useful tools for the identification of daylily accessions and molecular marker assisted breeding.