中国小家鼠Y染色体Sry基因遗传多样性分析
发布时间：2019-02-26 19:41
【摘要】：小家鼠(Mus musculus)属哺乳纲(Mammalia)啮齿目(Rodentia)、鼠科(Muridae)、小家鼠属(Mus),是全球分布的人类共栖种。小家鼠的实验室衍生品系作为重要的模式物种,被广泛应用于生物学和生物医学研究的各个领域。小家鼠和人类关系密切,其生物地理模式与遗传分化模式可能与人类的迁徙、贸易联系、文化交流、移民活动、古农业的发展等直接相关。中国疆域辽阔,地形复杂,全境都有小家鼠分布,但中国小家鼠群体遗传多样性,尤其是Y染色体遗传多样性缺乏系统研究。本工作首次以Y染色体上的Sry基因系统探究中国小家鼠父系遗传的生物地理分布及遗传进化格局。通过采集15个省23个地区的212个雄性小家鼠个体,并进行基因组DNA提取,Sry基因片段PCR进行扩增和序列测定,使用分子处理软件分析碱基组成、定义单倍型,进行多样性分析并利用单倍型构建NetWork网络图和贝叶斯系统发育树,从而系统地研究Sry基因的特点和父系遗传结构特征。结果显示扩增的Sry基因片段平均长856 bp,基因碱基的平均含量分别为:A27.5%;T 30.7%;G 22.5%;C 19.3%,AT含量58.2%,存在明显的AT偏好。该片段有73个多态位点,简约信息位点22个,基因多样性较低。核苷酸多样性(nucleotide diversity)平均为0.00356,各种群的核苷酸多样性值从0.00096(周口)到0.00657(南宁)。总的单倍型多样性hd(haplotype diversity)为0.729,9个种群hd值从0.249(上海)到0.833(南宁)之间。利用DAMBE软件共定义了28个单倍型,其中S1和S2为主频单倍型,16个地区的117个样品拥有S1单倍型,12个地区62个样品拥有S2单倍型,S1和S2单倍型分别占比50.5%和29.7%,其余26个单倍型只占19.8%。我们通过对各地区和组成单倍型序列的碱基组成进行对比,发现不同个体之间、不同单倍型之间碱基差异较小,并且遗传距离也较小。根据单倍型分析和核苷酸多样性分析确定Sry基因虽存在一定遗传多样性,但同时具有较高的保守性。通过构建单倍型网络关系图可知S1和S2位为中心单倍型,其它单倍型以S1和S2为中心发散分布。利用单倍型序列构建系统发育树表明中国境内小家鼠Sry没有明显支系,这与母系遗传的线粒体系统发育树分为2个支系不同,揭示父系遗传的Sry基因保守、进化缓慢、突变率较低,在近缘物种间分歧不大。本工作为我们进一步全面深入研究中国小家鼠的父系遗传特征及Sry基因演化特征奠定了基础。
[Abstract]:The (Mammalia) rodent of the genus (Mus musculus), (Mammalia), (Rodentia), (Muridae), (Mus), is a global human symbiotic species. Laboratory-derived strain of mice, as an important model species, has been widely used in various fields of biology and biomedicine research. The model of biogeography and genetic differentiation may be directly related to human migration, trade relations, cultural exchange, immigration activities and the development of ancient agriculture. The population genetic diversity of Chinese mice, especially Y chromosome, is lack of systematic study, because of its vast territory and complex terrain, and the distribution of domestic mice all over the country. For the first time, the Sry gene on Y chromosome was used to investigate the biogeographic distribution and genetic evolution pattern of Chinese mouse paternity. Two hundred and twelve male mouse individuals from 23 regions in 15 provinces were collected, and genomic DNA was extracted, Sry gene fragment PCR was amplified and sequenced, base composition was analyzed by molecular processing software and haplotype was defined. Diversity analysis was carried out and haplotypes were used to construct NetWork network map and Bayesian phylogenetic tree, so as to systematically study the characteristics of Sry gene and patrilineal genetic structure. The results showed that the average length of the amplified Sry gene was 856 bp, and the average content of the base was A27.5%, 30.7%, 22.5%, 19.3%, respectively, and the AT content was 58.2%. There was an obvious AT preference. There were 73 polymorphic sites, 22 reduced information sites and low gene diversity. The average (nucleotide diversity) of nucleotide diversity was 0.00356. The nucleotide diversity values of various groups ranged from 0.00096 (Zhoukou) to 0.00657 (Nanning). The total haplotype diversity hd (haplotype diversity) was 0.729, and the HD values of 9 populations ranged from 0.249 (Shanghai) to 0.833 (Nanning). A total of 28 haplotypes were defined by DAMBE software, among which S1 and S2 were dominant haplotypes, 117 samples from 16 regions had S1 haplotypes, and 62 samples from 12 regions had S2 haplotypes. S1 and S2 haplotypes accounted for 50.5% and 29.7% respectively, while the other 26 haplotypes only accounted for 19.8%. By comparing the base compositions of different regions and haplotypes, we found that the differences of bases and genetic distances between different individuals and different haplotypes were smaller. According to haplotype analysis and nucleotide diversity analysis, it was found that the Sry gene had some genetic diversity, but it was highly conservative at the same time. By constructing a haplotype network diagram, we can see that S1 and S2 are central haplotypes and other haplotypes are centered on S1 and S2. The phylogenetic tree constructed by haplotype sequence showed that there was no obvious clade of mouse Sry in China, which was different from that of mitochondrial phylogenetic tree inherited from maternal lineage. The results showed that the Sry gene of paternal inheritance was conserved and the evolution was slow. The mutation rate is low, and there is little divergence among relative species. This work lays a foundation for us to study the paternal genetic characteristics and Sry gene evolution of Chinese mice in an all-round way.
