【摘要】：玉米籽粒的物質(zhì)積累過程是影響玉米產(chǎn)量與品質(zhì)的重要因素之一。隨著測序技術(shù)與生物信息學(xué)的發(fā)展,以高通量測序數(shù)據(jù)為基礎(chǔ),在全基因組范圍內(nèi)發(fā)掘玉米籽粒物質(zhì)積累相關(guān)的功能基因,不僅對作物育種及改良具有重要的意義,同時(shí)也為作物功能基因組學(xué)研究提供了新的策略與方法。本研究通過構(gòu)建玉米轉(zhuǎn)錄組測序數(shù)據(jù)分析平臺,對368個(gè)玉米自交系籽粒的轉(zhuǎn)錄組測序數(shù)據(jù)進(jìn)行了分析,以玉米籽粒物質(zhì)積累過程為研究重點(diǎn),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(zhuǎn)錄組測序數(shù)據(jù)的從頭組裝,構(gòu)建了玉米的泛轉(zhuǎn)錄組,研究了其中與籽粒物質(zhì)積累過程相關(guān)的遺傳組分。主要研究結(jié)果如下:1.利用目前主流的轉(zhuǎn)錄組分析軟件,構(gòu)建了玉米轉(zhuǎn)錄組測序數(shù)據(jù)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(gòu)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(dá)分析三個(gè)子平臺,能夠滿足群體轉(zhuǎn)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(shù)據(jù)進(jìn)行從頭組裝,在玉米新基因挖掘及泛轉(zhuǎn)錄組的構(gòu)建上具有重要的應(yīng)用價(jià)值。此外,利用統(tǒng)計(jì)學(xué)及生物學(xué)的方法對平臺分析結(jié)果進(jìn)行驗(yàn)證,均顯示其具有較高的準(zhǔn)確性與可信度。2.根據(jù)群體結(jié)構(gòu)及適應(yīng)性將368份玉米自交系分為溫帶(190份)和熱帶(178份)兩個(gè)玉米類群,結(jié)合轉(zhuǎn)錄組分析所獲的558,579個(gè)高質(zhì)量SNP標(biāo)記,利用XP-EHH選擇信號檢測方法對群體間受選擇的情況進(jìn)行了研究。在溫帶和熱帶玉米中分別鑒定了 730個(gè)和421個(gè)選擇區(qū)域,其中溫帶玉米受到了更強(qiáng)的選擇作用。對選擇區(qū)域中受選擇的基因進(jìn)行功能注釋,發(fā)現(xiàn)調(diào)控相關(guān)基因在選擇區(qū)域內(nèi)顯著富集,并且在群體間存在表達(dá)差異(P-value0.05)。進(jìn)一步對其中與玉米籽粒物質(zhì)積累相關(guān)的基因進(jìn)行分析,發(fā)現(xiàn)蔗糖降解途徑兩個(gè)關(guān)鍵酶的編碼基因sus1和incw1在溫帶玉米中受到了強(qiáng)烈的選擇(top 0.5%),并且在溫帶玉米中的表達(dá)水平極顯著地高于熱帶玉米(P-value0.01)。同時(shí),在該途徑的其它基因及玉米油分合成途徑的相關(guān)基因中也檢測到了類似的選擇信號,表明玉米籽粒物質(zhì)積累相關(guān)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(dá)的存在/缺失變異(ePAV)模式進(jìn)行轉(zhuǎn)化,并設(shè)計(jì)了"先組裝后比對"的策略將玉米轉(zhuǎn)錄組測序數(shù)據(jù)進(jìn)行從頭組裝,分別獲得了 13,382個(gè)ePAV基因和2,355條高質(zhì)量的新序列(novel sequences),并以此構(gòu)建了玉米的泛轉(zhuǎn)錄組。序列數(shù)據(jù)分析與重測序?qū)嶒?yàn)驗(yàn)證表明,ePAV表達(dá)模式更能夠反映玉米基因在不同自交系中的表達(dá)差異,而"先組裝后比對"的策略也更適用于玉米轉(zhuǎn)錄組的從頭組裝。與嚴(yán)建兵教授實(shí)驗(yàn)室合作,利用玉米泛轉(zhuǎn)錄組中的遺傳變異,與玉米15個(gè)農(nóng)藝性狀表型和526個(gè)籽粒代謝相關(guān)性狀進(jìn)行全基因組關(guān)聯(lián)分析,發(fā)現(xiàn)類黃酮代謝途徑中相關(guān)基因的ePAV表達(dá)模式與該途徑中代謝物的含量顯著關(guān)聯(lián)(P-value7.49E-5),表明ePAV基因及ePAV模式對玉米籽粒物質(zhì)積累過程中代謝物合成調(diào)控過程具有重要的影響。本研究旨在利用轉(zhuǎn)錄組測序數(shù)據(jù),在全基因組的水平上發(fā)掘?qū)τ衩鬃蚜Ｎ镔|(zhì)積累過程具有重要影響的功能基因,并嘗試解析其遺傳機(jī)理和生物學(xué)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(xué)位授予單位】：中國農(nóng)業(yè)大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2017
【分類號】：S513

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