BackgroundThe ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment. Industrial microbes such as Saccharomyces cerevisiae are also faced with a large range of fermentation conditions that affect their technological properties. Finding the molecular determinism of such variations is a critical task for better understanding the genetic bases of phenotypic plasticity and can also be helpful in order to improve breeding methods.ResultsIn this study we implemented a QTL mapping program using two independent cross (~ 100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to whole genome sequencing approaches, both crosses were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the environmental conditions. Molecular dissection of a major QTL demonstrated that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits.ConclusionsThe detection of QTLs and their interactions with environment emphasizes the complexity of yeast industrial traits. The validation of the interaction of SSU1 allelic variants with the nature of the fermented juice increases knowledge about the impact of the sulfite pump during fermentation. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5145-4) contains supplementary material, which is available to authorized users.

The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasted response is due to allelic variations and is caused by gene-by-environment interactions (GxE). Finding the genes and the cellular functions that interact with the environment is a current challenge for better understanding the genetic bases of phenotypic plasticity. In order to study the impact of natural allelic variations having a contrasted but relevant effect in a changing environment, we investigated the phenotypic response of the wine yeast Saccharomyces cerevisiae fermented in various grape juices. In this study we implemented a QTL mapping program using two independent offspring (~100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to high throughput sequencing approaches, both populations were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the nature of the fermented juice or fermentation conditions. Molecular dissection of a major QTL showed that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits. Both alleles have positive effect according to external condition in phenotypes related to yeast fitness suggesting an example of balanced selection. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity.