過去本實驗室經由比較台灣原生種姬蝴蝶蘭(Phalaenopsis equestris)和白花蝴蝶蘭(P. aphrodite subsp. formosana)的葉綠體DNA，發現兩種蝴蝶蘭在演化過程產生變異的熱點區域，特別是在基因間隙和內插子區域中。本研究針對高變異的6個基因間隙和1個基因內插子區域進行定序，以分析19種蝴蝶蘭原生種間序列變異的情形，並探討親緣演化關係。為了開發蝴蝶蘭粒線體DNA標誌，首先鑑定白花蝴蝶蘭粒線體DNA含有的微衛星序列(microsatellite)，針對SSR共設計13組引子對，利用PCR產物長度的差異用以區別不同蝴蝶蘭原生種。多型性程度分析顯示，13組粒線體SSR標誌的PIC值介於0.12到0.85。結合5組SSR標誌可以成功鑑定18種蝴蝶蘭原生種。而利用串聯粒線體DNA或葉綠體DNA分子數據所建構的親緣演化樹有所不同。本研究也將胞器DNA標誌應用於鑑別11個姬蝴蝶蘭品系，結合3組葉綠體標誌可以將其全部區分出來。此外，藉由蝴蝶蘭粒線體DNA標誌得以確認蝴蝶蘭粒線體是母系遺傳，可應用於追朔蝴蝶蘭雜交種的原始母本來源。綜合以上結果，本研究開發的胞器DNA標誌可應用於品種鑑定、親本分析、親緣演化研究。

Previously, by comparative cpDNA analysis of two moth orchids, P. aphrodite and P. equestris, many evolutionary hot-spot regions were identified, particularly in intergenic spacer and intron regions. In this study, the polymorphic sites located in six intergenic spacers and one intron among 19 moth orchids were further determined and phylogenetically analyzed. To explore the mtDNA as markers, microsatellite located in the mtDNA of P. aphrodite were identified. In total, the primer pairs for 13 mtDNA markers were designed and subsequently been used to evaluate their amplification capability and transferability among moth orchids. The polymorphism information content (PIC) values of 13 mtDNA markers varied from 0.12 to 0.85 in native moth orchids. Based on the combination of 5 mtDNA markers, it could successfully identify 18 out of 19 moth orchids. Phylogenetic tree constructed on the basis of concatenated mtDNA or cpDNA showed distinct relationship among these moth orchids. Furthermore, cpDNA and mtDNA markers were also applied to distinguish the subspecies of P. equestris. The combination of 3 cpDNA markers could completely identify 11 subspecies of P. equestris. Furthermore, maternally inherited mode of mitochondrial DNA was confirmed based on mtDNA markers technology. In summary, we have developed a set of organellar DNA markers that can be used for the identification and phylogenetic studies in Phalaenopsis orchids.

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