Abstract
Quantitative trait locus (QTL) mapping by pooled-segregant whole-genome sequencing in yeast is a robust methodology for the simultaneous identification of superior genes involved in polygenic traits (e.g., high ethanol tolerance). By crossing two haploid strains with opposite phenotypes, being one of interest, the resulting diploid is sporulated, the meiotic segregants phenotyped, and a pool of selected segregants with the phenotype of interest assembled. The genotyping by pooled-segregant sequencing constitutes a fast and reliable methodology to map all QTL defining the trait of interest. The QTLs can be further analyzed by reciprocal hemizygosity analysis to identify the causative superior alleles that can subsequently be used for yeast strain improvement by targeted genetic engineering.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326–330
Deutschbauer AM, Davis RW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 37: 1333–1340
Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR et al (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294(5547):1719–1723
Winzeler EA et al (1998) Direct allelic variation scanning of the yeast genome. Science 281(5380):1194–1197
Kwok P-Y (2002) SNP genotyping with fluorescence polarization detection. Hum Mutat 19(4):315–323
Lechner D, Lathrop GM, Gut IG (2002) Large-scale genotyping by mass spectrometry: experience, advances and obstacles. Curr Opin Chem Biol 6(1):31–38
Hardenbol P, Banér J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H et al (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 21(6):673–678
Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464(7291):1039–1042
Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M (2011) Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 21:1131–1138
Swinnen S, Schaerlaekens T, Pais T, Claesen J, Hubmann G, Yang Y, Demeke M, Foulquie-Moreno M, Goovaerts A, Souvereyns K, Clement L, Dumortier F, Thevelein JM (2012) Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. Genome Res. doi:10.1101/gr.131698.111
Popolo L, Vanoni M, Alberghina L (1982) Control of the yeast cell cycle by protein synthesis. Exp Cell Res 142:69–78
Sherman F, Hicks J (1991) Micromanipulation and dissection of asci. Methods Enzymol 194: 21–37
Huxley C, Green ED, Dunham I (1990) Rapid assessment of S. cerevisiae mating type by PCR. Trends Genet 6:236
Duitama J et al (2014) An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Res. doi: 10.1093/nar/gkt1381
Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165–1188
Gietz RD, Schiestl RH, Willems AR, Woods RA (1995) Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast 11:355–360
Douglas AT, Fred W (2008) Growth and manipulation of yeast. Curr Protoc Mol Biol 82:13.2.1–13.2.12
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Pais, T.M., Foulquié-Moreno, M.R., Thevelein, J.M. (2014). QTL Mapping by Pooled-Segregant Whole-Genome Sequencing in Yeast. In: Mapelli, V. (eds) Yeast Metabolic Engineering. Methods in Molecular Biology, vol 1152. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0563-8_15
Download citation
DOI: https://doi.org/10.1007/978-1-4939-0563-8_15
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-0562-1
Online ISBN: 978-1-4939-0563-8
eBook Packages: Springer Protocols