Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti
Caron, Thibault | Crequer, Ewen | Le Piver, Mélanie | Le Prieur, Stéphanie | Brunel, Sammy | Snirc, Alodie | Cueff, Gwennina | Roueyre, Daniel | Place, Michel | Chassard, Christophe | Simon, Adeline | de la Vega, Ricardo, C Rodríguez | Coton, Monika | Coton, Emmanuel | Foulongne-Oriol, Marie | Branca, Antoine | Giraud, Tatiana | Ecologie, Société et Evolution (ex-Ecologie, Systématique et Evolution) (ESE) ; AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS) | Laboratoire Interprofessionnel de Production (SAS LIP) | Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM) ; Université de Brest (UBO EPE) | Unité Mixte de Recherche sur le Fromage (UMRF) ; VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA) | Département Microbiologie et Chaîne Alimentaire - INRAE (MICA) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | BIOlogie et GEstion des Risques en agriculture (BIOGER) ; Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Unité de recherche Mycologie et Sécurité des Aliments (MycSA) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | ANR-19-CE20-0002,FUNGADAPT,Mécanismes d'adaptation chez les Penicilllium utilisés dans les produits fermentés(2019)
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Показать больше [+] Меньше [-]Английский. Elucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms. Penicillium roqueforti is the mold used worldwide for the blue cheese maturation, contributing to flavors through proteolytic and lipolytic activities. The two domesticated cheese populations display very little genetic diversity, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to cheese and non-cheese populations. Analyses of high-quality genome assemblies of the parental strains revealed five large translocations, two having occurred via a circular intermediate, one with footprints of Starship giant mobile elements. Offspring genotyping with genotype-by-sequencing (GBS) revealed several genomic regions with segregation distortion, possibly linked to degeneration in cheese lineages. We found transgressions for several traits relevant for cheese making, with offspring having more extreme trait values than parental strains. We identified quantitative trait loci (QTLs) for colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, but not for growth rates. Some genomic regions appeared rich in QTLs for both lipid and protein metabolism, and other regions for the production of multiple extrolites, indicating that QTLs have pleiotropic effects. Some QTLs corresponded to known biosynthetic gene clusters, e.g., for the production of melanin or extrolites. F1 hybrids constitute valuable strains for cheese producers, with new traits and new allelic combinations, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation, revealing convergent adaptation targeting major gene regulators.
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