Chen Shi-An A, Kern Alexander F, Ang Roy Moh Lik, Xie Yihua, Fraser Hunter B
Department of Biology, Stanford University, Stanford, CA 94305, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Cell Genom. 2023 Feb 28;3(4):100273. doi: 10.1016/j.xgen.2023.100273. eCollection 2023 Apr 12.
Gene-by-environment (GxE) interactions, in which a genetic variant's phenotypic effect is condition specific, are fundamental for understanding fitness landscapes and evolution but have been difficult to identify at the single-nucleotide level. Although many condition-specific quantitative trait loci (QTLs) have been mapped, these typically contain numerous inconsequential variants in linkage, precluding understanding of the causal GxE variants. Here, we introduce BARcoded Cas9 retron precise parallel editing via homology (CRISPEY-BAR), a high-throughput precision genome editing strategy, and use it to map GxE interactions of naturally occurring genetic polymorphisms impacting yeast growth. We identified hundreds of GxE variants within condition-specific QTLs, revealing unexpected genetic complexity. Moreover, we found that 93.7% of non-neutral natural variants within ergosterol biosynthesis pathway genes showed GxE interactions, including many impacting antifungal drug resistance through diverse molecular mechanisms. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions while also demonstrating massively parallel genome editing as an effective means for investigating this complexity.
基因与环境（GxE）相互作用是指基因变异的表型效应具有条件特异性，这对于理解适应度景观和进化至关重要，但在单核苷酸水平上很难识别。尽管已经定位了许多条件特异性数量性状基因座（QTL），但这些基因座通常在连锁中包含大量无关紧要的变异，从而无法理解因果GxE变异。在这里，我们引入了通过同源性进行条形码Cas9逆转录子精确平行编辑（CRISPEY-BAR），这是一种高通量精确基因组编辑策略，并使用它来绘制影响酵母生长的自然发生的遗传多态性的GxE相互作用图谱。我们在条件特异性QTL中鉴定出数百个GxE变异，揭示了意想不到的遗传复杂性。此外，我们发现麦角固醇生物合成途径基因中93.7%的非中性自然变异显示出GxE相互作用，包括许多通过不同分子机制影响抗真菌药物抗性的变异。总之，我们的结果表明存在一个极其复杂、依赖于背景的适应度景观，其特征是普遍存在的GxE相互作用，同时也证明了大规模平行基因组编辑是研究这种复杂性的有效手段。
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