水稻种质资源重要农艺性状的全基因组关联分析

发布时间：2018-04-14 23:02

  本文选题：水稻 + 种质资源　； 参考：《中国农业科学院》2016年博士论文

【摘要】：本研究利用5,291个SNP标记,分析了523份稻种资源的遗传结构,采用全基因组关联分析方法,对株型、种子颜色、直播出苗以及苗期稻瘟病抗性等重要农艺性状进行遗传解析。主要结果如下:1.对523份品种进行群体结构分析,表明该群体可划分为籼(469)、粳(54)两个亚种,群体分化系数FST为0.56,表明存在明显的群体分化。而469份籼稻品种可划分为4个亚群(POP1-POP4)和1个混合群(Mixed),FST在0.05-0.25之间,表明各亚群间分化程度较小或处于中等分化水平。2.利用469份籼稻品种进行各性状的全基因组关联分析。在陵水和杭州环境下,株型相关性状分别找到114和161个显著性位点,两环境下共同检测到10个显著性位点;种子颜色相关性状,分别检测到12和11个显著性位点,两环境下共同检测到6个显著性位点;直播出苗相关性状,两环境下均检测到8个显著性位点,共同检测到2个显著性位点。在杭州环境下,苗期稻瘟病抗性共鉴定了16个稻瘟病菌株,检测到了127个显著性位点。3.对显著性位点进行一因多效分析。株型和种子颜色性状共有54个位点检测到了一因多效性,包括NAL1和Rc。此外,在第11染色体上有9个位点与剑叶长和剑叶长宽比显著相关,形成一个大的基因簇。对稻瘟病抗性位点分析发现Pi9、Pi5、Pi56(t)和Pita至少在两个以上菌株中检测到。此外,还有8个新位点至少能在3个以上的菌株中检测到,表明这些位点具有一定的广谱抗性。4.对于分蘖角度性状,找到了4个具有较大表达差异的候选基因,分别为LOC_Os08g33150、LOC_Os08g33160、LOC_Os08g33200和LOC_Os08g33420。分析LOC_Os08g33160在两组不同表型品种中的表达,其差异达到57倍左右。测序结果表明该基因在第4外显子存在一个C-T关键变异,导致mRNA由CAA变成UAA,翻译提前终止。该基因可能是控制水稻分蘖角度的最优候选基因。5.苗期稻瘟病抗性关联位点共找到45个抗性基因,包括4个已克隆基因。这些抗性基因主要分布在第11染色体(18个)、第6染色体(9个)和第12染色体(8个),具有成簇分布的特点。在这45个抗性基因中包含了本实验室在不同群体中已关联到的LOC_Os12g23930。RT-qPCR结果显示该基因在接菌后表达量显著下调5.6倍,这与之前的报道一致。6.对S182菌株接种的抗性品种进行转录组测序,共找282个上调和401个下调基因,包括有8个抗性基因,有报道表明LOC_Os01g66020可能参与水稻白叶枯抗性调控。结合S182苗期稻瘟病抗性关联分析,有3个基因在两种方法中都能检测到,分别为LOC_Os02g02850、LOC_Os02g41590和LOC_Os02g41630,其中LOC_Os02g41630属于phenylalanine ammonia-lyase gene family(PAL)家族成员之一(OsPAL1),与OsPAL5同源,而OsPAL4对白叶枯、纹枯病和稻瘟病具有一定的抗性,表明LOC_Os02g41630可能是重要候选基因。
[Abstract]:5291 SNP markers used in this study, analysis of the genetic structure of 523 rice germplasms, using genome-wide association analysis method of plant type, seed color, agronomic traits and seedling emergence of direct seeding rice blast resistance by genetic analysis. The main results are as follows: 1.. Population structure analysis of 523 cultivars, indicating that the population can be divided into indica japonica (469), (54) two subspecies, population differentiation coefficient FST is 0.56, show that there is obvious social differentiation. And 469 indica varieties could be divided into 4 subgroups (POP1-POP4) and 1 (Mixed), a mixed group of FST in 0.05-0.25, indicated that the differentiation between subpopulations a lesser degree or in a genome-wide association study of medium differentiation level.2. using 469 indica rice varieties were all traits. In Lingshui and Hangzhou environment, plant type traits were found 114 and 161 significant loci, two environment commonly detected 10 significant On site; seed color related traits were detected 12 and 11 significant loci, two environment commonly detected 6 significant loci; live seedling traits, two environment were detected 8 significant sites commonly detected 2 significant sites. In the Hangzhou environment at seedling stage of rice blast resistance were identified and 16 blast strains, detected 127 significant loci.3. on significant loci were pleiotropism. Analysis of plant type and seed color trait of a total of 54 loci were detected by pleiotropy, including NAL1 and Rc.. In addition, in eleventh there are 9 chromosomes. A site with the flag leaf length and flag leaf length width ratio was significantly related to the formation of a large gene cluster. The blast resistance loci analysis showed that Pi9, Pi5, Pi56 and Pita (T) at least in more than two strains detected. In addition, there are 8 new sites to at least 3 or more strains detected, These loci showed.4. with broad-spectrum resistance to certain tiller angle traits, 4 were found with large differential expression of candidate genes were LOC_Os08g33150, LOC_Os08g33160, LOC_Os08g33200 and LOC_Os08g33420. expression analysis of LOC_Os08g33160 in two groups of different phenotypes in cultivars, the difference reached about 57 times. The results of sequencing showed that the gene in exon fourth. There is a C-T key variation, leading to mRNA from CAA to UAA, translation termination. This gene may be associated with control of tiller angle in rice blast resistance gene.5. in rice seedling optimal sites found a total of 45 genes, including 4 genes that have been cloned. These resistance genes are mainly distributed in eleventh chromosomes (18) chromosome sixth, (9) and twelfth (8), with chromosome clustering distribution characteristics. In the 45 resistance genes included in our laboratory in different groups have been closed Linked to the results of LOC_Os12g23930.RT-qPCR showed that the gene expression after inoculation was significantly reduced by 5.6 times, reported.6. resistant varieties and before the inoculation of strain S182 by transcriptome sequencing, a total of 282 up-regulated and 401 down regulated genes, including 8 genes, it has been reported that LOC_Os01g66020 may be involved in rice white the leaf blight resistance regulation. According to the analysis of S182 at seedling stage of rice blast resistance, 3 genes can be detected in the two method, respectively LOC_Os02g02850, LOC_Os02g41590 and LOC_Os02g41630, which belongs to the LOC_Os02g41630 phenylalanine ammonia-lyase gene family (PAL) one of the members of the family (OsPAL1), and OsPAL5 and OsPAL4 on homologous, leaf blight, sheath blight and has a certain resistance to rice blast, suggest that LOC_Os02g41630 may be an important candidate gene.

【学位授予单位】：中国农业科学院
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S511
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本文编号：1751395