ArticleGenome research2011
Revealing the genetic structure of a trait by sequencing a population under selection.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
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Who cites it
153 citing papers in PubMed.
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- Discovery and validation of ASG1 as a novel determinant of NaCl tolerance in the yeast Saccharomyces cerevisiae through iterative crossing.G3 (Bethesda, Md.) · 2026Article
- Predicting natural variation in the yeast phenotypic landscape with machine learning.Molecular systems biology · 2025Article
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- A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection.bioRxiv : the preprint server for biology · 2024Article
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- Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network.EMBO reports · 2023Article
- Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation.Journal of molecular evolution · 2023Review
- Adaptive responses of yeast strains tolerant to acidic pH, acetate, and supraoptimal temperature.Applied microbiology and biotechnology · 2023Article
- A QTL on chromosome IV explains a natural variation of QR.pap final position inmicroPublication biology · 2023Article
- Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes.Molecular biology and evolution · 2022Article
- Bulk segregant linkage mapping for rodent and human malaria parasites.Parasitology international · 2022Review
- The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.Molecular biology and evolution · 2022Article
- Estimating the time since admixture from phased and unphased molecular data.Molecular ecology resources · 2022Article
93 more citing papers are in PubMed but not listed here.
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14 authors.
Funding
Abstract
One approach to understanding the genetic basis of traits is to study their pattern of inheritance among offspring of phenotypically different parents. Previously, such analysis has been limited by low mapping resolution, high labor costs, and large sample size requirements for detecting modest effects. Here, we present a novel approach to map trait loci using artificial selection. First, we generated populations of 10-100 million haploid and diploid segregants by crossing two budding yeast strains of different heat tolerance for up to 12 generations. We then subjected these large segregant pools to heat stress for up to 12 d, enriching for beneficial alleles. Finally, we sequenced total DNA from the pools before and during selection to measure the changes in parental allele frequency. We mapped 21 intervals with significant changes in genetic background in response to selection, which is several times more than found with traditional linkage methods. Nine of these regions contained two or fewer genes, yielding much higher resolution than previous genomic linkage studies. Multiple members of the RAS/cAMP signaling pathway were implicated, along with genes previously not annotated with heat stress response function. Surprisingly, at most selected loci, allele frequencies stopped changing before the end of the selection experiment, but alleles did not become fixed. Furthermore, we were able to detect the same set of trait loci in a population of diploid individuals with similar power and resolution, and observed primarily additive effects, similar to what is seen for complex trait genetics in other diploid organisms such as humans.
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