Comparative analysis of microsatellite, SNP, and InDel markers in four Rhododendron species based on RNA-seq

Rhododendron possesses valuable horticultural and medicinal properties. However, the genetic studies have been hindered due to the lack of genetic markers. Based on RNA-seq, large-scale molecular markers were developed from four Rhododendron species endemic to Dabie Mountains (central China): R. fortunei (5.25 Gb; SSRs, 12,756, one/2.37 kb, 147 types; SNPs, 38,313; InDels, 3,174), R. simsii (5.80 Gb; SSRs, 13,294, one/2.58 kb, 167 types; SNPs, 136,590; InDels, 6,258), R. mariesii (6.53 Gb; SSRs, 15,724, one/2.51 kb, 170 types; SNPs, 44,942; InDels, 4,126), and R. molle (4.35 Gb; SSRs, 10,214, one/2.49 kb, 110 types; SNPs, 77,829; InDels, 3,416). Di-nucleotide repeats were the main type (59.126%–64.314%), and AG/CT repeat (55.18%–61.22%) was the most. In particular, 89 species-specific types had been found. Furthermore, C:G→T:A mutation was the main SNP type (30.475%–34.99%). However, C:G→G:C mutation was the least type in R. fortunei, while T:A→G:C mutation was the least in the other three species. InDels with length of 3 nt was most in R. fortunei, but 1 nt InDels were the main type in the other three species. Twelve microsatellite markers developed from R. simsii reveled high genetic diversity in the four populations, and heterozygote excess was observed. This research would benefit the genetic study, molecular marker-assisted selection, and breeding studies in Rhododendron species.