Abstract
Premise Saxifraga fortunei (Saxifragaceae) includes several infraspecific taxa that are ecologically and morphologically distinct. To investigate the evolutionary history of phenotypic polymorphisms in this species, we developed expressed sequence tag–simple sequence repeat (EST‐SSR) markers for S. fortunei.Methods and ResultsWe developed 26 polymorphic markers based on transcriptome data obtained from Illumina HiSeq 2000. Within three populations of S. fortunei var. incisolobata, the number of alleles ranged from four to 25, and the levels of observed and expected heterozygosity ranged from 0.200 to 0.847 and from 0.209 to 0.930, respectively. Furthermore, all 26 loci showed transferability for S. fortunei var. obtusocuneata and S. fortunei var. suwoensis, and 18 loci were also successfully amplified in S. acerifolia.ConclusionsThese newly developed EST‐SSR markers will prove useful to infer the evolutionary history of S. fortunei var. incisolobata and its relatives in population genetic studies.
Highlights
METHODS AND RESULTSWe developed 26 polymorphic markers based on transcriptome data obtained from Illumina HiSeq 2000
All 26 loci showed transferability for S. fortunei var. obtusocuneata and S. fortunei var. suwoensis, and 18 loci were successfully amplified in S. acerifolia
These newly developed expressed sequence tag–simple sequence repeat (EST‐SSR) markers will prove useful to infer the evolutionary history of S. fortunei var. incisolobata and its relatives in population genetic studies
Summary
Fresh floral buds of S. fortunei var. incisolobata (population F42, Appendix 1) were frozen in liquid nitrogen and total RNA was extracted using the Agilent Plant RNA Isolation Mini Kit A total of 568 regions were obtained, and we selected 96 PCR primer pairs based on the repeat numbers of microsatellite motifs. Incisolobata individuals from each of three populations (F05, F35, and F38; Appendix 1) were used to evaluate the polymorphisms of the target loci. Of the 47 loci that were successfully amplified, 26 showed polymorphisms within each population of S. fortunei var. From three populations (F05, F35, and F38), the number of alleles ranged from four to 25 and the levels of observed and expected heterozygosity ranged from 0.200 to 0.847 and from 0.209 to 0.930, respectively (Table 2). Obtusocuneata, all 26 loci were successfully amplified and polymorphic. Suwoensis, all 26 loci were amplified, of which 22 showed polymorphisms. In S. acerifolia, 18 loci were amplified and 15 showed polymorphisms. Asterisks indicate significant deviation from Hardy–Weinberg equilibrium after Bonferroni correction (*P < 0.05, **P < 0.01, ***P < 0.001)
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