Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis
Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis
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DOI：
10.1371/journal.pcbi.1008082
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发表时间：
2020-02
影响因子：
4.3
通讯作者：
G. Schweizer;A. Wagner
中科院分区：
文献类型：
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作者：
G. Schweizer;A. Wagner
我们研究了模式植物拟南芥中80个数量表型的基因型-表型图谱，通过将影响每个表型的基因型表示为基因型网络。在这样的网络中，每个顶点或节点对应于个体在影响给定表型的所有那些基因组基因座处的基因型。如果相关的基因型恰好在一个核苷酸上不同，则两个顶点由边连接。我们分析的80个基因型网络是基于199个A. thaliana加入它们形成连接图，其拓扑结构在表型之间有很大差异。我们把我们的分析集中在上位性（突变之间的非加性相互作用）的发生率上，因为上位性的高发生率可以降低进化路径向高或低表型值的可及性。我们发现上位性相互作用在67个表型，在51个表型每对突变体的相互作用是上位性的。此外，我们发现表型特异性的差异，可访问的突变路径的最大表型值的分数。然而，尽管上位性影响最大表型值的可及性，但我们分析的表型的基因型和表型变化之间的关系足够平滑，即使在上位性普遍存在的情况下，大多数表型仍然可以获得一些进化路径。我们使用的基因型网络表示可以补充现有的方法来理解许多不同生物体中多基因性状的遗传结构。基因型变化与表型变化的关系是进化生物学中的一个基本问题。基因型和表型变化之间的平稳关系有利于表型进化，而崎岖的阻碍它，因为崎岖景观上的进化变化不允许表型值单调增加或减少。我们使用的数据从多个全基因组关联研究的80个不同的表型在塔勒水芹拟南芥构建80个基因型表型图这些表型。我们对每个图使用网络表示，其中一个顶点对应于一个基因型，如果两个顶点在单个核苷酸上不同，则它们是连接的。我们研究了突变之间的非加性相互作用的发生率，作为容易达到这些图的极端表型值的代理。这种发生率在表型之间变化很大，但即使在最高的地方，绝大多数表型都存在一些通往高或低表型值的单调途径，因此潜在的表型可以进行适应性进化。
We study the genotype-phenotype maps of 80 quantitative phenotypes in the model plant Arabidopsis thaliana, by representing the genotypes affecting each phenotype as a genotype network. In such a network, each vertex or node corresponds to an individual’s genotype at all those genomic loci that affect a given phenotype. Two vertices are connected by an edge if the associated genotypes differ in exactly one nucleotide. The 80 genotype networks we analyze are based on data from genome-wide association studies of 199 A. thaliana accessions. They form connected graphs whose topography differs substantially among phenotypes. We focus our analysis on the incidence of epistasis (non-additive interactions among mutations) because a high incidence of epistasis can reduce the accessibility of evolutionary paths towards high or low phenotypic values. We find epistatic interactions in 67 phenotypes, and in 51 phenotypes every pairwise mutant interaction is epistatic. Moreover, we find phenotype-specific differences in the fraction of accessible mutational paths to maximum phenotypic values. However, even though epistasis affects the accessibility of maximum phenotypic values, the relationships between genotypic and phenotypic change of our analyzed phenotypes are sufficiently smooth that some evolutionary paths remain accessible for most phenotypes, even where epistasis is pervasive. The genotype network representation we use can complement existing approaches to understand the genetic architecture of polygenic traits in many different organisms. Author summary How genotypic change relates to phenotypic change is a fundamental problem in evolutionary biology. A smooth relationship between genotypic and phenotypic change facilitates phenotypic evolution, whereas a rugged one hampers it, because evolutionary change on a rugged landscape does not allow a monotonic increase or decrease in phenotypic value. We use data from multiple genome-wide association studies for 80 different phenotypes in the thale cress Arabidopsis thaliana to construct 80 genotype-phenotype maps for these phenotypes. We use a network representation for each map, where a vertex corresponds to a genotype, and where two vertices are connected if they differ in a single nucleotide. We study the incidence of non-additive interactions between mutations as a proxy for the ease to reach extreme phenotypic values of these maps. This incidence varies greatly among phenotypes, but even where it is highest, some monotonic pathways to high or low phenotypic values exist for the vast majority of phenotypes, such that the underlying phenotypes are accessible to adaptive evolution.