【作者】 王旭峰；

【导师】 田丰；

【作者基本信息】 中国农业大学 ， 作物遗传育种， 2017， 博士

【摘要】 基因表达调控在控制生物体表型变异和物种进化过程中扮演着非常重要的作用。为在全基因组范围内解析玉米基因表达调控变异的遗传基础,本论文对由玉米自交系W22和其祖先种大刍草(Zea mays ssp.pargviglumis)杂交衍生而来的BC2S3渗入系群体进行了转录组测序,并结合覆盖全基因组的19,838个SNP分子标记,进行了全基因组表达数量性状位点(eQTL)的定位分析。获得如下主要结果:1.在玉米全基因组范围内,共检测到25,560个eQTL,其中包括13,148 local-eQTL和12,512 distant-eQTL。与distant-eQTL相比,local-eQTL能够解释较大的表达变异。这些eQTL可以调控17,311个基因的表达,平均每个基因定位到1.5个eQTL,呈现出相对比较简单的遗传结构。eQTL调控的基因中,local-eQTL参与调控的基因比例高达75%,表明local-eQTL在基因表达调控中扮演着非常重要的作用。2.对local-eQTL调控的基因在全基因组上的分布分析发现:相邻的基因更容易同时检测到local-eQTL,呈现出表达搭载效应(expression piggybacking)。这种表达搭载效应可以延伸到多个相邻基因,从而形成共调控的基因簇。相似的染色质修饰状态可能是引起基因组上表达搭载效应的重要原因。3.Distant-eQTL在基因组上并不是随机分布的,而是形成了 125个显著的表达调控热点。这些调控热点控制的基因趋向于在同一个或者相似的代谢途径中富集,表明这些热点区域内可能存在重要的调控因子。通过整合eQTL定位、基因注释信息以及已知的代谢途径信息,我们鉴定了一系列潜在的候选调控因子。4.在玉米第2染色体上,eQTL热点Hotspot 30可以调控9个参与苯并噁嗪代谢途径的Bx基因的表达变异。通过对该位点上Bx基因对应的eQTL置信区间进行重叠分析,我们把候选调控因子缩小到一个4.7Mb的区间内,包含76个注释的基因。其中,29个基因(包含6个转录因子)受到了 local-eQTL的调控。进一步的酵母单杂和瞬时表达实验鉴定了一个编码R2R3类型的MYB转录因子的基因,ZmMYB35,负向地调控了下游Bx基因的表达。5.通过综合本研究与先前两个研究中检测到的玉米与大刍草之间差异表达的基因,我们鉴定出了 5,223个玉米驯化过程中表达模式发生显著分化的基因。在这些基因所检测到的local-eQTL中,56%的eQTL使玉米的等位基因上调表达,表明驯化可能更频繁地导致了栽培玉米等位基因的上调表达。6.参与苯并噁嗪代谢途径的Bx基因在玉米和大刍草展现出显著的表达分化。进一步基因组序列分析和代谢分析结果表明:在玉米散布到温带环境过程中,参与苯并噁嗪代谢途径的基因可能发生了显著的表达分化以适应温带地区的虫害环境。更多还原

【Abstract】 The regulation of gene expression has been shown to play an important role in controlling organismic phenotypes and species evolution.Here,we report a comprehensive assessment of gene expression variation by sequencing the transcriptome of a large maize-teosinte experimental population.By combiningwith 19,838 SNP markers,eQTL mapping was performed.Major findings are as follows.1.Genome-wide genetic mapping identified 25,660 expression quantitative trait loci(eQTL)for 17,311 genes,including 13,148(51.2%)local-eQTL and 12,512(48.8%)distant-eQTL.Local-eQTL typically had larger effects than distant-eQTL.Of genes with eQTL mapped,76%had local-eQTL.These results suggested that local regulatory effects play a predominant role in determining expression variation of most genes.2.Local-eQTL more frequently mapped to adjacent genes,displaying a mode of expression piggybacking,which consequently created a number of co-regulated gene clusters.Genes within the co-regulated gene clusters tend to have related function and shared chromatin modification.3.Distant-eQTL are not evenly distributed along the maize genome,but form 125 significant distant-eQTL hotspots with their targets significantly enriched in specific functional categories.By integrating different sources of information,we identified putative trans-regulators for a variety of metabolic pathways.4.At Hotspot 30 on chromosome 2,significant distant-eQTL were detected for nine members of the benzoxazinoid metabolic pathway(Bx2-Bx8 and Bx11-Bx12),suggesting that Hotspot 30 might contain a trans-regulator that coordinately regulates the expression of the Bx genes.Through yeast-one-hybrid(Y1H)experiment and transient expression assay,we showed that a R2R3-MYB transcription factor,ZmMYB35,functions as a key regulator that negatively regulates the expression of Bx genes for the biosynthesis of benzoxazinoids.5.We compiled a list of 5,223 genes with local effects that were also detected in the DE or ASE study.At 56%of the local-eQTL mapped for these genes,the maize allele was more highly expressed than the teosinte allele,suggesting that domestication has significantly impacted the global gene expression,with many of genes targeted by selection.6.By integrating expression,genome sequence,and metabolic analyses,we demonstrated that the Bx genes for benzoxazinoid biosynthesis have been coordinately modified for the adaptation of maize to temperate environments with a distinct herbivore community.更多还原