Penicillium roqueforti Genome sequencing. Penicillium roqueforti

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 for the maturation of all types of blue cheeses worldwide, contributing to flavor through proteolytic and lipolytic activities. The two main domesticated cheese populations have lost most of their genetic diversities, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to the Roquefort and non-Roquefort cheese populations or to the silage and lumber/spoiled food populations. Analyses of high-quality genome assemblies of the parental strains revealed chromosomal rearrangements corresponding to five large translocations, two having occurred via a circular intermediate. The offspring were genotyped with GBS (genotype-by-sequencing and genetic maps indicated homogeneous crossing-over distributions along chromosomes, except in the translocated regions. Several genomic regions showed 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 impacts. 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 genetic diversity, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement and innovations for cheese production. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation of organisms to a new environment. The detection of the same QTLs between independently domesticated P. roqueforti lineages, and with pleiotropic effects, suggests convergent adaptation targeting major regulators.