水稻花发育相关的miRNA靶基因多态性和自然选择研究 
凌立贞 
学位类型博士
导师高立志 
2010-11
学位授予单位中国科学院研究生院
学位授予地点北京
学位专业植物学
摘要自然选择如何通过作用于重要调节因子而决定基因调节的进化方式,一直是进化生物学家感兴趣的话题。microRNA(miRNA)是一类内源转录后抑制因子,在植物的生长发育过程中发挥着重要作用。为了解花发育过程中miRNA调节层的自然选择机制,我们重测序了来自5个水稻群体的31个参与花发育的miRNA靶基因。研究发现负选择作用于保守的miRNA靶位点,在栽培稻及其野生祖先种中保持了低变异的、保守的靶序列。相反,正选择允许非保守的miRNA靶位点发生变异,且作用于特定的栽培群体。通过对非保守靶位点变异的分析,发现这些变异影响miRNA/target二聚体的稳定性和靶位点的得失,可能有助于miRNA功能的多样化。上述结果表明,保守miRNA靶位点的变异对水稻花的发育可能是有害的,而非保守靶位点的变异则有助于水稻花发育相关性状的表型多样化和群体对特定环境的适应。为进一步了解靶序列变异的等位基因的功能效应和进化意义,我们分析了粳稻、籼稻和普通野生稻群体中LOC_Os01g18850 (SPL 1)靶基因和两侧1.4M区域序列的单倍型和连锁不平衡(LD)结构。靶序列和两侧的SNP遗传谱表明两个栽培稻群体中包含靶序列SNP 3C/T的变异呈现很高的单倍型频率,低的单倍型多态性和严重的连锁不平衡,而普通野生稻群体则完全相反。LRT检测表明靶位点上的SNP 3C/T在整个栽培稻群体受到了近期正选择作用。两个栽培稻亚种群体间的比较表明,籼稻中一半的单倍型 (mh 2) 包含靶位点SNP 3C等位基因,而在粳稻中91%的核心单倍型mh 3中包含SNP 3T等位基因;而且该基因组区域的连锁不平衡程度粳稻群体较籼稻的高。这些差异表明,在进化过程中粳稻和籼稻的靶序列发生了独立的进化事件,而且粳稻群体受到了更强的近期正选择作用。最后,我们进一步调查了栽培稻中靶位点SNP3和SNP 4等位基因的生态地理分布,结果表明粳稻的SNP 3T和SNP 4A等位基因在花发育过程中可能与适应北方的气候相关。
资助项目How has natural selection determined the evolution of gene regulation by acting on major regulatory factors? This question has been attractive to many evolutionary biologists for a long time. MicroRNAs (miRNAs) are endogenous posttranscriptional repressors and play essential roles in diverse biological processes in plants. To understand how natural selection has targeted on the entire lay of miRNA regulatory modules during flower development, we resequenced 31 miRNA target sites involved in flower development from five rice populations. We found that purifying selection serves as a major evolutionary force to act on the conserved miRNA binding sites, leading to the globally reduced genetic variation in highly conserved miRNA binding sequences within the entire rice samples. Conversely, positive selection allows variations at nonconserved miRNA binding sites and acts on them in a population-specific behaviour. Further analysis revealed that the polymorphisms within target sites may serve as raw materials for diverse functions of miRNAs by means of the destabilization of duplex, abolishment of existing target sites, and creation of novel ones. Together, the above-mentioned results indicate that variations at conserved binding sites are likely deleterious during rice flower development, whereas variants at nonconserved binding sites may be conductive to flower development-related phenotypic diversities and rice population adaption to variable environmental conditions as well. To further assess functional effects and evolutionary significance of variable alleles at the target genes, we reported the detailed characterization of the haplotype and linkage disequilibrium (LD) patterns of the entire target gene (LOC_Os01g18850,SPL 1) and the 1.4 Mb flanking regions in three rice populations, namely japonica, indica and O. rufipogon. The genetic profile of SNPs at target site and its flanking regions revealed high haplotype frequency, low haplotype diversity and strong LD in two cultivatedricepopulations. By contrast, we observed the opposite phenomena in O. rufipogon. Using the long-range haplotype (LRT) test, we found strong evidence of recent positive selection for SNP 3C/T alleles at target site in the combined O. sativa. Comparsion between the two rice subpopulations indicated that the major haplotype mh 2 containing SNP 3C accounts for half of all haplotypes in indica, while mh 3 containing SNP 3T is 91% in japonica. Moreover, the extent of LD is stronger in japonica than that in inidca. These differences suggest that independent evolutionary events may have occurred in target sequences of two cultivated rice populations and stronger positive selection acted on japonica. Next, we examined geographic distribution of polymorphic variants at target sites. We found that the major alleles SNP 3T and tightly linked SNP 4A in japonica appear to be associated with the adaption to the northern climates during rice flower development.
文献类型学位论文
条目标识符http://ir.kib.ac.cn/handle/151853/16170
专题昆明植物所硕博研究生毕业学位论文
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凌立贞 . 水稻花发育相关的miRNA靶基因多态性和自然选择研究 [D]. 北京. 中国科学院研究生院,2010.
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