RNA-Seq SSRs of Moth Orchid and Screeningfor Molecular Markers across GenusPhalaenopsis (Orchidaceae)

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Title:	RNA-Seq SSRs of Moth Orchid and Screeningfor Molecular Markers across GenusPhalaenopsis (Orchidaceae)
Authors:	Tsai, Chi-Chu;Shih, Huei-Chuan;Wang4☯, Hao-Ven;Lin, Yu-Shium;Chang, Chia-Hung;Chiang, Yu-Chung;Chou, Chang-Hung
Date:	2015-11-12
Issue Date:	2015-11-12T07:23:57Z (UTC)
Abstract:	Background The moth orchid (Phalaenopsis species) is an ornamental crop that is highly commercialized worldwide. Over 30,000 cultivars of moth orchids have been registered at the Royal Horticultural Society (RHS). These cultivars were obtained by artificial pollination of interspecific hybridization. Therefore, the identification of different cultivars is highly important in the worldwide market. Methods/Results We used Illumina sequencing technology to analyze an important species for breeding, Phalaenopsis aphrodite subsp. formosana and develop the expressed sequence tag (EST)- simple sequence repeat (SSR) markers. After de novo assembly, the obtained sequence covered 29.1 Mb, approximately 2.2% of the P. aphrodite subsp. formosana genome (1,300 Mb), and a total of 1,439 EST-SSR loci were detected. SSR occurs in the exon region, including the 5’ untranslated region (UTR), coding region (CDS), and 3’UTR, on average every 20.22 kb. The di- and tri-nucleotide motifs (51.49% and 35.23%, respectively) were the two most frequent motifs in the P. aphrodite subsp. formosana. To validate the developed EST-SSR loci and to evaluate the transferability to the genus Phalaenopsis, thirty trinucleotide motifs of the EST-SSR loci were randomly selected to design EST-SSR primers and to evaluate the polymorphism and transferability across 22 native Phalaenopsis species that are usually used as parents for moth orchid breeding. Of the 30 EST-SSR loci, ten polymorphic and transferable SSR loci across the 22 native taxa can be obtained. The validated EST-SSR markers were further proven to discriminate 12 closely related Phalaenopsis cultivars. The results show that it is not difficult to obtain universal SSR markers by transcriptome deep sequencing in Phalaenopsis species.
Appears in Collections:	[Department of Nursing] Papers

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