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研究生: 宋雅琇
Ya-Hsiu Sung
論文名稱: 臺灣杜鵑之低變異Non-TIR-NBS-LRR基因亞家族族群遺傳與演化模式
Population genetics and molecular evolution in low genetic variation Non-TIR-NBS-LRR gene subfamily of the Rhododendron formosanum Hemsl.
指導教授: 黃士穎
Hwang, Shih-Ying
學位類別: 碩士
Master
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2010
畢業學年度: 98
語文別: 中文
論文頁數: 72
中文關鍵詞: 抗病基因臺灣杜鵑軍備競賽正向天擇
英文關鍵詞: resistance gene, Rhododendron formosanum Hemsl., arms race, positive selection, Non-TIR-NBS-LRR
論文種類: 學術論文
相關次數: 點閱:131下載:1
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  • 植物抗病基因適合使用於分子族群遺傳的處理,以偵測並了解分子層次的天擇作用。而植物的抗病基因家族中以NBS-LRR (nucleotide-binding site plus Leucine-rich repeats)為最大成員。目前用來解釋植物與病原體交互作用之共演化的模式,以軍備競賽(arms race)以及壕溝戰(trench warfare)為主軸。這兩種模式分別是受到正向天擇(positive selection)和均衡天擇(balancing selection)影響。本研究選殖了先前研究得知為低度遺傳變異之Non-TIR-NBS-LRR基因亞家族之抗病基因成員。我們調查了臺灣杜鵑的10個野生族群在NBS譯碼區的歧異度,發現NBS序列的大多變異發生在族群內,顯示族群之間沒有明顯分化。此外利用CODEML分析位點模式的比較結果,偵測到NBS序列受到天擇的位點,這些區域顯示可能影響NBS與ATP結合能力,進而提高抵抗疾病的訊息傳遞和辨識病原的能力或效率有關。在本研究中支持了軍備競賽的假說,而非只是族群動態變化所致,因此在族群中抗病基因之變異是暫時的,對偶基因是因為selective sweeps而呈現高頻率。

    Plant disease resistance genes are promising candidates for using molecular population genetic approaches to detect and understand natural selection at the molecular level. The nucleotide-binding site plus Leucine-rich repeats (NBS-LRR) gene family is one of the major plant resistance genes. Two evolutionary models, an ‘arms race’ and a ‘trench warfare’, are often invoked to explain co-evolution of host-pathogen interactions. The selective forces act on these two models positive selection and balancing selection, respectively. We cloned NBS sequences which were considered low genetic variation in previous research. Then individuals from each of ten natural populations of plant Rhododendron formosanum Hemsl. were examined for the patterns of nucleotide diversity at NBS-encoding genes. Most variation of NBS sequences were found within populations indicated low population differentiation. Results from site model comparisons of the CODEML analyses detected positively selected codon sites. Regions with positively selected were might be related to ATP binding ability which promoted resistance signal transduction and enhanced pathogen recognition efficiency. This research supports an ‘arms race’ hypothesis, in which variation for resistance will be transient, and that alleles spread to high frequency because of selective sweeps.

    摘要 1 Abstract 2 壹、 前言 3 貳、 文獻探討 5 一、 基因重複與演化的關聯 5 二、 植物的抗病基因 6 三、 抗病基因的作用機制—基因對基因學說 8 四、 抗病基因的演化模式 9 (一) 軍備競賽演化模式 10 (二) 壕溝戰演化模式 11 參、 材料與方法 13 一、 研究材料 13 二、 實驗方法 13 (一) 基因組DNA萃取 13 (二) Non-TIR-NBS gene subfamily類抗病基因之PCR擴增 14 (三) NBS區域的基因cloning 16 三、 分析方法 18 (一) DNA序列比對與排序 18 (二) 族群遺傳分析 19 (三) 重建基因樹 21 (四) 序列之演化分析 22 肆、 結果 25 一、 臺灣杜鵑低變異之類抗病基因結果整理 25 (一) 偽基因數量 25 (二) Consensus sequence 25 二、 族群遺傳分析 26 (一) 遺傳歧異度 26 (二) 中性檢測 29 三、 低變異之類抗病基因的分群與親緣關係分析 30 四、 低變異NBS抗病基因之選汰壓力分析結果 31 (一) 偵測特殊演化支系的正向天擇作用之結果 31 (二) 偵測特殊位點的正向天擇作用之結果 32 (三) 偵測特殊演化支系之特殊位點的正向天擇作用結果 33 伍、 討論 36 一、 臺灣杜鵑NBS序列的族群遺傳 36 二、 選汰壓力對NBS區域之作用 38 三、 受到正向天擇的位點之區域 39 四、 軍備競賽的演化模式 41 陸、 參考文獻 44 柒、 表附錄 51 捌、 圖附錄 65 表目錄 表一、基因對基因學說於單一基因座的交互作用 51 表二、族群採樣點之資料 52 表三、引子序列 53 表四、PCR反應試劑 53 表六、Colony PCR反應試劑 54 表八、族群序列總表 55 表九、族群單套基因型的數量及種類 56 表十、各族群的遺傳歧異度和中性檢測總表 57 表十一、族群核苷酸和胺基酸歧異度的百分比(p-distance) 58 表十二、族群兩兩的差異(Pairwise difference),看其族群分化指數FST 59 表十三、AMOVA分析結果 60 表十四、各群間的遺傳歧異度和中性檢測總表 61 表十五、各群核苷酸和胺基酸歧異度的百分比(p-distance) 61 表十六、CODEML程式中branch model 和site model的分析和LRT比較不同模式的結果 62 表十七、CODEML的branch-site model A與LRT的結果 64 圖目錄 圖一、本研究中臺灣杜鵑之採樣族群地理位置圖。 65 圖二、NBS保守區與引子設計區域。 65 圖三、核苷酸歧異度在各族群的分布。 66 圖四、在各族群中πa/πs的分布。 66 圖五、(A)利用sliding-window 分析Tajima's D和(B)Fu and Li's D。 67 圖六、臺灣杜鵑低變異類抗病基因的核苷酸序列所建構產生的neighbor-joining tree。 68 圖七、臺灣杜鵑低變異類抗病基因的胺基酸序列所建構產生的neighbor-joining tree。 69 圖八、NJ tree標記上ω > 1的演化支系。 70 圖九、將各演化分支的Ka與Ks作圖。 71 圖十、在site model中偵測到受到正向天擇的位點之區域分布。 72 圖十一、在branch-site model中偵測到受到正向天擇的位點之區域分布。 72

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