Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti

• DOI: 10.1371/journal.pgen.1011669
• Publication Date: 2025-04-15T17:34:02Z
• Authors: Thibault Caron; Ewen Crequer; Mélanie Le Piver; Stéphanie Le Prieur; Sammy Brunel; Alodie Snirc; Gwennina Cueff; Daniel Roueyre; Michel Place; Christophe Chassard; Adeline Simon; Ricardo C. Rodríg...; Monika Coton; Emmanuel Coton; Marie Foulongne-O...; Antoine Branca; Tatiana Giraud
• Keywords: Genetic architecture; Penicillium roqueforti

Elucidating the genomic architecture of quantitative traits is essential for our understanding adaptation and breeding in domesticated organisms. Penicillium roqueforti mold used worldwide blue cheese maturation, contributing to flavors through proteolytic lipolytic activities. The two populations display very little genetic diversity, but are differentiated carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging non-cheese populations. Analyses high-quality genome assemblies parental strains revealed large translocations, having occurred via a circular intermediate, one with footprints Starship giant mobile elements. Offspring genotyping genotype-by-sequencing (GBS) several regions segregation distortion, possibly linked degeneration lineages. found transgressions relevant making, offspring more extreme trait values than strains. identified loci (QTLs) colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, not growth rates. Some appeared rich QTLs both lipid protein metabolism, other production multiple extrolites, indicating that have pleiotropic effects. corresponded known biosynthetic gene clusters, e.g., melanin or extrolites. hybrids constitute valuable producers, new allelic combinations, allowed identifying target important paving way strain improvement. findings further contribute mechanisms underlying rapid adaptation, revealing convergent targeting major regulators.