全基因组扫描筛选德保矮马矮小性状相关候选基因研究

发布时间：2019-06-09 20:41

【摘要】：德保矮马分布于我国南方广西山区的体型显著矮小的马品种,是全世界矮马品种里比较古老的矮马资源之一。它的矮小体型是长期驯化过程中人类的定向培育和适应自然环境的结果。对德保矮马来说,矮小体型是适应山路托运的优势性状,因此对德保矮马的长期培育和保护十分重要。目前,对德保矮马的历史起源以及矮小性的分子遗传机理的研究起步比较晚,尤其是在基因组水平上研究报道极为稀少。本研究利用马高密度基因芯片(GeneSeek Equine SNP 65K)对中国体高差异较大的三个品种(德保矮马,蒙古马,伊犁马)进行选择信号筛选,单拷贝序列(CNV)以及体高关联分析研究。同时整合了来32个国外马品种729个个体的50K基因芯片分型数据。进一步确认了德保矮马与国外马品种系统进化关系以及对矮小性状的遗传机理提供了分子遗传学依据。本研究利用普氏野马做为外群,构建国内外马品种的进化树,结果发现中国三个马品种在进化树上形成独立的分支。从遗传距离来看中国马品种和国外蒙古马比较近。这对理解中国三个马品种系统进化提供了分子基础。为进一步了解中国三个马品种和国外32个马品种之间的系统发生关系以及群体遗传结构情况同样进行主成分分析(PCA)和遗传结构分析,发现中国马品种和国外蒙古马及北西伯利亚(TUVA)马聚在一起属于古老的小型马品种。连锁不平衡分析结果也支持了中国马属于比较古老品种。为了解中国三个马品种遗传关系和遗传结构,进行主成分分析(PCA)和遗传结构分析。结果显示德保矮马与其它两个中国马品种(伊犁马和蒙古马)明显分离。说明德保矮马遗传背景与中国这两个马品种有比较大的差别。本研究在中国三个马品种全基因组上通过基于群体分化系数FST为基础的di分析,基于单倍型为基础的XP-EHH分析以及德保矮马与伊犁马体高全基因组关联分析(GWAS),在德保矮马基因组上分别检测到523个和505个显著的di和XP-EHH值的选择信号位点。结合两种方法筛选到了与体高显著相关的SNP位点进行关联分析。最终筛选了与体高显著相关的22个SNP位点。通过基因注释确认了两个候选基因HMGA2和TBX3基因与德保矮马体高显著相关。其中HMGA2基因是以前人和马研究中报道过的体高相关的基因,但是TBX3基因在国外马品种没有报道过。并且我们没有检测到德保矮马与国外矮马的基因交流情况。因此,我们认为德保矮马很可能经历了与国外矮马不同的独立的矮化驯化过程。说明德保矮马矮小性分子遗传机理不同于国外矮马品种。本研究将会为世界矮马矮小遗传机理解提供一些新的分子证据。最近研究表明寻找直接影响个体表型差异的DNA变异的研究中,仅关注单核苷酸多态性(SNPs)是不够的,在基因组中有重要功能意义的变异还有其他形式,如拷贝数变异(copy number variation,CNV)。我们在德保矮马以及其他国内两个品种马全基因组水平上进行单拷贝序列(CNV)多态性分析,发现只有在11号染色上包含生长发育相关基因的CNVR。这可能与我们检测CNV方法的单一性或者芯片密度的限制检测不到更多的CNVR的原因。将来更高密度芯片以及重测序技术的开发会进一步发现在德保矮马体高相关CNVR的可能。综上所述,本研究发现德保矮马体高相关正向选择位点与国外马品种选择位点有所不同。说明德保矮马矮小性可能存在独立的的分子遗传学机理。
[Abstract]:The dwarf horse of Debao is a kind of large and small horse variety in the mountainous area of Guangxi, and is one of the ancient dwarf horse resources in the world's short horse variety. Its short stature is the result of the directional cultivation and adaptation of the natural environment in the process of long-term domestication. The short stature is the dominant character to adapt to the consignment of the mountain road, so it is very important for the long-term cultivation and protection of the Dwara. At present, the research on the historical origin and the molecular genetic mechanism of the dwarf horse is relatively late, especially at the genomic level. In this study, the selection signal screening, single copy sequence (CNV) and high correlation analysis of three varieties (Debao Dwarf, Mongolian horse and Ili horse) with a large difference in Chinese body height were studied by using a high-density gene chip (Genetek Equine SNP 65K). At the same time, the data of 50 K gene chips of 729 individuals from 32 foreign horses were also integrated. The genetic mechanism of the dwarf horse and the foreign horse variety system is further confirmed, and the molecular genetic basis is provided for the genetic mechanism of the small characters. In this study, the wild Mustang was used as the outer group to construct the wild tree of the horse variety at home and abroad. The results showed that the three horses in China form an independent branch on the evolutionary tree. From the genetic distance, the Chinese horse variety is close to the other Mongolian horse. This provides a molecular basis for understanding the evolution of three Chinese species systems. The main component analysis (PCA) and the genetic structure analysis were also carried out in order to further understand the relationship between the three horses in China and the 32 horses in the country and the genetic structure of the population. It is found that the Chinese horse variety and the overseas Mongolian horse and the North Siberia (TUVA) horse come together to belong to the ancient small-scale horse variety. The results of the linkage disequilibrium analysis also support the Chinese horse as a relatively old variety. In order to understand the genetic relationship and the genetic structure of the three horses in China, the principal component analysis (PCA) and the genetic structure analysis were carried out. The results show that Debao Dwarf is obviously separated from the other two Chinese horse breeds (Ili horse and Mongolian horse). There is a great difference between the genetic background and the two kinds of horses in China. Based on the population differentiation factor (FST) based on the population differentiation factor (FST) based on the population differentiation factor (FST), this study is based on the haplotype-based XP-EHH analysis and the high-genome association analysis (GWAS) of the Debao dwarf horse and the Ili horse. The selection signal sites of 523 and 505 significant di and XP-EHH values were respectively detected on the genome of the Debao Dwarf horse. The association analysis of SNP sites associated with a significant body height was screened in combination with two methods. The 22 SNP sites associated with the body height were finally screened. Two candidate genes, such as HMGA2 and TBX3, were confirmed to be highly correlated with DPPH. The HMGA2 gene is the body-high-related gene reported in the previous human and horse studies, but the TBX3 gene has not been reported in the foreign horse variety. And we didn't have a sense of the gene exchange between Dbao Dwarf and the foreign dwarf. Therefore, we think that Debao Dwarf is very likely to experience a separate, dwarfed, acclimatization process that is different from that of a foreign dwarf. The genetic mechanism of dwarfed dwarf horse is different from that of foreign dwarf horse. The study will provide some new molecular evidence for the understanding of the world's dwarf genetic machine. Recent studies have shown that it is not sufficient to look for DNA variants that directly affect the individual phenotypic differences, and there are other forms, such as copy number variation (CNV), that are important in the genome. We carried out a single copy sequence (CNV) polymorphism analysis on both German and other domestic two breeds, and found that only CNVR with the development-related genes was included in the No.11 staining. This may not be the cause of more CNVR than we can detect the uniformity of the CNV method or the limitation of the chip density. The development of higher density chips and heavy sequencing techniques in the future will further identify the potential for high-related CNVR in Debao dwarfs. In conclusion, the present study found that the highly correlated forward selection site of Densin Dwarf is different from that of the foreign horse. It is suggested that there may be an independent molecular genetic mechanism in the dwarfism of Densin.
【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】：2015
【分类号】：S821

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