Phylogeny, Polymorphism, and SSR Markers of Phalaenopsis

Molecular identification is an essential technology that establishes microsatellite loci in order to improve the commercial breeding of the moth orchid (Phalaenopsis species). In this chapter, phylogenetic reconstruction revealed the relationship of Phalaenopsis species. Microsatellite primer sets, including genomic-SSR and EST-SSR, were generated from Phalaenopsis aphrodite subsp. formosana to further investigate the transferability across Phalaenopsis species. Ten and twenty-eight polymorphic EST-SSRs and genomic-SSRs markers were collected by magnetic bead enrichment method and next-generation sequencing technology, which revealed 21 species of the genus Phalaenopsis with high transferability, particularly in the subgenus Phalaenopsis. The result indicated that these microsatellite markers are distinct to subgenus Phalaenopsis. Therefore, the genetic relationships among species of subgenus Phalaenopsis could be differentiated and constructed on the assignment test. These molecular markers can be used to assess the paternity of Phalaenopsis and investigate the hybridization among Phalaenopsis species.