转录组测序数据分析在玉米籽粒功能基因挖掘中的应用

发布时间：2018-08-05 15:57

【摘要】：玉米籽粒的物质积累过程是影响玉米产量与品质的重要因素之一。随着测序技术与生物信息学的发展,以高通量测序数据为基础,在全基因组范围内发掘玉米籽粒物质积累相关的功能基因,不仅对作物育种及改良具有重要的意义,同时也为作物功能基因组学研究提供了新的策略与方法。本研究通过构建玉米转录组测序数据分析平台,对368个玉米自交系籽粒的转录组测序数据进行了分析,以玉米籽粒物质积累过程为研究重点,从中找到了在玉米改良过程中受选择作用的功能基因。此外,本研究也通过转录组测序数据的从头组装,构建了玉米的泛转录组,研究了其中与籽粒物质积累过程相关的遗传组分。主要研究结果如下:1.利用目前主流的转录组分析软件,构建了玉米转录组测序数据分析平台。该平台主要由基于参考基因组的比对分析平台和无参考基因组的Denovo组装平台构成。其中,基于参考基因组的平台中又包含了序列比对、SNP Calling和表达分析三个子平台,能够满足群体转录组分析的多种需求。无参考基因组的Denovo组装平台则可以对测序数据进行从头组装,在玉米新基因挖掘及泛转录组的构建上具有重要的应用价值。此外,利用统计学及生物学的方法对平台分析结果进行验证,均显示其具有较高的准确性与可信度。2.根据群体结构及适应性将368份玉米自交系分为温带(190份)和热带(178份)两个玉米类群,结合转录组分析所获的558,579个高质量SNP标记,利用XP-EHH选择信号检测方法对群体间受选择的情况进行了研究。在温带和热带玉米中分别鉴定了 730个和421个选择区域,其中温带玉米受到了更强的选择作用。对选择区域中受选择的基因进行功能注释,发现调控相关基因在选择区域内显著富集,并且在群体间存在表达差异(P-value0.05)。进一步对其中与玉米籽粒物质积累相关的基因进行分析,发现蔗糖降解途径两个关键酶的编码基因sus1和incw1在温带玉米中受到了强烈的选择(top 0.5%),并且在温带玉米中的表达水平极显著地高于热带玉米(P-value0.01)。同时,在该途径的其它基因及玉米油分合成途径的相关基因中也检测到了类似的选择信号,表明玉米籽粒物质积累相关基因在玉米育种改良过程中受到了明显的人工选择作用。3.通过对玉米基因表达的存在/缺失变异(ePAV)模式进行转化,并设计了"先组装后比对"的策略将玉米转录组测序数据进行从头组装,分别获得了 13,382个ePAV基因和2,355条高质量的新序列(novel sequences),并以此构建了玉米的泛转录组。序列数据分析与重测序实验验证表明,ePAV表达模式更能够反映玉米基因在不同自交系中的表达差异,而"先组装后比对"的策略也更适用于玉米转录组的从头组装。与严建兵教授实验室合作,利用玉米泛转录组中的遗传变异,与玉米15个农艺性状表型和526个籽粒代谢相关性状进行全基因组关联分析,发现类黄酮代谢途径中相关基因的ePAV表达模式与该途径中代谢物的含量显著关联(P-value7.49E-5),表明ePAV基因及ePAV模式对玉米籽粒物质积累过程中代谢物合成调控过程具有重要的影响。本研究旨在利用转录组测序数据,在全基因组的水平上发掘对玉米籽粒物质积累过程具有重要影响的功能基因,并尝试解析其遗传机理和生物学功能,从而为玉米育种改良工作提供重要的遗传资源。
[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.
【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：S513

【参考文献】