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標題: | 利用RNA-seq探討秈稻F1子代之對偶基因不平衡現象 Allelic imbalance in the F1 hybrid of Oryza sativa, ssp. indica revealed by RNA-seq data |
作者: | Yu-Shen Tsai 蔡鈺深 |
指導教授: | 劉力瑜 |
關鍵字: | 次世代定序技術,對偶基因不平衡,單一核?酸多型性,虛擬參考序列, RNA-Seq,Allelic imbalance,Single nucleotide polymorphism,Pseudo Reference,NGS, |
出版年 : | 2014 |
學位: | 碩士 |
摘要: | 水稻品種間的外表型受到了基因表現量的影響,不同的基因表現會讓一個品種能擁有獨特的性狀或特性,藉由研究雜交種中的對偶基因表現量是否不平衡,能提供訊息讓我們了解遺傳變異的機制。本研究藉由次世代定序技術,將分別種植於正常環境與乾旱環境下的兩個秈稻品種APO與IR64及其雜交後代F1定序,接著進行表現量分析,以了解雜交水稻對偶基因表現量不平衡的現象。APO、IR64為秈稻品種,目前尚未完成完整的基因體序列,目前僅有稉稻cDNA可作為參考序列。但由於秈稻與稉稻之間仍然有些許變異,會影響分析的結果,所以本研究利用定序資料所得之核苷酸多型性 (SNPs) 以及序列插入與缺失位置來修改稉稻參考序列,產生虛擬參考序列,作為後續分析的依據。接著,本研究利用定序資料找出APO、IR64之間有48175個SNPs位點,藉由SNPs資訊判別F1定序片段的來源親,進而檢定F1中的基因是否有對偶基因表現不平衡的現象。研究結果發現,虛擬參考序列確實能增加秈稻定序片段的比對率,而使用本研究提出的方法辨別子代的定序片段確實能減少計算偏差所造成的影響。利用卡方檢定以及二項式檢定進行對偶基因不平衡分析,顯示APO與IR64兩秈稻品種在正常環境下有750個基因有對偶基因不平衡現象,而在乾旱環境下有882個基因有對偶基因不平衡現象,這些具有對偶基因不平衡現象的基因大多與光合作用、抗逆境、膜狀胞器等有關。 Allelic imbalance refers to the preferential expression of one of the two alleles in a diploid genome, and it is suggested to play important roles in determining phenotypic diversity. This study aims to analyze allelic imbalance in hybrid rice using next generation sequencing (NGS) results of transcriptome of two indica rice varieties, APO and IR64, and their F1 hybrid under control and drought conditions. To improve the mapping rate of the sequenced reads, we first modified the japonica rice reference (MSU7 cDNA) to a pseudo reference that better represent the studied indica rice popultaion. This approach relied on detecting single nucleotide polymorphisms (SNPs) and insertion-deletion sites between japonica and two indica rice species of interest. After mapping sequencing data of APO and IR64, respectively, to the pseudo reference, 48,175 SNPs were identified between two parents, which were further used to distinguish the origins of the F1 reads. The chi-square test and binomial test were adopted to compare the read counts of F1 from either parent to identify allelic imbalanced genes. As the results, we found 750 genes imbalanced in control, and 882 genes in drought condition. The gene annotation showed that function of allelic imbalanced genes were related to photosynthesis, response to stress, and membrane-bounded organelle. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/57887 |
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顯示於系所單位: | 農藝學系 |
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