【学位授予单位】：鲁东大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q953
本文编号：2431089
[Abstract]:The (Mammalia) rodent of the genus (Mus musculus), (Mammalia), (Rodentia), (Muridae), (Mus), is a global human symbiotic species. Laboratory-derived strain of mice, as an important model species, has been widely used in various fields of biology and biomedicine research. The model of biogeography and genetic differentiation may be directly related to human migration, trade relations, cultural exchange, immigration activities and the development of ancient agriculture. The population genetic diversity of Chinese mice, especially Y chromosome, is lack of systematic study, because of its vast territory and complex terrain, and the distribution of domestic mice all over the country. For the first time, the Sry gene on Y chromosome was used to investigate the biogeographic distribution and genetic evolution pattern of Chinese mouse paternity. Two hundred and twelve male mouse individuals from 23 regions in 15 provinces were collected, and genomic DNA was extracted, Sry gene fragment PCR was amplified and sequenced, base composition was analyzed by molecular processing software and haplotype was defined. Diversity analysis was carried out and haplotypes were used to construct NetWork network map and Bayesian phylogenetic tree, so as to systematically study the characteristics of Sry gene and patrilineal genetic structure. The results showed that the average length of the amplified Sry gene was 856 bp, and the average content of the base was A27.5%, 30.7%, 22.5%, 19.3%, respectively, and the AT content was 58.2%. There was an obvious AT preference. There were 73 polymorphic sites, 22 reduced information sites and low gene diversity. The average (nucleotide diversity) of nucleotide diversity was 0.00356. The nucleotide diversity values of various groups ranged from 0.00096 (Zhoukou) to 0.00657 (Nanning). The total haplotype diversity hd (haplotype diversity) was 0.729, and the HD values of 9 populations ranged from 0.249 (Shanghai) to 0.833 (Nanning). A total of 28 haplotypes were defined by DAMBE software, among which S1 and S2 were dominant haplotypes, 117 samples from 16 regions had S1 haplotypes, and 62 samples from 12 regions had S2 haplotypes. S1 and S2 haplotypes accounted for 50.5% and 29.7% respectively, while the other 26 haplotypes only accounted for 19.8%. By comparing the base compositions of different regions and haplotypes, we found that the differences of bases and genetic distances between different individuals and different haplotypes were smaller. According to haplotype analysis and nucleotide diversity analysis, it was found that the Sry gene had some genetic diversity, but it was highly conservative at the same time. By constructing a haplotype network diagram, we can see that S1 and S2 are central haplotypes and other haplotypes are centered on S1 and S2. The phylogenetic tree constructed by haplotype sequence showed that there was no obvious clade of mouse Sry in China, which was different from that of mitochondrial phylogenetic tree inherited from maternal lineage. The results showed that the Sry gene of paternal inheritance was conserved and the evolution was slow. The mutation rate is low, and there is little divergence among relative species. This work lays a foundation for us to study the paternal genetic characteristics and Sry gene evolution of Chinese mice in an all-round way.
【学位授予单位】：鲁东大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q953
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1 王金鹏;中国小家鼠Y染色体Sry基因遗传多样性分析[D];鲁东大学;2017年
，本文编号：2431089
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