臺灣博碩士論文加值系統

本試驗旨在應用cDNA微陣列晶片尋找菜鴨腦下垂體中可能參與蛋形成的差異表現基因，並藉由探討基因多態性與菜鴨產蛋性能之關聯性來開發菜鴨分子選種標記。試驗一：抽取菜鴨產蛋後0、4、8、12、16、20及22小時腦下垂體之total RNA，經反轉錄標定後，再與自製腦下垂體cDNA微陣列晶片（共8736點）進行雜交反應，並放大雜交的螢光訊號。晶片經螢光掃描、擷取影像及數字化後，利用分析軟體進行正規化、對數轉換及統計分析。試驗共發現167個差異表現之cDNA株系（fold change ≥ 2.0；P < 0.05），萃取其質體DNA進行定序後即可得表現序列標誌（expressed sequence tag, EST）序列。經去除載體覆蓋、品質不良或過短序列後，將相似EST序列進行接合，最後共得16個contig與71個singleton。經基因身分比對後，去除重複及粒線體基因序列，共發現37個已知身分基因，這些基因可能參與菜鴨蛋形成的過程與調解卵巢濾泡生長。透過基因功能分類體系（Gene Ontology, GO）資料庫，對各基因可能扮演生理角色之功能性做分類預測分析。分析結果顯示，上述基因可被歸納參與生物過程（biological process）、分子功能（molecular function）及細胞組成（cellular component）三大類，百分率分別為35.1%、54.0%及37.8%。生物過程分類顯示差異表現基因主要以參與代謝與轉譯過程；分子功能分類顯示差異表現基因功能主要涉及分子結合（molecular binding）與催化活性；在細胞組成分類顯示差異表現基因的表現位置主要以細胞內為主。試驗二：依據試驗所得之EST序列或GeneBank基因庫上基因全長序列設計特異引子對以擴增標的基因PCR產物，利用單股構形多態性（single strand conformation polymorphism, SSCP）技術、核酸定序（DNA sequencing）及微序列法（minisequencing）完成基因多態性之分析，並搭配SAS統計方法探討基因多態性與菜鴨產蛋性能的關聯性。結果顯示，在生長激素（growth hormone, GH）、泌乳素（prolactin, PRL）、細胞骨架蛋白（destrin, DSTN）、富含脯胺酸核受器輔活化因子1（proline-rich nuclear receptor coactivator 1, PNRC1）及細胞週期素依賴激酶2-相關蛋白1（cyclin-dependent kinase 2-associated protein 1, CDK2AP1）中，共發現32個單一核苷酸多態性（single nucleotide polymorphism, SNP），其中1個SNP座落在5’-非轉譯區、3個SNP座落在外顯子、20個SNP座落在介入子及8個SNP座落在
3’-非轉譯區。此外，在GH基因之C3169T、C3700T及C5058G所組成的雙套型中，以H1H1雙套型者之受精相關性能的表現顯著較佳（P < 0.05）。在PRL基因之T213C、T295C、G309T、C381A、G3941T及A3975C所組成的雙套型中，以H1H1雙套型較有利於受精相關性能的表現，另以H1H2雙套型較有利於40週齡蛋重的表現（P < 0.05）。在DSTN基因之T92C、C93A、G100T及T106C所組成的雙套型中，以H6H7雙套型者之40週齡蛋重的表現顯著較佳，另以H6H6雙套型者之受精相關性能的表現顯著較佳（P < 0.05）；在PNRC1基因之G98T中，不同基因型的性狀表現會受到品系影響，又在品系獨立分析下，在對照品系中以GG基因型者之初產蛋重顯著較重；在選拔品系中以GG基因型者之孵化率顯著較低（P < 0.05）。在CDK2AP1基因之93_94insA中，以－/A基因型者之最長持續受精天數顯著較－/－基因型者為長（P < 0.05）。本試驗所得結果可供將SNP標記應用在輔助菜鴨選種之參考。

The purpose of this study was to identify a set of differentially expressed genes with potential involvement in duck egg formation process using cDNA microarray analysis; and to develop the molecular DNA markers by investigating the associations of gene polymorphisms with duck egg production. In experiment 1, the pituitary target RNA were obtained at 0, 4, 8, 12, 16, 20 and 22 h after laying and labeled for hybridization with in-house cDNA microarray (8736 spots). The hybridization signals were amplified by Tyramide signal amplification technology and scanned by fluorescent scanner at 532 nm for image acquisition and quantification. Data normalization, log transformation and statistics were carried out by Avadis software. One hundred sixty-seven differentially expressed cDNAs were observed in fold change ≥ 2.0 at 4, 8, 12, 16, 20, 22 h relative to 0 h (P < 0.05). Raw sequences of the cDNAs were processed through sequence analysis including trimming vector sequence, and removing low quality and short sequence (< 100 bp), thus resulted in 136 expressed sequences tag (EST) sequences. There were 16 contigs assembled along with 71 singletons separated after cluster analysis. The results of cluster analysis were used for sequence indentify and functional annotation. Removing repeat and mitochondrial DNA sequences, 37 known genes with potential involvement in ovarian follicles development and egg formation were acquired based on BLASTN (GeneBlank). These known gene sequences were annotated in Gene Ontology (GO); they included biological process (35.1%), molecular function (54.0%), and cellular component (37.8%). For these known genes that mapped to biological processes, most of them with their functional annotations were related to metabolic processes and translation. For molecular function, most of the known genes were related to macromolecule binding and catalytic activity, and for these cellular component genes were expressed in intracellular region. In experiment 2, the specific-primers were designed for target gene amplification according to the EST and complete sequences obtained from our laboratory and GeneBank database, respectively. Identification of the expressed gene polymorphisms was performed by single strand conformation polymorphism (SSCP) technology, DNA sequencing, and SNaPshot minisequencing. Furthermore, the association between the gene polymorphisms and duck traits was analyzed. Total of 32 single nucleotide polymorphisms (SNPs) within growth hormone (GH), prolactin (PRL), destrin (DSTN), proline-rich nuclear receptor coactivator 1 (PNRC1), cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) genes were found, of which 1, 3, 20 and 8 SNPs were located in 5’-untranslated region (UTR), exons, introns and 3’-UTR, respectively. The SNP-trait association analysis showed that the GH gene diplotypes constructed on C3169T, C3700T, and C5058G were associated with maximum duration of fertility (MDF) (P < 0.05), and the H1H1 diplotype was advantage for duck fertility. In PRL gene, the diplotypes constructed on T213C, T295C, G309T, C381A, G3941T, and A3975C were associated with egg weight at 40 wk of age (EW40) and MDF (P < 0.05). Within all diplotypes, the ducks with H1H1 diplotype had the highest MDF, and the H1H2 diplotype had the highest EW40. In DSTN gene, the H6H7 diplotype was dominant for EW40, and the H3H3, H3H8, and H6H6 diplotypes were dominant for MDF within all diplotypes constructed on T92C, C93A, G100T, and T106C. In PNRC1 gene, the G98T genotype effects were line-specific that the ducks with GG genotype had higher egg weight at first egg than ducks with GT genotype in control line, whereas the ducks with GG had lower hatchability rate than ducks with GT genotype in selected line (P < 0.05). Moreover, the ducks with －/A genotype had higher MDF than ducks with －/－ genotype in CDK2AP1 gene (P < 0.05). The results showed that these SNP markers will be helpful for marker-assisted selection in the breeding program of Tsaiya ducks.

中文摘要 ------------------------------------------------------------------------------------- i
英文摘要 ------------------------------------------------------------------------------------- iii
壹、文獻探討 ------------------------------------------------------------------------------- 1
一、褐色菜鴨 ------------------------------------------------------------------------- 1
二、腦下垂體 ------------------------------------------------------------------------- 2
三、生物晶片技術 ------------------------------------------------------------------- 4
四、單一核苷酸多態性 ------------------------------------------------------------- 15
貳、試驗研究 -------------------------------------------------------------------------------- 19
試驗一、應用微陣列晶片技術尋找菜鴨腦下垂體之差異表現基因 -------- 19
一、前言 -------------------------------------------------------------------------------- 19
二、材料與方法 ---------------------------------------------------------------------- 20
（一）試驗動物 ------------------------------------------------------------------- 20
（二）cDNA基因庫之建立 ---------------------------------------------------- 20
（三）cDNA 微陣列晶片之產製 ---------------------------------------------- 25
（四）cDNA微陣列晶片雜交反應 ------------------------------------------- 27
（五）晶片影像擷取與資料分析 ---------------------------------------------- 29
（六）序列分析與基因身分註解 ---------------------------------------------- 29
三、結果與討論 ----------------------------------------------------------------------- 31
（一）產蛋菜鴨腦下垂體cDNA基因庫 ------------------------------------- 31
（二）cDNA微陣列晶片分析 ------------------------------------------------- 31
（三）差異表現基因之身分確認 ---------------------------------------------- 37
試驗二、探討腦下垂體差異表現基因多態性與菜鴨產蛋性能之關聯性 -- 49
一、前言 -------------------------------------------------------------------------------- 49
二、材料與方法 ----------------------------------------------------------------------- 50
（一）試驗動物 -------------------------------------------------------------------- 50
（二）性狀紀錄 -------------------------------------------------------------------- 50
（三）血液基因組DNA之萃取與定量---------------------------------------- 52
（四）標的基因之PCR擴增與電泳確認 ------------------------------------- 52
（五）單股構形多態性分析 ----------------------------------------------------- 55
（六）序列分析 -------------------------------------------------------------------- 57
（七）微序列分析 ----------------------------------------------------------------- 58
（八）單套型分析 ----------------------------------------------------------------- 59
（九）統計分析 -------------------------------------------------------------------- 59
三、結果與討論 ----------------------------------------------------------------------- 60
（一）生長激素（growth hormone, GH）基因 --------------------------------- 60
（二）泌乳素（prolactin, PRL）基因 ------------------------------------------ 112
（三）細胞骨架蛋白（destrin, DSTN）基因 ---------------------------------- 143
（四）烯醇酶1（enolase 1, ENO1）基因 -------------------------------------- 160
（五）醯基輔酶A結合區域7（acyl-coenzyme A binding domain containing 7, ACBD7）基因 --------------------------------------------- 160
（六）富含脯胺酸核受器輔活化因子1（proline-rich nuclear receptor coactivator 1, PNRC1）基因 --------------------------------------------- 160
（七）H3組蛋白家族3B（H3 histone, family 3B, H3F3B）基因 -------- 169
（八）胸腺素β4（thymosin β4, Tβ4）基因 ---------------------------------- 169
（九）細胞週期素依賴激酶2-相關蛋白1（cyclin-dependant kinase 2-associated protein 1, CDK2AP1）基因 ----------------------------- 169
（十）乳酸脫氫酶B（lactate dehydrogenase B, LDHB）基因 ------------ 176
參、結論 -------------------------------------------------------------------------------------- 180
肆、參考文獻 ------------------------------------------------------------------------------- 181
伍、附錄 ------------------------------------------------------------------------------------- 215

台灣畜產種原資訊網 http://www.angrin.tlri.gov.tw/。行政院農業委員會畜產試驗所。
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