野生型和人工选育全蓝型七彩神仙鱼群体的遗传多样性分析
S931.5%S917.4; [目的]研究七彩神仙鱼(Symphysodon aequifasciatus)的遗传多样性,分析野生型和两种人工选育蓝色群体的亲缘关系和遗传差异,获得与体色形成相关的候选基因组区域及位点,同时为七彩神仙鱼分类系统的制订提供参考.[方法]对9尾野生型(WF)、8尾全蓝型(BF)和10尾白化蓝型(ABF)七彩神仙鱼个体进行全基因组重测序,获得单核苷酸多态性(SNP)位点,计算群体遗传多样性指标,分析群体遗传结构,进行群体间的选择消除分析.考虑SNP注释和突变率,结合PCR和Sanger测序,验证候选SNP.[结果]在3个七彩神仙鱼群体中共鉴定出1 360 293个SN...
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| Published in | 广东农业科学 Vol. 51; no. 4; pp. 65 - 78 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | Chinese |
| Published |
上海海洋大学水产与生命学院/农业农村部淡水水产种质资源重点实验室/水产种质资源发掘与利用教育部重点实验室/上海水产养殖工程技术研究中心/水产科学国家级实验教学示范中心,上海 201306
01.04.2024
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1004-874X |
| DOI | 10.16768/j.issn.1004-874X.2024.04.006 |
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| Abstract | S931.5%S917.4; [目的]研究七彩神仙鱼(Symphysodon aequifasciatus)的遗传多样性,分析野生型和两种人工选育蓝色群体的亲缘关系和遗传差异,获得与体色形成相关的候选基因组区域及位点,同时为七彩神仙鱼分类系统的制订提供参考.[方法]对9尾野生型(WF)、8尾全蓝型(BF)和10尾白化蓝型(ABF)七彩神仙鱼个体进行全基因组重测序,获得单核苷酸多态性(SNP)位点,计算群体遗传多样性指标,分析群体遗传结构,进行群体间的选择消除分析.考虑SNP注释和突变率,结合PCR和Sanger测序,验证候选SNP.[结果]在3个七彩神仙鱼群体中共鉴定出1 360 293个SNP,PIC、Pi、Ho、He表明,野生型、全蓝型和白化蓝型的遗传多样性递减,选育群体的杂合度很低.系统发育进化树、群体结构分析和多态性位点主成分分析结果均显示,3个群体之间相互独立,且群体内部聚集明显.连锁不平衡衰减分析结果表明,白化蓝型群体承受着巨大的选择压力,其次是全蓝型群体.基于群体分化指数FST和Pi进行选择消除分析,结果表明,全蓝型群体的第3、12、13、18、20号染色体和白化蓝型群体的第1、16、18、19号染色体的较大区域内存在强烈的选择信号.在全蓝型群体和白化蓝型群体中分别鉴定出13个和9个候选SNP.[结论]3个七彩神仙鱼群体的遗传多样性较低,遗传关系显示出与人工选育进程的一致性.USP43、FGFR2、DENND4、MLL1基因可能与七彩神仙鱼体色形成密切相关. |
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| AbstractList | S931.5%S917.4; [目的]研究七彩神仙鱼(Symphysodon aequifasciatus)的遗传多样性,分析野生型和两种人工选育蓝色群体的亲缘关系和遗传差异,获得与体色形成相关的候选基因组区域及位点,同时为七彩神仙鱼分类系统的制订提供参考.[方法]对9尾野生型(WF)、8尾全蓝型(BF)和10尾白化蓝型(ABF)七彩神仙鱼个体进行全基因组重测序,获得单核苷酸多态性(SNP)位点,计算群体遗传多样性指标,分析群体遗传结构,进行群体间的选择消除分析.考虑SNP注释和突变率,结合PCR和Sanger测序,验证候选SNP.[结果]在3个七彩神仙鱼群体中共鉴定出1 360 293个SNP,PIC、Pi、Ho、He表明,野生型、全蓝型和白化蓝型的遗传多样性递减,选育群体的杂合度很低.系统发育进化树、群体结构分析和多态性位点主成分分析结果均显示,3个群体之间相互独立,且群体内部聚集明显.连锁不平衡衰减分析结果表明,白化蓝型群体承受着巨大的选择压力,其次是全蓝型群体.基于群体分化指数FST和Pi进行选择消除分析,结果表明,全蓝型群体的第3、12、13、18、20号染色体和白化蓝型群体的第1、16、18、19号染色体的较大区域内存在强烈的选择信号.在全蓝型群体和白化蓝型群体中分别鉴定出13个和9个候选SNP.[结论]3个七彩神仙鱼群体的遗传多样性较低,遗传关系显示出与人工选育进程的一致性.USP43、FGFR2、DENND4、MLL1基因可能与七彩神仙鱼体色形成密切相关. |
| Abstract_FL | [Objective]The study was conducted to investigate the genetic diversity of Symphysodon aequifasciatus,analyze the kinship and the genetic differences of a wild population and two artificially bred blue populations,identify candidate genomic regions and loci associated with body color,and provide references for the formulation of classification system of discus fish.