Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics
Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics
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DOI：
10.1093/molbev/msx151
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发表时间：
2017-10-01
影响因子：
10.7
通讯作者：
Zhang, Jianzhi
中科院分区：
文献类型：
--
作者：
Maclean, Calum J.;Metzger, Brian P. H.;Zhang, Jianzhi
芽殖酵母酿酒酵母是分子和细胞生物学中研究最深入的真核生物，但由于群体结构强大而复杂，其在理解自然群体表型变异遗传基础方面的效用受到低效关联图谱的限制。为了克服这一挑战，我们生成了 85 个菌株的基因组序列，并对总共 190 个不同菌株进行了全面的群体基因组调查。我们确定了染色体之间群体结构的显着差异，并确定了参考基因组中缺少的 181 个基因。许多这些非参考基因都得到了表达，我们在功能上证实了其中两个基因增强了抗真菌药物的耐药性。接下来，我们使用每个菌株中存在的独特 DNA 条形码，同时测量了 4,500 多个实验室菌株（每个菌株都缺乏非必需基因）和跨多个环境的 81 个天然菌株的生长率。通过将从基因缺失菌株获得的全基因组反向遗传信息与自然菌株的全基因组关联分析相结合，我们确定了与自然种群适应性变异相关的基因组区域。为了通过实验验证这些关联的子集，我们使用了相互半合性测试，发现虽然组合的正向和反向遗传方法可以识别单个因果基因，但自然遗传变异的表型后果通常遵循复杂的模式。所提供的资源和方法概述了酵母关联图谱的有效且可靠的途径，并显着增强了其作为理解自然群体表型变异和进化的遗传机制的模型的价值。
The budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of phenotypic variation in natural populations is limited by inefficient association mapping due to strong and complex population structure. To overcome this challenge, we generated genome sequences for 85 strains and performed a comprehensive population genomic survey of a total of 190 diverse strains. We identified considerable variation in population structure among chromosomes and identified 181 genes that are absent from the reference genome. Many of these nonreference genes are expressed and we functionally confirmed that two of these genes confer increased resistance to antifungals. Next, we simultaneously measured the growth rates of over 4,500 laboratory strains, each of which lacks a nonessential gene, and 81 natural strains across multiple environments using unique DNA barcode present in each strain. By combining the genome-wide reverse genetic information gained from the gene deletion strains with a genome-wide association analysis from the natural strains, we identified genomic regions associated with fitness variation in natural populations. To experimentally validate a subset of these associations, we used reciprocal hemizygosity tests, finding that while the combined forward and reverse genetic approaches can identify a single causal gene, the phenotypic consequences of natural genetic variation often follow a complicated pattern. The resources and approach provided outline an efficient and reliable route to association mapping in yeast and significantly enhance its value as a model for understanding the genetic mechanisms underlying phenotypic variation and evolution in natural populations.