The Origin of Diversity in Begonia: Genome Dynamism, Population Processes and Phylogenetic Patterns

秋海棠屬(Begonia L.) 是維管束植物中第六大屬有超過1500種原生種遍布於熱帶與亞熱帶地區。台灣共有18種已被記錄的原生秋海棠其中的14種分別屬於3個組(section)秋海棠組(sect. Diplocinium)、扁果組(sect. Platycentrum) 以及無翅組(sect. Sphenanthera)另外4種為天然雜交種。台灣為世界已知秋海棠天然雜交種和物種特有率最多的地區也是秋海棠染色體型態最複雜的亞洲地區此外台灣原生秋海棠具有觀賞和藥用之價值因此物種的鑑別和多樣性研究對原生秋海棠的應用具有重要性。本試驗利用120個來自單子葉作物的SSR分子標誌進行台灣原生秋海棠的遺傳多樣性分析以測試單子葉SSR分子標誌應用於遠緣植物的可行性並且藉此了解台灣原生秋海棠的親緣關係。結果顯示平均60.6%的單子葉SSR分子標誌可以增幅秋海棠各原生種的基因組而單子葉SSR分子標誌的轉移率會受到SSR重複序列的重複類型、長度、以及分布於基因區與否所影響其中以SSR分子標誌在基因組的分布對轉移率影響最為明顯位於基因區的SSR分子標誌增幅秋海棠基因組的能力和多型性程度顯著的高於位於非基因區的SSR分子標誌。進一步分別以基因區分子標誌、非基因區分子標誌、以及綜合以上兩者的增幅結果進行親緣性分析可將台灣原生秋海棠成功地分成三群而蘭嶼秋海棠(B. fenicis)、岩生秋海棠(B. ravenii)、以及裂葉秋海棠(B. palmata)與此三群原生秋海棠的親緣關係較遠。利用分子標誌分類結果與型態分類不一致但與染色體數目相關推測可能是由於台灣原生秋海棠發生種間雜交和平行演化的結果。本篇論文證明單子葉SSR分子標誌可跨物種轉移的可行性未來將可提供序列資訊缺乏之植物作為種源多樣性與親緣關係研究的工具。Begonia is the sixth-largest genus of vascular plants in the world. There are fourteen native species and four endemic natural hybrids in Taiwan in which the highest density of natural hybrids and species containing the most complex chromosome numbers in Asia have been reported. Besides, the native Begonia species in Taiwan show great potential as ornamental and medical plants. However, very few molecular tools have been conducted in Begonia species identification and diversity investigation. This study had employed 120 SSR markers designed from monocot genomes to test transferability on Begonia species in Taiwan. An average of 60.6% transferability and multi-unique loci with 100% polymorphism were obtained. In addition, the degree of transferability was influenced by SSR motif types, length and distribution in coding or noncoding regions especially. Simple and imperfect type showed higher transferability. Meanwhile, transferability values of tetra- and dinucleotide repeats were higher than those of tri-nucleotide. Markers derived from coding region revealed higher polymorphism and transferability than those of noncoding region markers. The dendrograms penetrated by data from coding region markers was more similar to total region markers than those of noncoding region markers in diversity analysis. Three groups of dendrograms based on coding, noncoding and total markers were in accordance with previous studies of phylogeny of Begonia species in Taiwan. It demonstrated that SSR markers derived from monocot genomes can be applied in genetic diversity and phylogenetic analysis of distantly related dicotyledons.ContentsPage摘要 iAbstract iiContents iiiContents of table ivContents of figure v1. Introduction 12. Materials and methods 6Plant materials 6Selection and classification of SSR markers 6Genomic DNA extraction and PCR amplification 7Gel electrophoresis analysis 8Data analysis 8Genetic similarity, diversity analysis and clustering.. 103. Results 11Transferability and polymorphism of monocot SSR markers across native Begonia species in Taiwan 11Correlation between transferability of monocot SSR markers and motif categories 12Comparison of PIC values of SSR markers derived from coding and noncoding regions for Begonia genetic diversity analysis 14Genetic relationships of Taiwan native Begonia species 154. Discussion 18Patterns of transferring genomic SSR markers into distantly-related taxa 18Effects of targets species characters on transferability 21Effects of marker types and distributions on transferability 24Polymorphism and diversity of SSR markers from coding and noncoding regions 27Genetic relationship among Taiwanese Begonia species by monocot SSR markers 295. Conclusion 336. References 347. Appendix 4