[Method]Whole-genome resequencing was conducted on 9 individuals from the wild population(WF),8 individuals from the solid blue population(BF)and 10 individuals from the albino blue population(ABF),respectively.Single nucleotide polymorphism(SNP)loci were obtained to calculate population genetic diversity indices,analyze population genetic structure,and perform selective sweep analysis between populations.The candidate SNPs were validated by considering SNP annotation and mutation rates combined with PCR and Sanger sequencing.[Result]A total of 1 360 293 SNPs are identified among the 3 Symphysodon aequifasciatus populations.Genetic diversity,as measured by PIC,Pi,Ho,and He,indicates a decreasing trend from the wild population to the solid blue and albino blue populations,with low heterozygosity in the selected populations.Phylogenetic tree,population structure analysis,and principal component analysis of polymorphic loci all indicate that the three populations are independent of each other and cluster within themselves.Linkage disequilibrium decay analysis indicates that the albino blue population is under significant selection pressure,followed by the solid blue population.The result of population selective sweep based on the population differentiation index(FST)and nucleotide polymorphism(Pi)reveals strong selection signals in large regions of chromosomes 3,12,13,18,and 20 in the solid blue population and chromosomes 1,16,18,and 19 in the albino blue population.Thirteen and nine candidate SNPs are identified in the solid blue and albino blue populations,respectively.[Conclusion]The genetic diversity of the 3 Symphysodon aequifasciatus populations is relatively low,and the genetic relationships are consistent with the process of artificial breeding.USP43,FGFR2,DENND4,and MLL1 genes may be closely related to the body color formation of Symphysodon aequifasciatus. |
| Author | 陈再忠 吉钰 温彬 高建忠 |
| AuthorAffiliation | 上海海洋大学水产与生命学院/农业农村部淡水水产种质资源重点实验室/水产种质资源发掘与利用教育部重点实验室/上海水产养殖工程技术研究中心/水产科学国家级实验教学示范中心,上海 201306 |
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| Author_FL | WEN Bin JI Yu GAO Jianzhong CHEN Zaizhong |
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| DocumentTitle_FL | Genetic Diversity Analysis of Wild and Artificially Bred Blue Populations in Symphysodon aequifasciatus |
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| Keywords | population genetics genetic diversity 遗传多样性 选择消除分析 single nucleotide polymorphism(SNP) 群体遗传学 单核苷酸多态性(SNP) Symphysodon aequifasciatus selective sweep analysis 七彩神仙鱼 |
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| Publisher | 上海海洋大学水产与生命学院/农业农村部淡水水产种质资源重点实验室/水产种质资源发掘与利用教育部重点实验室/上海水产养殖工程技术研究中心/水产科学国家级实验教学示范中心,上海 201306 |
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| Title | 野生型和人工选育全蓝型七彩神仙鱼群体的遗传多样性分析 |
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