Torija MJ, Rozés N, Poblet M, Guillamón JM, Mas A. Effects of fermentation temperature on the strain population of Saccharomyces cerevisiae. Int J Food Microbiol. 2003;80:47–53.
Beltran G, Torija MJ, Novo M, Ferrer NN, Poblet M, Guillamón JM, et al. Analysis of yeast populations during alcoholic fermentation: a six year follow-up study. Syst Appl Microbiol. 2002;25:287–93.
Salvadó Z, Arroyo-López FN, Guillamón JM, Salazar G, Querol A, Barrio E, et al. Temperature adaptation Markedly Determines evolution within the genus Saccharomyces. Appl Environ Microbiol. 2011;77:2292–302.
Bisson LF. Stuck and sluggish fermentations. Am J Enol Vitic. 1999;50:107–19.
Infante JJ, Dombek KM, Rebordinos L, Cantoral JM, Young ET. Genome-wide amplifications caused by chromosomal rearrangements play a major role in the adaptive evolution of natural yeast. Genetics. 2003;165:1745–59.
Marullo P, Bely M, Masneuf-Pomarede I, Aigle M, Dubourdieu D. Inheritable nature of enological quantitative traits is demonstrated by meiotic segregation of industrial wine yeast strains. FEMS Yeast Res. 2004;4:711–9.
Mackay TFC, Stone EA, Ayroles JF. The genetics of quantitative traits: challenges and prospects. Nat Rev Genet. 2009;10:565–77.
Parts L. Genome-wide mapping of cellular traits using yeast. Yeast. 2014;31:197–205.
Yang Y, Foulquié-Moreno MR, Clement L, Erdei É, Tanghe A, Schaerlaekens K, et al. QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing. PLoS Genet. 2013;9:e1003693.
Sinha H, David L, Pascon RC, Clauder-Münster S, Krishnakumar S, Nguyen M, et al. Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics. 2008;180:1661–70.
Shapira R, David L. Genes with a combination of over-dominant and epistatic effects underlie heterosis in growth of Saccharomyces cerevisiae at high temperature. Front Genet. 2016;7:72.
Ben-Ari G, Zenvirth D, Sherman A, David L, Klutstein M, Lavi U, et al. Four linked genes participate in controlling sporulation efficiency in budding yeast. PLoS Genet. 2006;2:1815–23.
Deutschbauer AM, Davis RW. Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet. 2005;37:1333–40.
Ehrenreich IM, Gerke JP, Kruglyak L. Genetic dissection of complex traits in yeast: Insights from studies of gene expression and other phenotypes in the BYxRM cross. Cold Spring Harb Symp Quant Biol. 2009;74:145–53.
Katou T, Namise M, Kitagaki H, Akao T, Shimoi H. QTL mapping of sake brewing characteristics of yeast. J Biosci Bioeng. 2009;107:383–93.
Nogami S, Ohya Y, Yvert G. Genetic complexity and quantitative trait loci mapping of yeast morphological traits. PLoS Genet. 2007;3:0305–18.
Kim HS, Fay JC. Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compounds. Proc Natl Acad Sci U S A. 2007;104:19387–91.
Voordeckers K, Kominek J, Das A, Espinosa-Cantú A, De Maeyer D, Arslan A, et al. Adaptation to high ethanol reveals complex evolutionary pathways. PLoS Genet. 2015;11:e1005635.
Greetham D, Wimalasena TT, Leung K, Marvin ME, Chandelia Y, Hart AJ, et al. The genetic basis of variation in clean lineages of Saccharomyces cerevisiae in response to stresses encountered during bioethanol fermentations. PLoS One. 2014;9:e103233.
Albert FW, Treusch S, Shockley AH, Bloom JS, Kruglyak L. Genetics of single-cell protein abundance variation in large yeast populations. Nature. 2014;506:1–19.
Parts L, Liu Y-C, Tekkedil MM, Steinmetz LM, Caudy AA, Fraser AG, et al. Heritability and genetic basis of protein level variation in an outbred population. Genome Res. 2014;24:1363–70.
Brauer MJ, Christianson CM, Pai DA, Dunham MJ. Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics. 2006;173:1813–6.
Li J, Wang L, Wu X, Fang O, Wang L, Lu C, et al. Polygenic molecular architecture underlying non-sexual cell aggregation in budding yeast. DNA Res. 2013;20:55–66.
Marullo P, Bely M, Masneuf-Pomarède I, Pons M, Aigle M, Dubourdieu D. Breeding strategies for combining fermentative qualities and reducing off-flavor production in a wine yeast model. FEMS Yeast Res. 2006;6:268–79.
Ambroset C, Petit M, Brion C, Sanchez I, Delobel P, Guérin C, et al. Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. G3Genes|Genomes|Genetics. 2011;1:263–81.
Salinas F, Cubillos FA, Soto D, Garcia V, Bergström A, Warringer J, et al. The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae. PLoS One. 2012;7:e49640.
