我国籼稻品种遗传结构与多样性的SNP分析

发布时间：2018-03-28 11:22

本文选题：水稻　切入点：单核苷酸多态性　出处：《中国农业科学院》2016年博士论文

【摘要】：水稻是超过35亿人、约占世界范围内一半人口的主要粮食作物。水稻品种资源,尤其是地方品种资源,从其野生祖先在自然和人为的选择下不断进化,形成高水平的遗传多样性,是进行遗传改良的生物或非生物胁迫耐受性的主要来源。因此,比较地方品种和国外引进品种、选育品种的遗传多样性和结构,可为选育良种亲本提供可靠的依据,有助于改变我国现有选育品种遗传基础狭窄的现状,实现农业可持续发展。单核苷酸多态性(SNP)具有密度高、分布均匀的特点,已成为一种成熟有效的遗传变异检测技术,广泛应用于遗传多样性结构研究以及分子育种。本研究利用Illumina的Infinium技术手段定制全基因组SNP芯片,对471份中国籼稻品种(其中地方品种285份、国外引进品种94份、选育品种92份)进行遗传多样性和结构分析。主要结果如下:1.对本研究定制芯片包含的5291个SNPs位点进行了特征分析,结果表明大部分的SNPs位于基因间,其中42%位于非翻译区、内含子以及编码区等基因内,58%位于非基因区间。72.33%的SNPs标记间距少于75 kb并且所有的间距都大于0.5 kb。2.利用主成分分析、基于Nei距离的NJ树和基于模型的群体结构对本研究试验材料进行了遗传结构分析,结果均表明本研究所采用的地方品种、国外引进品种和选育品种等材料被明显分成3个亚群,并存在一定的重叠。3.对地方品种、国外引进品种和选育品种的遗传多样性进行了分析,结果表明地方品种的多态信息含量(PIC)和遗传多样性(GD)最高,并且72%SNPs标记在地方品种亚群内的最小等位基因频率(MAF)≥0.2,明显高于其中两个亚群。4.利用分子方差分析对地方品种、国外引进品种和选育品种三个亚群的进行了群体间遗传分化分析,结果表明亚群内的遗传分化高达90.61%。5.比较SNPs标记亚群间的PIC值分布,结果揭示它们之间的差异并非表现在全基因组整体上,而是某个位点或者某个染色体区段。6.对亚群间PIC值存在明显变化的3个染色体片段进行分析,将片段上的SNPs位点进行基因本体富集分析,结果发现不同亚群间的某些位点有着不同的分子功能或性状,并已被克隆或报道。7.分析不同亚群间如选育品种/地方品种、国外引进品种/地方品种、地方品种/选育品种和地方品种/国外引进品种的ROD值,分别找到了23、24、20、21个遗传多样性显著下降的非重叠窗口,其中有56、47、45、40个基因。
[Abstract]:Rice is the main food crop of more than 3.5 billion people and accounts for about half of the world's population. Rice varieties, especially local varieties, have evolved from their wild ancestors, both naturally and artificially. The formation of a high level of genetic diversity is the main source of tolerance to biological or abiotic stress for genetic improvement. It can provide reliable basis for breeding improved parents, and help to change the current situation of narrow genetic basis of selected varieties in China and realize the sustainable development of agriculture. SNPs have the characteristics of high density and uniform distribution. It has become a mature and effective technique for detection of genetic variation, which has been widely used in genetic diversity structure research and molecular breeding. In this study, the whole genome SNP chip was customized by Infinium technology of Illumina. 471 Chinese indica rice varieties (285 local varieties and 94 imported varieties from abroad) were studied. The main results were as follows: 1. The 5291 SNPs loci contained in the microarray were analyzed. The results showed that most of the SNPs were located between genes, 42% of which were located in the untranslated region. In intron and coding region, 58% of the SNPs markers located in non-gene interval. 72.33% had less than 75 kb spacing and all the distances were greater than 0.5 kb. The genetic structure of NJ tree based on Nei distance and population structure based on model were analyzed. The results showed that the local varieties, imported varieties and selected varieties were obviously divided into three subgroups. The genetic diversity of local varieties, imported varieties and selected varieties were analyzed. The results showed that local varieties had the highest polymorphic information content (Pi) and genetic diversity (GD). The minimum allelic frequency of 72%SNPs markers in subpopulations of local cultivars was higher than that of two subgroups (0.2), which was significantly higher than that of two subgroups (.4.The analysis of molecular variance was used to analyze the local varieties). The genetic differentiation of three subpopulations of imported and selected varieties was analyzed. The results showed that the genetic differentiation in subpopulations was as high as 90.61.5.The distribution of PIC values among subpopulations with SNPs markers was compared. The results showed that the difference between them was not expressed in the whole genome, but in a single locus or chromosome segment. 6. Three chromosomal fragments with significant changes in PIC values among subpopulations were analyzed. The results of gene bulk enrichment analysis of SNPs loci on the fragments showed that some loci of different subpopulations had different molecular functions or traits, and had been cloned or reported. 7. Analysis of different subpopulations, such as breeding varieties / local varieties, was carried out. The ROD values of imported varieties / local varieties, local varieties / breeding varieties and local varieties / foreign introduced varieties were found, respectively, and 21 non-overlapping windows for the significant decrease of genetic diversity were found, among which there were 56, 474, 45, 40 genes, respectively.
【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】：S511.21

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