Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses
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.
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dig-cirad-fr-5898122021-11-09T09:57:33Z http://agritrop.cirad.fr/589812/ http://agritrop.cirad.fr/589812/ Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses. Cubillos Francisco A., Brice Claire, Molinet Jennifer, Tisne Sébastien, Abarca Valentina, Tapia Sebastián, Oporto Christian, García Verónica, Liti Gianni, Martínez Claudio. 2017. G3 - Genes Genomes Genetics, 7 (6) : 1693-1705.https://doi.org/10.1534/g3.117.042127 <https://doi.org/10.1534/g3.117.042127> Researchers Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses Cubillos, Francisco A. Brice, Claire Molinet, Jennifer Tisne, Sébastien Abarca, Valentina Tapia, Sebastián Oporto, Christian García, Verónica Liti, Gianni Martínez, Claudio eng 2017 G3 - Genes Genomes Genetics Q02 - Traitement et conservation des produits alimentaires 000 - Autres thèmes Amérique du Nord Afrique occidentale http://aims.fao.org/aos/agrovoc/c_5219 http://aims.fao.org/aos/agrovoc/c_8355 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/589812/1/1693.full.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1534/g3.117.042127 10.1534/g3.117.042127 info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.117.042127 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1534/g3.117.042127 |
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Q02 - Traitement et conservation des produits alimentaires 000 - Autres thèmes http://aims.fao.org/aos/agrovoc/c_5219 http://aims.fao.org/aos/agrovoc/c_8355 Q02 - Traitement et conservation des produits alimentaires 000 - Autres thèmes http://aims.fao.org/aos/agrovoc/c_5219 http://aims.fao.org/aos/agrovoc/c_8355 |
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Q02 - Traitement et conservation des produits alimentaires 000 - Autres thèmes http://aims.fao.org/aos/agrovoc/c_5219 http://aims.fao.org/aos/agrovoc/c_8355 Q02 - Traitement et conservation des produits alimentaires 000 - Autres thèmes http://aims.fao.org/aos/agrovoc/c_5219 http://aims.fao.org/aos/agrovoc/c_8355 Cubillos, Francisco A. Brice, Claire Molinet, Jennifer Tisne, Sébastien Abarca, Valentina Tapia, Sebastián Oporto, Christian García, Verónica Liti, Gianni Martínez, Claudio Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses |
description |
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. |
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Q02 - Traitement et conservation des produits alimentaires 000 - Autres thèmes http://aims.fao.org/aos/agrovoc/c_5219 http://aims.fao.org/aos/agrovoc/c_8355 |
author |
Cubillos, Francisco A. Brice, Claire Molinet, Jennifer Tisne, Sébastien Abarca, Valentina Tapia, Sebastián Oporto, Christian García, Verónica Liti, Gianni Martínez, Claudio |
author_facet |
Cubillos, Francisco A. Brice, Claire Molinet, Jennifer Tisne, Sébastien Abarca, Valentina Tapia, Sebastián Oporto, Christian García, Verónica Liti, Gianni Martínez, Claudio |
author_sort |
Cubillos, Francisco A. |
title |
Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses |
title_short |
Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses |
title_full |
Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses |
title_fullStr |
Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses |
title_full_unstemmed |
Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-Seq analyses |
title_sort |
identification of nitrogen consumption genetic variants in yeast through qtl mapping and bulk segregant rna-seq analyses |
url |
http://agritrop.cirad.fr/589812/ http://agritrop.cirad.fr/589812/1/1693.full.pdf |
work_keys_str_mv |
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1758025939920355328 |