Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait

Genetics: A Periodical Record of Investigations Bearing on Heredity and Variation

Amy Shen^1¹  Alessandro L. V. Coradini^2²  Jonathan T. Lee^1³ 

[1] Laboratory of Genomics and Bioenergy, Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, São Paulo 13083-970, Brazil^2;Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910;Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910^1

关键词: cryptic genetic variation;    epistasis;    genotype–environment interaction;    complex traits;    genetic architecture;    genetic background effects;   

DOI  :  10.1534/genetics.119.301907

学科分类：医学（综合）

来源: Genetics Society of America

【 摘 要 】

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic genetic variation underlying a Saccharomyces cerevisiae colony phenotype that is typically suppressed in a cross of the laboratory strain BY4716 (BY) and a derivative of the clinical isolate 322134S (3S). To do this, we comprehensively dissect the trait’s genetic basis in the BYx3S cross in the presence of three different genetic perturbations that enable its expression. This allows us to detect and compare the specific loci that interact with each perturbation to produce the trait. In total, we identify 21 loci, all but one of which interact with just a subset of the perturbations. Beyond impacting which loci contribute to the trait, the genetic perturbations also alter the extent of additivity, epistasis, and genotype–environment interaction among the detected loci. Additionally, we show that the single locus interacting with all three perturbations corresponds to the coding region of the cell surface gene FLO11 . While nearly all of the other remaining loci influence FLO11 transcription in cis or trans , the perturbations tend to interact with loci in different pathways and subpathways. Our work shows how layers of cryptic genetic variation can influence complex traits. Here, these layers mainly represent different regulatory inputs into the transcription of a single key gene.

【 授权许可】

CC BY