轉錄組測序數據分析在玉米籽粒功能基因挖掘中的應用
發(fā)布時間：2018-08-05 15:57
【摘要】：玉米籽粒的物質積累過程是影響玉米產量與品質的重要因素之一。隨著測序技術與生物信息學的發(fā)展,以高通量測序數據為基礎,在全基因組范圍內發(fā)掘玉米籽粒物質積累相關的功能基因,不僅對作物育種及改良具有重要的意義,同時也為作物功能基因組學研究提供了新的策略與方法。本研究通過構建玉米轉錄組測序數據分析平臺,對368個玉米自交系籽粒的轉錄組測序數據進行了分析,以玉米籽粒物質積累過程為研究重點,從中找到了在玉米改良過程中受選擇作用的功能基因。此外,本研究也通過轉錄組測序數據的從頭組裝,構建了玉米的泛轉錄組,研究了其中與籽粒物質積累過程相關的遺傳組分。主要研究結果如下:1.利用目前主流的轉錄組分析軟件,構建了玉米轉錄組測序數據分析平臺。該平臺主要由基于參考基因組的比對分析平臺和無參考基因組的Denovo組裝平臺構成。其中,基于參考基因組的平臺中又包含了序列比對、SNP Calling和表達分析三個子平臺,能夠滿足群體轉錄組分析的多種需求。無參考基因組的Denovo組裝平臺則可以對測序數據進行從頭組裝,在玉米新基因挖掘及泛轉錄組的構建上具有重要的應用價值。此外,利用統(tǒng)計學及生物學的方法對平臺分析結果進行驗證,均顯示其具有較高的準確性與可信度。2.根據群體結構及適應性將368份玉米自交系分為溫帶(190份)和熱帶(178份)兩個玉米類群,結合轉錄組分析所獲的558,579個高質量SNP標記,利用XP-EHH選擇信號檢測方法對群體間受選擇的情況進行了研究。在溫帶和熱帶玉米中分別鑒定了 730個和421個選擇區(qū)域,其中溫帶玉米受到了更強的選擇作用。對選擇區(qū)域中受選擇的基因進行功能注釋,發(fā)現調控相關基因在選擇區(qū)域內顯著富集,并且在群體間存在表達差異(P-value0.05)。進一步對其中與玉米籽粒物質積累相關的基因進行分析,發(fā)現蔗糖降解途徑兩個關鍵酶的編碼基因sus1和incw1在溫帶玉米中受到了強烈的選擇(top 0.5%),并且在溫帶玉米中的表達水平極顯著地高于熱帶玉米(P-value0.01)。同時,在該途徑的其它基因及玉米油分合成途徑的相關基因中也檢測到了類似的選擇信號,表明玉米籽粒物質積累相關基因在玉米育種改良過程中受到了明顯的人工選擇作用。3.通過對玉米基因表達的存在/缺失變異(ePAV)模式進行轉化,并設計了"先組裝后比對"的策略將玉米轉錄組測序數據進行從頭組裝,分別獲得了 13,382個ePAV基因和2,355條高質量的新序列(novel sequences),并以此構建了玉米的泛轉錄組。序列數據分析與重測序實驗驗證表明,ePAV表達模式更能夠反映玉米基因在不同自交系中的表達差異,而"先組裝后比對"的策略也更適用于玉米轉錄組的從頭組裝。與嚴建兵教授實驗室合作,利用玉米泛轉錄組中的遺傳變異,與玉米15個農藝性狀表型和526個籽粒代謝相關性狀進行全基因組關聯分析,發(fā)現類黃酮代謝途徑中相關基因的ePAV表達模式與該途徑中代謝物的含量顯著關聯(P-value7.49E-5),表明ePAV基因及ePAV模式對玉米籽粒物質積累過程中代謝物合成調控過程具有重要的影響。本研究旨在利用轉錄組測序數據,在全基因組的水平上發(fā)掘對玉米籽粒物質積累過程具有重要影響的功能基因,并嘗試解析其遺傳機理和生物學功能,從而為玉米育種改良工作提供重要的遺傳資源。
[Abstract]:The accumulation process of corn grain is one of the important factors that affect the yield and quality of maize. With the development of sequencing and bioinformatics, it is of great significance not only to crop breeding and improvement, but also to explore the functional genes related to the accumulation of corn grain in the whole genome based on the high flux sequencing data. A new strategy and method was provided for the research of crop functional genomics. This study analyzed the sequence data of 368 maize inbred lines by constructing the sequencing data analysis platform of maize transcriptional group. In addition, this study also constructed the pan transcriptional group of maize and studied the genetic components related to the accumulation process of grain. The main results were as follows: 1. using the current mainstream transcriptional analysis software, the analysis platform for the sequencing data of the maize transcriptome was constructed. The platform is mainly composed of the reference genome based comparative analysis platform and the Denovo assembly platform without reference genome. Among them, the platform based on the reference genome contains sequence alignment, SNP Calling and expression analysis three sub platforms, which can meet the various needs of the group transcriptome analysis. The Denovo assembly without reference genome is flat. In addition, the platform analysis results are verified by statistical and biological methods. The results show that the platform has a high accuracy and credibility of.2. based on the population structure and adaptability of 368 copies of corn. The inbred lines were divided into temperate (190) and 178 tropical (178) maize groups, combined with 558579 high quality SNP markers obtained by the transcriptional analysis, and studied the selection among populations using XP-EHH selection signal detection methods. 