發(fā)布時間：2018-01-16 00:05

  本文關鍵詞：DUF1313基因家族和C2H2鋅指基因家族的進化分析及其與玉米農藝性狀的關聯(lián)　出處：《四川農業(yè)大學》2016年博士論文　論文類型：學位論文

  更多相關文章： 玉米 DUF1313基因家族 C2H2鋅指基因家族 系統(tǒng)發(fā)育分析 關聯(lián)分析

【摘要】：玉米是我國重要的糧飼作物,也是遺傳學研究的模式作物之一。隨著測序技術的發(fā)展和公共數(shù)據(jù)庫的構建,使得人們利用生物信息學手段探索分子生物學中未知的信息成為可能。未知功能的結構域(Domain of unknown function,DUF)是一種蛋白結構域,但是目前為止不知道其所具有的功能。所有蛋白結構域中超過20%的蛋白結構域被注釋為“DUF”,這類結構域很多都是高度保守的,說明這類結構域在生物進程中扮演重要的功能。DUF1313基因家族蛋白只在植物中發(fā)現(xiàn),且含有一個高度保守的未知功能的結構域,在植物生長發(fā)育過程中起重要作用。由于該結構域功能未知,目前對該家族的研究報道比較少。C2H2型鋅指轉錄因子家族是植物中最大的轉錄因子家族之一,基因成員廣泛參與植物多種生物過程的調控。C2H2鋅指結構域及其側翼序列是主要的DNA結合位點,是該類轉錄因子的活性中心,對調控其靶基因具有重要作用。目前,對擬南芥、水稻和楊樹C2H2鋅指家族的研究已有報道,但是玉米作為遺傳研究的模式作物,該類轉錄因子在玉米基因組的分布規(guī)律、表達模式及參與何種調控等都知之甚少。本課題對以上兩類基因家族進行了系統(tǒng)的進化分析以及家族成員與玉米農藝性狀的關聯(lián)分析。主要研究結果如下：1.DUF1313基因家族在植物中的進化及其與玉米成株期農藝性狀的關聯(lián)：(1)本研究從81個光白養(yǎng)型植物中鑒定到269個DUF1313基因,該基因家族只存在于植物中,分布范圍從海洋單細胞藻類到陸生高大喬木；(2)對DUF1313結構域的序列分析發(fā)現(xiàn),該結構域中有4個氨基酸殘基在進化過程中發(fā)生規(guī)律性的變異,根據(jù)該變異規(guī)律可以將269個DUF1313基因分為三種主要類型：IARV、 I(S/T/F)(K/R)V和IRRV型；(3)系統(tǒng)發(fā)育分析結果表明,IARV型基因是比較原始的類型,可能是由藻類基因進化而來,禾本科植物保留了該類型基因；雙子葉植物保留了I(S/T/F)(K/R)V類型的基因,IRRV型基因是最大的一類DUF1313家族基因,雙子葉和單子葉植物都含有該類型基因,說明該類型基因是最近的DUF1313基因家族擴張的產物；(4)對禾本科植物DUF1313家族基因進行選擇壓分析,結果表明B1分化枝檢測到了4個顯著受到正選擇的氨基酸位點,推測該家族基因在禾本科植物中出現(xiàn)了功能分化；(5)利用514份玉米自交系的表型和基因型,對4個玉米DUF1313基因進行關聯(lián)分析表明,三個分化較早的DUF1313基因與8個玉米成株期農藝性狀(開花期等性狀)顯著關聯(lián),而分化較晚的一個基因關聯(lián)結果不顯著；利用25個RILs群體驗證的結果與關聯(lián)分析結果一致,說明4個玉米DUF1313基因在進化過程中出現(xiàn)了功能分化；(6) ELF4-like4基因是玉米中最原始并且高度保守的DUF1313基因。利用103條玉米、大芻草和摩擦禾ELF4-like4基因序列重構系統(tǒng)發(fā)育樹,根據(jù)bootstrap值可以將玉米及其近緣種分為四個類群,這與前人根據(jù)形態(tài)學對玉蜀黍族的分類是一致的。因此,這個基因能夠用來對玉米及其近緣種進行系統(tǒng)分類。2.玉米C2H2轉錄因子家族的系統(tǒng)發(fā)育及與玉米成株期農藝性狀的關聯(lián)：(1)該家族基因分布于玉米染色體的所有區(qū)域,但并不均勻,多數(shù)成簇分布于染色體的兩端；玉米C2H2鋅指基因以全基因組復制為主,部分基因存在串聯(lián)復制；(2)玉米C2H2鋅指基因系統(tǒng)發(fā)育分析表明,該家族基因分化為4個類群,其中Ⅱ類群為植物特有的鋅指基因,該類型基因在DNA識別區(qū)包含一個保守的"QALGGH"序列,被稱為Q型鋅指；(3)植物特有的鋅指基因的基因結構比較保守,很少有內含子的插入,其他類型的基因有豐富的內含子數(shù)量和插入類型；蛋白序列結構顯示,植物特有的鋅指基因的蛋白序列結構也比較保守,只含有單個或多個鋅指結構域,幾乎不含其他類型的保守結構域；(4)對C2H2鋅指結構域的系統(tǒng)發(fā)育分析表明,多鋅指基因在進化過程中其鋅指結構域的位置和順序比較保守,位置相同的鋅指結構域在序列上高度保守一致； (5)C2H2鋅指基因家族在B73自交系不同生長階段的11種組織中的表達分析表明,該家族基因在各個組織中都能表達,可以分為高表達、差異表達和低表達三個類群；(6)對玉米C2H2家族基因進行功能預測表明,該家族基因主要參與玉米的生殖和發(fā)育,尤其與玉米產量形成重要農藝性狀顯著關聯(lián)；(7)克隆了109條玉米ZMF155基因序列,利用該基因的SNPs和Indels與玉米成株期農藝性狀進行關聯(lián)分析,結果表明該基因與穗行數(shù)性狀顯著關聯(lián),說明該基因在玉米產量形成中發(fā)揮一定的作用。
[Abstract]:Maize is an important crop for food and feed, is also one of the patterns of crop genetics research. Along with the construction of the development of sequencing technology and public databases, making people using bioinformatics tools to explore unknown molecular biology information possible. Domain of unknown function (Domain of unknown function, DUF) is a kind of protein structure domain, but so far do not know its function. More than 20% of the protein domain structure of all protein domains is annotated as "DUF", this kind of domain are highly conserved, suggesting that this type of domain play an important function of.DUF1313 gene family proteins in biological processes only found in plants domain, and contains an unknown function highly conserved, plays an important role in plant growth and development. Due to the domain of unknown function, the family research report ratio Little.C2H2 type zinc finger transcription factor family is one of the largest family of transcription factors in plants, the regulation of.C2H2 gene is involved in many members of the zinc finger domain of plant biological processes and its flanking sequence is the main DNA binding site, is the center of the activity of transcription factors, plays an important role in the regulation of its target genes. At present, the in Arabidopsis, rice and poplar C2H2 zinc finger family studies have been reported, but the maize as a model crop genetic research, the transcription factor distribution in maize genome, expression pattern and regulation in which are poorly understood. This paper analyzed system evolution analysis and family members with maize agronomic traits correlation on the above two types of gene family. The main results are as follows: 1.DUF1313 gene family evolution in plants and their associated plant agronomic traits and corn: (1) This