Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

IF 3.6 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Katy Paul, Gwendal Restoux, Florence Phocas
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引用次数: 0

Abstract

Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.
在全基因组范围内检测四个驯化虹鳟种群(Oncorhynchus mykiss)共有的正平衡选择特征
随着时间的推移,进化过程会在基因组上留下足迹。高同源区可能与有利等位基因的正向选择相对应,而杂合区的维持可能是由于平衡选择现象。我们分析了来自四个互不相连的国内虹鳟种群的 176 条鱼的数据,这些鱼是用高密度 Axiom Trout 基因分型 665K 单核苷酸多态性阵列进行基因分型的,其中 20 条来自美国,156 条来自三个法国品系。利用基于同源性和扩展单倍型同源性的方法,我们在这四个种群中检测到了选择的特征。在所有四个种群中,包括 253 个基因在内的九个基因组区域被确定为处于正选择状态,其中大部分位于 2 号染色体上,也有的位于 12、15、16 和 20 号染色体上。此外,四个种群还共有四个杂合区域,其中包含 29 个基因,这些基因可能处于平衡选择之下。它们分别位于 10、13 和 19 号染色体上。无论这些区域是同源还是异源,我们都在每个区域中检测到了几个在脊椎动物中高度保守的基因,这些基因在细胞和核组织、胚胎发育或免疫中起着关键作用。我们发现了与虹鳟健康有关的新候选基因,以及之前发现的17个正选择基因,其中10个在其他鱼类中(auts2、atp1b3、zp4、znf135、igf-1α、brd2、col9a2、mrap2、pbx1和emilin-3)。通过使用来自不同起源、互不相连的种群的材料,我们绘制出了这些虹鳟种群之间共享的正向选择特征的全基因组图谱,并确定了几个可能处于平衡选择下的区域。这些结果为今后研究驯化过程中遗传多样性和基因组进化的动态提供了宝贵的资源。
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来源期刊
Genetics Selection Evolution
Genetics Selection Evolution 生物-奶制品与动物科学
CiteScore
6.50
自引率
9.80%
发文量
74
审稿时长
1 months
期刊介绍: Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.
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