730 and 421 selected regions were identified in temperate and tropical maize, of which temperate maize was affected. The selection of selected genes in the selected area was annotated, and it was found that the regulated genes were enriched in the selected regions, and there was a difference of expression among the populations (P-value0.05). Two key factors related to the accumulation of corn kernel matter accumulation were analyzed, and the two key points of the sucrose degradation pathway were found. The encoding genes sus1 and incw1 were strongly selected in temperate maize (top 0.5%), and the expression level in temperate maize was significantly higher than that of Tropical Maize (P-value0.01). At the same time, a similar selection signal was detected in other genes in this pathway and in the related genes of corn oil synthesis pathway, indicating corn seed. In the process of maize breeding improvement, grain material accumulation related genes were obviously selected by artificial selection,.3. was transformed through the existence / ePAV model of maize gene expression, and the strategy of "first assembly and comparison" was designed to assemble the sequence data of maize transcriptional group into 13382 ePAV genes and 2 respectively. 355 high quality new sequences (novel sequences) were used to construct the pan transcriptional group of maize. Sequence data analysis and resequencing experiments showed that ePAV expression pattern could reflect the difference of maize gene expression in different inbred lines, and the strategy of "first assembly and comparison" was also more suitable for the head assembly of Maize transcriptome. By using the genetic variation in the maize pan transcriptional group, the whole genome association analysis was carried out with 15 agronomic traits and 526 grain metabolism in maize. It was found that the ePAV expression pattern of the related genes in the flavonoid metabolic pathway was significantly associated with the content of the metabolites in this pathway (P-value7.49E-5), indicating that ePA V gene and ePAV model have an important influence on the regulation of metabolite synthesis during the accumulation of corn kernel. This study aims to explore the functional genes which have important effects on the accumulation process of corn grain by using the sequence of transcriptional sequences, and try to analyze the genetic mechanism and biological function of maize. So as to provide important genetic resources for maize breeding and improvement.
