Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

Abstract

Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.

Indirect monitoring of TORC1 signalling pathway reveals molecular diversity among different yeast strains

“…In this scenario, an alternative to study the TORC1 pathway is the use of genetic approaches, such as those that have been used to shed light into the molecular bases that underlie the phenotypic variability in nitrogen consumption in yeasts (Brice, Sanchez, Bigey, Legras, & Blondin, ; Contreras et al, ; Cubillos et al, ; Gutierrez, Beltran, Warringer, & Guillamon, ; Ibstedt et al, ; Jara et al, ). However, linkage approaches require phenotyping of a larger number of strains, which is unaffordable for monitoring TORC1 activity using the abovementioned methodologies based on immunoblot detection.…”

“…In this scenario, an alternative to study the TORC1 pathway is the use of genetic approaches, such as those that have been used to shed light into the molecular bases that underlie the phenotypic variability in nitrogen consumption in yeasts (Brice, Sanchez, Bigey, Legras, & Blondin, 2014;Contreras et al, 2012;Cubillos et al, 2017;Gutierrez, Beltran, Warringer, & Guillamon, 2013;Ibstedt et al, 2015;Jara et al, 2014).…”

Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross

“…The set of lines destined for extinction is a valuable, but transient, population that is only available during the creation of a multi-parental population (MPP). To our knowledge, this is a unique resource as other similar research populations do not retain this level of information during inbreeding (Kover et al 2009;McMullen et al 2009;Huang et al 2011;King et al 2012;Pekkala et al 2012;Pool et al 2012;Bouchet et al 2017;Cubillos et al 2017;Mangandi et al 2017;Raghavan et al 2017;Tisné et al 2017). With detailed genotyping and reproductive phenotyping of CC lines that were declared extinct, we can address questions related to survivability and line extinction during the process of inbreeding.…”

Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae

“…We selected 22 genes involved in nitrogen associated phenotypes during the fermentation process, identified by QTL mapping and validated by reciprocal hemizygosity analyses (i.e., with a demonstrated effect over the phenotype) [26,35,[38][39][40]52]. Importantly, most of the selected genes were mapped using yeast populations where the founder strains are the DBVPG6765 (WE), DBVPG6044 (WA), YPS128 (NA) and Y12 (SA) strains [22,23].…”

“…Among these phenotypes, our group has systematically focused its interest on nitrogen associated phenotypes, due to the importance of nitrogen sources for the fermentation process, being its deficiencies the principal cause of stuck and sluggish fermentations (reviewed in [36,37]). In this sense, we have mapped multiple QTLs related to nitrogen consumption using yeast populations derived from the four representative strains (WE, WA, NA and SA), validating the specific causative genes by reciprocal hemizygosity approaches [35,[38][39][40]. However, it is not fully understood which fraction of the genetic diversity observed in the species is represented by the alleles mapped in these QTL experiments, making necessary performing bioinformatic analyses to assess these contributions.…”