study from the 81 white light type plants identified 269 DUF1313 genes, the gene family exists only in plants, ranging from marine unicellular algae to terrestrial tall trees; (2) sequence of DUF1313 domain analysis shows that the variation of 4 amino acid residues occur in the evolutionary regularity in the process of the domain, according to the variation of 269 DUF1313 genes can be divided into three main types: IARV, I (S/T/F) (K/R) V and IRRV; (3) the results of phylogenetic analysis showed that IARV gene is a primitive type, possibly by algae and gene evolution to gramineous plants retained this type of gene; Dicotyledoneae retained I (S/T/F) (K/R) type V gene, IRRV gene is one of the largest gene DUF1313 family, twin Ye He monocotyledonous plants contain the type of gene, the gene type is DUF1313 based recently Because of the expansion of product family; (4) to gramineous plant DUF1313 genes selection pressure analysis, the results show that the B1 clade detected 4 distinct amino acid sites by positive selection, suggesting that the gene family in grasses had functional differentiation; (5) using 514 maize inbred lines phenotype and the genotype of 4 maize DUF1313 gene association analysis showed that three of the DUF1313 gene and early differentiation of 8 Maize Seedling agronomic traits (flowering traits) significant correlation, a result of late differentiation gene association is not significant; with a population of 25 RILs results and correlation analysis results indicated that 4 maize DUF1313 gene functional differentiation in the evolutionary process; (6) ELF4-like4 gene DUF1313 gene in maize is most primitive and highly conserved. Using 103 maize, Teosinte and Tripsacum ELF4-l Phylogenetic tree reconstruction system according to the gene sequence of ike4, bootstrap value of maize and its relatives can be divided into four groups, and the previous classification according to the morphology of maydeae is consistent. Therefore, this gene can be used for corn and its phylogenetic relatives of the classification system of.2. maize C2H2 transcription factor family and with the corn plant related agronomic traits: (1) all regions of the gene family in maize chromosome distribution, but not uniform, both ends of most clusters on chromosomes; maize C2H2 zinc finger gene by whole genome duplication as the main part of the gene tandem duplication; (2) maize C2H2 zinc finger gene phylogeny analysis showed that the gene family is divided into 4 groups, which were II plant specific zinc finger gene, this gene contains a conserved QALGGH sequence in the DNA zone, known as the Q type zinc finger ; (3) the plant specific zinc finger gene structure gene is conservative, there is little intron insertion, a number of rich introns and other types of insertion type gene; protein sequence structure, plant specific zinc finger protein gene sequence structure are conservative, contains only a single or multiple zinc finger domain, conserved domain almost does not contain other types; (4) the C2H2 zinc finger domain system development analysis showed that many zinc finger genes in the evolutionary process of the zinc finger position and order domain is more conservative, the same location of zinc finger domain in the highly conserved sequence; (5) expression of 11 gene family in different tissues of B73 inbred lines in the growth phase of the analysis showed that the C2H2 zinc finger family, the gene can be expressed in various tissues, can be divided into high expression, differential expression and low expression of the three groups; (6) of maize C2H2 Gene function prediction showed that the genes mainly involved in maize reproduction and development, especially the formation of important agronomic traits associated with maize yield; (7) cloning of 109 maize ZMF155 gene sequence, the gene of SNPs and Indels and corn plant agronomic traits correlation analysis, the results show that the gene with the number of rows per ear traits was significantly associated, indicating that the gene plays a role in maize yield formation.

【學位授予單位】：四川農業(yè)大學
【學位級別】：博士
【學位授予年份】：2016
【分類號】：S513;Q943.2

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