Maclean CJ~Zhang J, 2017

Pubmed ID 28472365
Title Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics.
Authors Calum J Maclean, Brian P H Metzger, Jian-Rong Yang, Wei-Chin Ho, Bryan Moyers, Jianzhi Zhang
Abstract 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.
Citation Mol Biol Evol 2017; 34:2486-2502

Datasets

Download the list of datasets
Paper Phenotype Condition Medium Collection Tested mutants Data Details
Maclean CJ~Zhang J, 2017 growth (pooled culture) temperature [40ÂșC] YPD hom 4,481 Quantitative
Maclean CJ~Zhang J, 2017 growth (pooled culture) sodium chloride [1.25 M], sodium chloride [1.25 M] YPD hom 4,481 Quantitative
Maclean CJ~Zhang J, 2017 growth (pooled culture) ethanol [7%] YPD hom 4,481 Quantitative
Maclean CJ~Zhang J, 2017 growth (pooled culture) paraquat [4 mM] YPD hom 4,481 Quantitative
Maclean CJ~Zhang J, 2017 growth (pooled culture) hydrogen peroxide [3 mM] YPD hom 4,481 Quantitative
Maclean CJ~Zhang J, 2017 growth (pooled culture) cobalt chloride [1 mM] YPD hom 4,481 Quantitative

Curation history

Tested strains

March 24, 2020 Ready to load.
April 17, 2020 Loaded.

Data

March 24, 2020 Ready to load.
April 17, 2020 Loaded.