An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae

Wilkening S, Lin G, Fritsch ES, Tekkedil MM, Anders S, Kuehn R, Michelle Nguyen , Aiyar RS, Proctor M, Sakhanenko NA, Galas DJ, Gagneur J, Deutschbauer A, Steinmetz LM (2014)

Publication Type: Journal article

Publication year: 2014

Journal

Genetics Genetics Society of America

Book Volume: 196

Pages Range: 853-865

Journal Issue: 3

DOI: 10.1534/genetics.113.160291

Abstract

Dissecting the molecular basis of quantitative traits is a significant challenge and is essential for understanding complex diseases. Even in model organisms, precisely determining causative genes and their interactions has remained elusive, due in part to difficulty in narrowing intervals to single genes and in detecting epistasis or linked quantitative trait loci. These difficulties are exacerbated by limitations in experimental design, such as low numbers of analyzed individuals or of polymorphisms between parental genomes. We address these challenges by applying three independent high-throughput approaches for QTL mapping to map the genetic variants underlying 11 phenotypes in two genetically distant Saccharomyces cerevisiae strains, namely (1) individual analysis of >700 meiotic segregants, (2) bulk segregant analysis, and (3) reciprocal hemizygosity scanning, a new genome-wide method that we developed. We reveal differences in the performance of each approach and, by combining them, identify eight polymorphic genes that affect eight different phenotypes: colony shape, flocculation, growth on two nonfermentable carbon sources, and resistance to two drugs, salt, and high temperature. Our results demonstrate the power of individual segregant analysis to dissect QTL and address the underestimated contribution of interactions between variants. We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies. © 2014 by the Genetics Society of America.

Involved external institutions

European Molecular Biology Laboratory (EMBL) DE Germany (DE) Stanford Genome Technology Center (SGTC) US United States (USA) (US) Pacific Northwest Research Institute (PNRI) US United States (USA) (US) University of California, Berkeley US United States (USA) (US)

How to cite

APA:

Wilkening, S., Lin, G., Fritsch, E.S., Tekkedil, M.M., Anders, S., Kuehn, R.,... Steinmetz, L.M. (2014). An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae. Genetics, 196(3), 853-865. https://doi.org/10.1534/genetics.113.160291

MLA:

Wilkening, Stefan, et al. "An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae." Genetics 196.3 (2014): 853-865.

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