吉钰,陈再忠,温彬,等.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[J].广东农业科学,2023,(6-7):- |
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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 |
Genetic diversity analysis of wild and artificially bred blue populations in discus fish |
投稿时间:2023-03-23 修订日期:2023-11-06 |
DOI: |
中文关键词: 七彩神仙鱼 群体遗传学 遗传多样性 单核苷酸多态性 全基因组重测序 选择消除分析 |
英文关键词: discus fish population genetics genetic diversity Single Nucleotide Polymorphism whole genome re-sequencing selective sweep analysis |
基金项目:上海市自然科学基金(20ZR1423600) |
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中文摘要: |
【目的】研究七彩神仙鱼(Symphysodon spp.)的遗传多样性,分析野生型和两种人工选育型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。【方法】对野生型(WF)、全蓝型(BF)和白化蓝型(ABF)群体中的9个、8个和10个个体进行了全基因组重测序,获得单核苷酸多态性(SNP)位点,由此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,结合聚合酶链式反应(PCR)和Sanger测序,验证了候选SNP。【结果】3个群体中共鉴定出1360293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都显示,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)和核苷酸多态性(Pi)进行的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了13个和9个候选SNP。【结论】3个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,蓝色七彩神仙鱼尤其是其中的白化类型,可以作为研究研究体色变异的良好模型。 |
英文摘要: |
【Objective】To investigate the genetic diversity of discus fish (Symphysodon spp.), analyze the kinship and genetic differences of a wild population and two artificially bred blue populations, and obtain candidate genomic regions and loci associated with coloration.【Method】A 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. Candidate SNPs were validated by combining SNP annotation and mutation rates, as well as polymerase chain reaction (PCR) and Sanger sequencing.【Result】A total of 1,360,293 SNPs are identified across the three populations. Genetic diversity, as measured by PIC, Pi, Ho, and He, exhibits a decreasing trend from the wild 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 from 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. 13 and 9 candidate SNPs are identified in the solid blue and albino blue populations, respectively.【Conclusion】The genetic diversity of the three groups was relatively low, and the genetic relationships were consistent with the history of artificial breeding. The blue discus fish, especially the albino variant, can serve as a good model for studying color variation. |
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