【摘要】：棉花是世界上重要的經(jīng)濟(jì)作物,棉花纖維是重要的天然紡織纖維。棉花纖維作為高度分化的單細(xì)胞,是研究細(xì)胞分化、細(xì)胞伸長和細(xì)胞壁合成的良好模型。本研究以組裝和分析海島棉基因組為基礎(chǔ),分析棉花纖維馴化歷程和鑒定控制纖維品質(zhì)性狀形成的重要位點(diǎn),并且分析纖維發(fā)育過程中的長鏈非編碼RNA,進(jìn)一步比較纖維和非纖維組織中可變剪接的差異,最后結(jié)合多組學(xué)數(shù)據(jù),從表觀遺傳角度揭示纖維發(fā)育的動(dòng)態(tài)過程。主要結(jié)果如下:1.海島棉基因組測(cè)序和纖維細(xì)胞壁合成的重要基因家族分析本研究利用全基因組鳥槍法測(cè)序拼接四倍體海島棉基因組。海島棉基因組編碼80876個(gè)基因,含有69%以上的重復(fù)序列。通過分析纖維素合酶(CesA)基因家族在棉花中的進(jìn)化和各個(gè)成員在纖維發(fā)育過程中的表達(dá)模式,我們創(chuàng)造性地提出海島棉纖維發(fā)育過程中CesA基因家族的接力模型,即At、Dt亞基因組合作調(diào)控四倍體棉花纖維發(fā)育。研究重點(diǎn)分析了果膠去甲酯化酶(PME)和果膠去甲酯化酶抑制基因家族(PMEI),發(fā)現(xiàn)PME的進(jìn)化起源與細(xì)胞壁中果膠出現(xiàn)的時(shí)間一致。此外,研究發(fā)現(xiàn)這兩個(gè)基因家族在高等植物中大量擴(kuò)增,并且進(jìn)化速率很快。我們推測(cè)PMEI結(jié)構(gòu)域的起源可能是全基因組復(fù)制之后pro結(jié)構(gòu)域的新功能化。這些結(jié)果促進(jìn)了棉花基因組研究,加深了對(duì)植物細(xì)胞壁進(jìn)化的理解。2.基因組重測(cè)序揭示了大量變異,這些變異是棉花馴化和順式調(diào)控分化的基礎(chǔ)本研究收集了352份陸地棉材料,包括半野生種和馴化種,構(gòu)建了一個(gè)綜合性的基因組變異圖譜。研究鑒定了93個(gè)馴化選擇區(qū)域,覆蓋At亞基因組的74 Mb,Dt亞基因組的104 Mb,同時(shí)通過全基因組關(guān)聯(lián)分析鑒定了19個(gè)與纖維品質(zhì)性狀相關(guān)的候選位點(diǎn)。結(jié)果表明長纖維的馴化與非對(duì)稱的亞基因組選擇相關(guān)。通過系統(tǒng)地分析DNase I酶切超敏感位點(diǎn)和三維基因組圖譜,我們將一些可能存在的功能變異與基因轉(zhuǎn)錄聯(lián)系起來,從而揭示了馴化對(duì)群體順式調(diào)控元件分化的影響。本研究提出了一個(gè)重要作物中基因組的進(jìn)化、調(diào)控和適應(yīng)的新觀點(diǎn),為基于基因組的棉花遺傳改良提供了豐富資源。3.棉花長鏈非編碼RNA的鑒定和在纖維中的功能分析通過整合大量的轉(zhuǎn)錄組數(shù)據(jù),本研究鑒定了30550個(gè)基因間區(qū)的長鏈非編碼RNA(lincRNA)和4718個(gè)反義長鏈非編碼RNA(lncNAT)位點(diǎn)。lncRNA的表達(dá)量比較低,并且大多數(shù)呈現(xiàn)出組織特異性表達(dá)模式。與蛋白質(zhì)編碼基因相比,lncRNA在基因區(qū)域的甲基化水平明顯更高,并且其表達(dá)水平受基因區(qū)域甲基化影響較小。我們利用實(shí)驗(yàn)驗(yàn)證了一部分在棉花纖維發(fā)育起始期表達(dá)的lncRNA,發(fā)現(xiàn)這些lncRNA在纖維發(fā)育突變體和正常表型材料中差異表達(dá),推測(cè)其可能與棉花纖維起始相關(guān)。最后,我們構(gòu)建了共表達(dá)網(wǎng)絡(luò),對(duì)在纖維伸長和次生壁合成時(shí)期的lncRNA進(jìn)行功能注釋。4.棉花可變剪接圖譜的建立及其復(fù)雜性和調(diào)控機(jī)制本研究利用單分子長讀段轉(zhuǎn)錄本測(cè)序技術(shù)(Iso-Seq)對(duì)海島棉進(jìn)行轉(zhuǎn)錄組測(cè)序,開發(fā)了一套分析Iso-Seq數(shù)據(jù)的流程。我們從44968個(gè)基因中鑒定了176849個(gè)全長轉(zhuǎn)錄本,并更新了基因模型;同時(shí),鑒定了15102個(gè)纖維特異的可變剪接事件,估計(jì)大約51.4%的亞基因組間的同源基因會(huì)通過可變剪接產(chǎn)生結(jié)構(gòu)差異的轉(zhuǎn)錄本。進(jìn)一步研究發(fā)現(xiàn),同一個(gè)基因由可變剪接產(chǎn)生的轉(zhuǎn)錄本會(huì)受到miRNA的差異性調(diào)控。最后,我們發(fā)現(xiàn)核小體密度和DNA甲基化會(huì)在染色質(zhì)水平定義外顯子。本研究揭示了四倍體棉花中可變剪接的復(fù)雜性和新的調(diào)控機(jī)制,進(jìn)一步增強(qiáng)了人們對(duì)多倍體植物中可變剪接的認(rèn)識(shí)。5.棉花纖維發(fā)育動(dòng)態(tài)表觀組的建立和重要調(diào)控基因分析本研究建立了棉花纖維發(fā)育過程中的動(dòng)態(tài)DNA甲基化組。隨著纖維發(fā)育,DNA甲基化的比例會(huì)逐漸升高,呈現(xiàn)出與RNA介導(dǎo)的DNA甲基化相反的趨勢(shì)。核小體定位分析表明發(fā)育中的纖維不斷異染色質(zhì)化,其可能與DNA甲基化的動(dòng)態(tài)變化相關(guān)。絕大部分DNA高甲基化是由H3K9me2依賴的途徑建立,與RNA介導(dǎo)的DNA甲基化不相關(guān)。通過分析四倍體棉花At和Dt亞組同源基因甲基化和表達(dá)量之間的關(guān)系,我們推測(cè)不同亞組基因的表觀修飾差異可能會(huì)是基因偏向性表達(dá)的原因之一。最后,我們利用多組學(xué)數(shù)據(jù)的整合分析,揭示了DNA甲基化的動(dòng)態(tài)變化可能會(huì)調(diào)控纖維細(xì)胞伸長和次生壁加厚時(shí)期活性氧含量的動(dòng)態(tài)平衡。本研究首次繪制了棉花纖維發(fā)育過程中表觀遺傳修飾的動(dòng)態(tài)圖譜。
[Abstract]:Cotton is an important economic crop in the world, and cotton fiber is an important natural textile fiber. As a highly differentiated single cell, cotton fiber is a good model for studying cell differentiation, cell elongation and cell wall synthesis. The main results are as follows: 1. Sequencing of island cotton genome and the dynamic process of fiber development in terms of epigenetics. The tetraploid island cotton genome encodes 80876 genes with more than 69% repetitive sequences. The evolution of cellulose synthase (CesA) gene family in cotton and the expression patterns of each member during fiber development were analyzed. In this paper, we creatively proposed a model of the CesA gene family during fiber development in island cotton, i.e. at, Dt subgenomes cooperate to regulate fiber development in tetraploid cotton. We speculate that the origin of the PMEI domain may be a new functionalization of the pro domain after whole-genome replication. These results promote cotton genome research and deepen the understanding of plant cell wall evolution. 2. Genome re-sequencing revealed a large number of mutations, which were the basis of domestication and cis-regulation of cotton differentiation. This study collected 352 upland cotton materials, including semi-wild species and domesticated species, to construct a comprehensive genomic variation map. 93 domesticated selection regions covering 74 Mb and Dt subgenomes of the At subgenome were identified. 104 Mb. Nineteen candidate sites related to fiber quality traits were identified by genome-wide association analysis. The results showed that domestication of long fibers was associated with asymmetric subgenome selection. By systematically analyzing the DNase I digestion supersensitive sites and three-dimensional genome maps, we have identified some possible functional variations and gene transduction. This study proposes a new viewpoint on the evolution, regulation and adaptation of the genome in an important crop, which provides abundant resources for genome-based genetic improvement of cotton. 3. Identification of long-stranded non-coding RNA in cotton and functional analysis in fiber Integrating a large number of transcriptome data, we identified 30550 long-stranded non-coding RNA (lincRNA) and 4718 antisense long-stranded non-coding RNA (lncNAT) loci. The expression of lncRNA was relatively low, and most of them showed tissue-specific expression patterns. The expression level of some lncRNA expressed at the initial stage of cotton fiber development was verified by experiments. It was found that these lncRNA were differentially expressed in fiber development mutants and normal phenotypic materials. It was speculated that the expression level might be related to cotton fiber initiation. Establishment of cotton alternative splicing map and its complexity and regulation mechanism. In this study, Iso-Seq was used to sequence the transcripts of island cotton, and a procedure for analyzing Iso-Seq data was developed. 176,849 full-length transcripts were identified from 44,968 genes and the gene model was updated. Meanwhile, 1512 fiber-specific alternative splicing events were identified. It is estimated that about 51.4% of the homologous genes among subgenomes will produce transcripts with structural differences through alternative splicing. Further studies have shown that the same gene is produced by alternative splicing. Finally, we found that nucleosome density and DNA methylation define exons at the chromatin level. This study revealed the complexity of variable splicing in tetraploid cotton and new regulatory mechanisms, further enhancing the understanding of variable splicing in polyploid plants. 5. Cotton fiber hair Dynamic DNA methylation group was established during cotton fiber development. With the development of cotton fiber, the proportion of DNA methylation increased gradually, showing the opposite trend to RNA-mediated DNA methylation. Most of the DNA hypermethylation is established by H3K9me2-dependent pathway and is not related to RNA-mediated DNA methylation. Finally, the dynamic changes of DNA methylation may regulate the dynamic balance of reactive oxygen species (ROS) content during fiber elongation and secondary wall thickening. This study is the first time to map epigenetic modification in cotton fiber development.
【學(xué)位授予單位】：華中農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2017
【分類號(hào)】：S562

【參考文獻(xiàn)】

相關(guān)期刊論文 前5條

1 王鵬;張凱;孟憲寶;;基因組選擇技術(shù)在奶牛育種規(guī)劃中的應(yīng)用[J];黑龍江畜牧獸醫(yī);2014年15期

2 陳歡;張文英;樊龍江;;作物育種方法研究進(jìn)展與展望[J];科技通報(bào);2011年01期

3 黎裕;王建康;邱麗娟;馬有志;李新海;萬建民;;中國作物分子育種現(xiàn)狀與發(fā)展前景[J];作物學(xué)報(bào);2010年09期

4 ;Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis[J];Cell Research;2007年05期

5 李寶健,朱華晨;論應(yīng)用多基因轉(zhuǎn)化策略綜合改良生物體遺傳性研究方向的前景 Ⅰ .多基因轉(zhuǎn)化的基因來源與技術(shù)平臺(tái)[J];中山大學(xué)學(xué)報(bào)(自然科學(xué)版);2004年06期

，

本文編號(hào)：2210865