The mitochondrial dna markers for distinguishing phalaenopsis species and revealing maternal phylogeny

We explored the mitochondrial DNA (mtDNA) markers for species identification via located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana, and then pre-screened for polymorphic markers by comparison with the corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish the 15 endemic moth orchids. The five most variable markers with polymorphic information content (PIC) ≥ 0.7, could be combined to classify 18 of the 19 endemic moth orchids, including the parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids; evolutionary hotspots such as variable SSRs and minisatellite repeats were identified as useful markers. Furthermore, marker technology was applied to reveal the maternal inheritance mode of mtDNA in moth orchids. Moreover, phylogenetic analysis indicates that mtDNA is non-monophyletic below Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.