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BMC Genomics

, 14:681

Eukaryote microbial genomics


BackgroundVariation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast Saccharomyces cerevisiae properties. However, the molecular bases of this variation of gene expression are unknown. We addressed these questions by carrying out an integrated genetical-genomic study in fermentation conditions. We report here quantitative trait loci QTL mapping based on expression profiling in a segregating population generated by a cross between a derivative of the popular wine strain EC1118 and the laboratory strain S288c.

ResultsMost of the fermentation traits studied appeared to be under multi-allelic control. We mapped five phenotypic QTLs and 1465 expression QTLs. Several expression QTLs overlapped in hotspots. Among the linkages unraveled here, several were associated with metabolic processes essential for wine fermentation such as glucose sensing or nitrogen and vitamin metabolism. Variations affecting the regulation of drug detoxification and export TPO1, PDR12 or QDR2 were linked to variation in four genes encoding transcription factors PDR8, WAR1, YRR1 and HAP1. We demonstrated that the allelic variation of WAR1 and TPO1 affected sorbic and octanoic acid resistance, respectively. Moreover, analysis of the transcription factors phylogeny suggests they evolved with a specific adaptation of the strains to wine fermentation conditions. Unexpectedly, we found that the variation of fermentation rates was associated with a partial disomy of chromosome 16. This disomy resulted from the well known 8–16 translocation.

ConclusionsThis large data set made it possible to decipher the effects of genetic variation on gene expression during fermentation and certain wine fermentation properties. Our findings shed a new light on the adaptation mechanisms required by yeast to cope with the multiple stresses generated by wine fermentation. In this context, the detoxification and export systems appear to be of particular importance, probably due to nitrogen starvation. Furthermore, we show that the well characterized 8–16 translocation located in SSU1, which is associated with sulfite resistance, can lead to a partial chromosomic amplification in the progeny of strains that carry it, greatly improving fermentation kinetics. This amplification has been detected among other wine yeasts.

KeywordsWine yeast Fermentation QTL Transcriptome Partial disomy Detoxification AbbreviationsQTLQuantitative trait locus

X-QTLExtreme QTL

eQTLExpression QTL

cis-eQTLeQTL closer than 40 kbp to the localization of the gene -local- eQTL

trans-eQTLeQTL farer than 40 kbp to the localization of the gene -distant- eQTL

aCGHComparative genomic hybridization in array

logFCLog2 of Fold-Change

FDRFalse discovery rate

LODLogarithm of odds

SAdMS-adenosyl methionine

PABAPara-amino benzoate

RmaxMaximal fermentation rate

R70Fermentation rate at 70% of fermentation progress

OD600Optic density at 600 nm


adjPvAdjusted P-value

kbpKilo base-pair.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-681 contains supplementary material, which is available to authorized users.

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Autor: Christian Brion - Chloé Ambroset - Isabelle Sanchez - Jean-Luc Legras - Bruno Blondin

Fuente: https://link.springer.com/

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