DUF1313基因家族和C2H2锌指基因家族的进化分析及其与玉米农艺性状的关联

发布时间：2018-01-16 00:05

本文关键词：DUF1313基因家族和C2H2锌指基因家族的进化分析及其与玉米农艺性状的关联　出处：《四川农业大学》2016年博士论文　论文类型：学位论文

【摘要】：玉米是我国重要的粮饲作物,也是遗传学研究的模式作物之一。随着测序技术的发展和公共数据库的构建,使得人们利用生物信息学手段探索分子生物学中未知的信息成为可能。未知功能的结构域(Domain of unknown function,DUF)是一种蛋白结构域,但是目前为止不知道其所具有的功能。所有蛋白结构域中超过20%的蛋白结构域被注释为“DUF”,这类结构域很多都是高度保守的,说明这类结构域在生物进程中扮演重要的功能。DUF1313基因家族蛋白只在植物中发现,且含有一个高度保守的未知功能的结构域,在植物生长发育过程中起重要作用。由于该结构域功能未知,目前对该家族的研究报道比较少。C2H2型锌指转录因子家族是植物中最大的转录因子家族之一,基因成员广泛参与植物多种生物过程的调控。C2H2锌指结构域及其侧翼序列是主要的DNA结合位点,是该类转录因子的活性中心,对调控其靶基因具有重要作用。目前,对拟南芥、水稻和杨树C2H2锌指家族的研究已有报道,但是玉米作为遗传研究的模式作物,该类转录因子在玉米基因组的分布规律、表达模式及参与何种调控等都知之甚少。本课题对以上两类基因家族进行了系统的进化分析以及家族成员与玉米农艺性状的关联分析。主要研究结果如下：1.DUF1313基因家族在植物中的进化及其与玉米成株期农艺性状的关联：(1)本研究从81个光白养型植物中鉴定到269个DUF1313基因,该基因家族只存在于植物中,分布范围从海洋单细胞藻类到陆生高大乔木；(2)对DUF1313结构域的序列分析发现,该结构域中有4个氨基酸残基在进化过程中发生规律性的变异,根据该变异规律可以将269个DUF1313基因分为三种主要类型：IARV、 I(S/T/F)(K/R)V和IRRV型；(3)系统发育分析结果表明,IARV型基因是比较原始的类型,可能是由藻类基因进化而来,禾本科植物保留了该类型基因；双子叶植物保留了I(S/T/F)(K/R)V类型的基因,IRRV型基因是最大的一类DUF1313家族基因,双子叶和单子叶植物都含有该类型基因,说明该类型基因是最近的DUF1313基因家族扩张的产物；(4)对禾本科植物DUF1313家族基因进行选择压分析,结果表明B1分化枝检测到了4个显著受到正选择的氨基酸位点,推测该家族基因在禾本科植物中出现了功能分化；(5)利用514份玉米自交系的表型和基因型,对4个玉米DUF1313基因进行关联分析表明,三个分化较早的DUF1313基因与8个玉米成株期农艺性状(开花期等性状)显著关联,而分化较晚的一个基因关联结果不显著；利用25个RILs群体验证的结果与关联分析结果一致,说明4个玉米DUF1313基因在进化过程中出现了功能分化；(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条玉米、大刍草和摩擦禾ELF4-like4基因序列重构系统发育树,根据bootstrap值可以将玉米及其近缘种分为四个类群,这与前人根据形态学对玉蜀黍族的分类是一致的。因此,这个基因能够用来对玉米及其近缘种进行系统分类。2.玉米C2H2转录因子家族的系统发育及与玉米成株期农艺性状的关联：(1)该家族基因分布于玉米染色体的所有区域,但并不均匀,多数成簇分布于染色体的两端；玉米C2H2锌指基因以全基因组复制为主,部分基因存在串联复制；(2)玉米C2H2锌指基因系统发育分析表明,该家族基因分化为4个类群,其中Ⅱ类群为植物特有的锌指基因,该类型基因在DNA识别区包含一个保守的"QALGGH"序列,被称为Q型锌指；(3)植物特有的锌指基因的基因结构比较保守,很少有内含子的插入,其他类型的基因有丰富的内含子数量和插入类型；蛋白序列结构显示,植物特有的锌指基因的蛋白序列结构也比较保守,只含有单个或多个锌指结构域,几乎不含其他类型的保守结构域；(4)对C2H2锌指结构域的系统发育分析表明,多锌指基因在进化过程中其锌指结构域的位置和顺序比较保守,位置相同的锌指结构域在序列上高度保守一致； (5)C2H2锌指基因家族在B73自交系不同生长阶段的11种组织中的表达分析表明,该家族基因在各个组织中都能表达,可以分为高表达、差异表达和低表达三个类群；(6)对玉米C2H2家族基因进行功能预测表明,该家族基因主要参与玉米的生殖和发育,尤其与玉米产量形成重要农艺性状显著关联；(7)克隆了109条玉米ZMF155基因序列,利用该基因的SNPs和Indels与玉米成株期农艺性状进行关联分析,结果表明该基因与穗行数性状显著关联,说明该基因在玉米产量形成中发挥一定的作用。
[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.

【学位授予单位】：四川农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S513;Q943.2

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