【學位授予單位】：中國農業(yè)大學
【學位級別】：博士
【學位授予年份】：2017
【分類號】：S513
本文編號：2166273
[Abstract]:The accumulation process of corn grain is one of the important factors that affect the yield and quality of maize. With the development of sequencing and bioinformatics, it is of great significance not only to crop breeding and improvement, but also to explore the functional genes related to the accumulation of corn grain in the whole genome based on the high flux sequencing data. A new strategy and method was provided for the research of crop functional genomics. This study analyzed the sequence data of 368 maize inbred lines by constructing the sequencing data analysis platform of maize transcriptional group. In addition, this study also constructed the pan transcriptional group of maize and studied the genetic components related to the accumulation process of grain. The main results were as follows: 1. using the current mainstream transcriptional analysis software, the analysis platform for the sequencing data of the maize transcriptome was constructed. The platform is mainly composed of the reference genome based comparative analysis platform and the Denovo assembly platform without reference genome. Among them, the platform based on the reference genome contains sequence alignment, SNP Calling and expression analysis three sub platforms, which can meet the various needs of the group transcriptome analysis. The Denovo assembly without reference genome is flat. In addition, the platform analysis results are verified by statistical and biological methods. The results show that the platform has a high accuracy and credibility of.2. based on the population structure and adaptability of 368 copies of corn. The inbred lines were divided into temperate (190) and 178 tropical (178) maize groups, combined with 558579 high quality SNP markers obtained by the transcriptional analysis, and studied the selection among populations using XP-EHH selection signal detection methods. 730 and 421 selected regions were identified in temperate and tropical maize, of which temperate maize was affected. The selection of selected genes in the selected area was annotated, and it was found that the regulated genes were enriched in the selected regions, and there was a difference of expression among the populations (P-value0.05). Two key factors related to the accumulation of corn kernel matter accumulation were analyzed, and the two key points of the sucrose degradation pathway were found. The encoding genes sus1 and incw1 were strongly selected in temperate maize (top 0.5%), and the expression level in temperate maize was significantly higher than that of Tropical Maize (P-value0.01). At the same time, a similar selection signal was detected in other genes in this pathway and in the related genes of corn oil synthesis pathway, indicating corn seed. In the process of maize breeding improvement, grain material accumulation related genes were obviously selected by artificial selection,.3. was transformed through the existence / ePAV model of maize gene expression, and the strategy of "first assembly and comparison" was designed to assemble the sequence data of maize transcriptional group into 13382 ePAV genes and 2 respectively. 355 high quality new sequences (novel sequences) were used to construct the pan transcriptional group of maize. Sequence data analysis and resequencing experiments showed that ePAV expression pattern could reflect the difference of maize gene expression in different inbred lines, and the strategy of "first assembly and comparison" was also more suitable for the head assembly of Maize transcriptome. By using the genetic variation in the maize pan transcriptional group, the whole genome association analysis was carried out with 15 agronomic traits and 526 grain metabolism in maize. It was found that the ePAV expression pattern of the related genes in the flavonoid metabolic pathway was significantly associated with the content of the metabolites in this pathway (P-value7.49E-5), indicating that ePA V gene and ePAV model have an important influence on the regulation of metabolite synthesis during the accumulation of corn kernel. This study aims to explore the functional genes which have important effects on the accumulation process of corn grain by using the sequence of transcriptional sequences, and try to analyze the genetic mechanism and biological function of maize. So as to provide important genetic resources for maize breeding and improvement.
【學位授予單位】：中國農業(yè)大學
【學位級別】：博士
【學位授予年份】：2017
【分類號】：S513
【參考文獻】
相關期刊論文 前10條
1 許波;張偉強;馮曉曦;王成業(yè);張海申;許海濤;王友華;張今瀚;;轉錄組測序技術在玉米中的應用研究進展[J];玉米科學;2014年01期
2 仇煥廣;張世煌;楊軍;井月;;中國玉米產業(yè)的發(fā)展趨勢、面臨的挑戰(zhàn)與政策建議[J];中國農業(yè)科技導報;2013年01期
3 徐雷;賈飛飛;王利琳;;擬南芥開花誘導途徑分子機制研究進展[J];西北植物學報;2011年05期
4 解增言;林俊華;譚軍;舒坤賢;;DNA測序技術的發(fā)展歷史與最新進展[J];生物技術通報;2010年08期
5 陳福祿;傅永福;林辰濤;;CO/FT調節(jié)元件與植物開花時間調節(jié)研究進展[J];中國農業(yè)科技導報;2009年02期
6 吳東東;張亞平;;人類群體中的達爾文正選擇[J];科學通報;2008年07期
7 鄧立彬;湯曉麗;康健;王青蕓;曾長青;;利用群體基因組學策略掃描人群特異的自然選擇信號[J];科學通報;2007年18期
8 唐祈林;榮廷昭;;玉米的起源與演化[J];玉米科學;2007年04期
9 王曉燕,高榮岐,董樹亭;玉米胚乳發(fā)育研究進展[J];中國農學通報;2005年06期
10 李明順,張世煌,李新海,田清震,白麗;優(yōu)質蛋白玉米(QPM)選育方法和發(fā)展策略[J];玉米科學;2004年03期
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