García-Ríos E, López-Malo M, Guillamón JM. Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations. BMC Genomics. 2014;15:1059.
Liti G, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, et al. Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast. PLoS Genet. 2009;5:e1000659.
Ramazzotti M, Berná L, Stefanini I, Cavalieri D. A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains. Nucleic Acids Res. 2012;40:3834–48.
Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, et al. Population genomics of domestic and wild yeasts. Nature. 2009;458:337–41.
Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, et al. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol. 2014;31:872–88.
Liti G, Louis EJ. Advances in quantitative trait analysis in yeast. PLoS Genet. 2012;8:e1002912.
Naithani S, Saracco SA, Butler CA, Fox TD. Interactions among COX1, COX2, and COX3 mRNA-specific translational activator proteins on the inner surface of the mitochondrial inner membrane of Saccharomyces cerevisiae. Mol Biol Cell. 2003;14:324–33.
Ashbysb MN, Kutsunais SY, Ackermany S, Tzagoloffll A, Edwards PA. COQ2 is a candidate for the structural gene encoding puru-hydroxybenzoate: polyprenyltransferase. J Biol Chem. 1992;267:4128–36.
Kim HS, Huh J, Riles L, Reyes A, Fay JC. A noncomplementation screen for quantitative trait alleles in Saccharomyces cerevisiae. G3 (Bethesda). 2012;2:753–60.
Lendenmann MH, Croll D, Palma-Guerrero J, Stewart EL, McDonald BA. QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici. Heredity (Edinb). 2016;116:384–94.
Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, et al. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res. 2011;21:1131–8.
Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, et al. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature. 2010;15:1030–42.
Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, et al. Assessing the complex architecture of polygenic traits in diverged yeast populations. Mol Ecol. 2011;20:1401–13.
Ames RM, Rash BM, Hentges KE, Robertson DL, Delneri D, Lovell SC. Gene duplication and environmental adaptation within yeast populations. Genome Biol Evol. 2010;2:591–601.
Brown CA, Murray AW, Verstrepen KJ. Rapid expansion and functional divergence of subtelomeric gene families in yeasts. Curr Biol. 2010;20:895–903.
Grant CM, MacIver FH, Dawes IW. Glutathione is an essential metabolite required for resistance to oxidative stress in the yeast Saccharomyces cerevisiae. FEBS Lett. 1997;29:511–5.
García-Ríos E, Ramos-Alonso L, Guillamón JM. Correlation between low temperature adaptation and oxidative stress in Saccharomyces cerevisiae. Front Microbiol. 2016;7:1–11.
Beltran G, Novo M, Leberre V, Sokol S, Labourdette D, Guillamón JM, et al. Integration of transcriptomic and metabolic analyses for understanding the global responses of low-temperature winemaking fermentations. FEMS Yeast Res. 2006;6:1167–83.
Redón M, Guillamón JM, Mas A, Rozés N. Effect of growth temperature on yeast lipid composition and alcoholic fermentation at low temperature. Eur Food Res Technol. 2011;232:517–27.
Tronchoni J, Rozès N, Querol A, Guillamón JM. Lipid composition of wine strains of Saccharomyces kudriavzevii and Saccharomyces cerevisiae grown at low temperature. Int J Food Microbiol. 2012;155:191–8.
Henderson CM, Lozada-Contreras M, Jiranek V, Longo ML, Block DE. Ethanol production and maximum cell growth are highly correlated with membrane lipid composition during fermentation as determined by lipidomic analysis of 22 Saccharomyces cerevisiae strains. Appl Environ Microbiol. 2013;79:91–104.
Dawes IW, Hardie ID. Selective killing of vegetative cells in sporulated yeast cultures by exposure to diethyl ether. Mol Gen Genet. 1974;131:281–9.
Riou C, Nicaud JM, Barre P, Gaillardin C. Stationary-phase gene expression in Saccharomyces cerevisiae during wine fermentation. Yeast. 1997;13:903–15.
Zwietering MH, Jongenburger I, Rombouts FM, Van K. Modeling of the bacterial growth curve modeling of the bacterial growth curve. Appl Environ Microbiol. 1990;56:1875–81.
Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol. 2014;1151:165–88.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Xie C, Tammi MT. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics. 2009;10:80.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, et al. Dissecting the architecture of a quantitative trait locus in yeast. Nature. 2002;416:326–30.
Upshall A, Giddings B, Mortimore ID. The use of benlate for distinguishing between haploid and diploid strains of Aspergillus nidulans and Aspergillus terreus. J Gen Microbiol. 1977;100:413–8.
Stearns T, Hoyt MA, Botstein D. Yeast mutants sensitive to antimicrotubule drugs define three genes that affect microtubule function. Genetics. 1990;124:251–62.
Huxley C, Green ED, Dunham I. Rapid assessment of S. cerevisiae mating type by PCR. Trends Genet. 1990;6:236.
Brem RB, Kruglyak L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A. 2005;102:1572–7.