{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T03:16:17Z","timestamp":1788318977110,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.pgen.1011669","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T00:00:00Z","timestamp":1746144000000}}],"reference-count":167,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T00:00:00Z","timestamp":1744675200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-19-CE20-0002-02 Fungadapt"],"award-info":[{"award-number":["ANR-19-CE20-0002-02 Fungadapt"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["Genomefun 309403"],"award-info":[{"award-number":["Genomefun 309403"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["Blue Proof of Concept"],"award-info":[{"award-number":["Blue Proof of Concept"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015118","name":"French Academy of Sciences","doi-asserted-by":"crossref","award":["Fondation Louis D"],"award-info":[{"award-number":["Fondation Louis D"]}],"id":[{"id":"10.13039\/100015118","id-type":"DOI","asserted-by":"crossref"}]},{"name":"LIP SAS"},{"DOI":"10.13039\/501100003032","name":"ANRT","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003032","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    Elucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms.\n                    <jats:italic>Penicillium roqueforti<\/jats:italic>\n                    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\n                    <jats:italic>Starship<\/jats:italic>\n                    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.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1011669","type":"journal-article","created":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T13:34:02Z","timestamp":1744724042000},"page":"e1011669","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0212-7756","authenticated-orcid":true,"given":"Thibault","family":"Caron","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6336-8226","authenticated-orcid":true,"given":"Ewen","family":"Crequer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e9lanie","family":"Le Piver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phanie","family":"Le Prieur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sammy","family":"Brunel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2121-0197","authenticated-orcid":true,"given":"Alodie","family":"Snirc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gwennina","family":"Cueff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Roueyre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michel","family":"Place","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Chassard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0020-6442","authenticated-orcid":true,"given":"Adeline","family":"Simon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9852-6654","authenticated-orcid":true,"given":"Ricardo C. Rodr\u00edguez","family":"de la Vega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0148-6802","authenticated-orcid":true,"given":"Monika","family":"Coton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0912-8804","authenticated-orcid":true,"given":"Emmanuel","family":"Coton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5668-5286","authenticated-orcid":true,"given":"Marie","family":"Foulongne-Oriol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antoine","family":"Branca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8475-1386","authenticated-orcid":true,"given":"Tatiana","family":"Giraud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,4,15]]},"reference":[{"key":"pgen.1011669.ref001","volume-title":"Introduction to Quantitative Genetics","author":"DS Falconer","year":"1995"},{"key":"pgen.1011669.ref002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.livsci.2013.01.016","article-title":"Genetic analysis and evaluation of behavioural traits in cattle","volume":"154","author":"K Adamczyk","year":"2013","journal-title":"Livest Sci"},{"issue":"8","key":"pgen.1011669.ref003","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1007\/s00299-017-2127-y","article-title":"Quantitative trait loci from identification to exploitation for crop improvement","volume":"36","author":"J Kumar","year":"2017","journal-title":"Plant Cell Rep"},{"issue":"1","key":"pgen.1011669.ref004","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.livsci.2014.05.017","article-title":"The development of genomics applied to dairy breeding","volume":"166","author":"MVB Silva","year":"2014","journal-title":"Livest Sci"},{"issue":"3","key":"pgen.1011669.ref005","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1007\/s10681-014-1170-9","article-title":"Molecular mapping of QTLs for domestication-related traits in cowpea (V. unguiculata (L.) 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Langmead","year":"2019","journal-title":"Bioinformatics"},{"issue":"15","key":"pgen.1011669.ref104","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pgen.1011669.ref105","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol"},{"issue":"1","key":"pgen.1011669.ref106","first-page":"18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"R Luo","year":"2012","journal-title":"GigaScience"},{"issue":"11","key":"pgen.1011669.ref107","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1101\/gr.236273.118","article-title":"Chromosome 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high-throughput genome editing","volume":"23","author":"M Alonge","year":"2022","journal-title":"Genome Biol"},{"issue":"8","key":"pgen.1011669.ref111","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics"},{"issue":"10","key":"pgen.1011669.ref112","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Kelley J, editor","volume":"38","author":"M Manni","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pgen.1011669.ref113","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s13059-024-03198-7","article-title":"Rapid and sensitive detection of genome contamination at scale with FCS-GX","volume":"25","author":"A Astashyn","year":"2024","journal-title":"Genome Biol"},{"issue":"1","key":"pgen.1011669.ref114","doi-asserted-by":"crossref","first-page":"e16526","DOI":"10.1371\/journal.pone.0016526","article-title":"Considering transposable element diversification in de novo annotation approaches","volume":"6","author":"T Flutre","year":"2011","journal-title":"PLoS ONE"},{"issue":"5","key":"pgen.1011669.ref115","doi-asserted-by":"crossref","first-page":"e91929","DOI":"10.1371\/journal.pone.0091929","article-title":"PASTEC: An Automatic Transposable Element Classification Tool. 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Res"},{"issue":"3","key":"pgen.1011669.ref127","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"pgen.1011669.ref128","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"pgen.1011669.ref129","doi-asserted-by":"crossref","first-page":"lqaa026","DOI":"10.1093\/nargab\/lqaa026","article-title":"GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins","volume":"2","author":"T Br\u016fna","year":"2020","journal-title":"NAR Genomics Bioinforma"},{"issue":"1","key":"pgen.1011669.ref130","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and 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in novel eukaryotic genomes by self-training algorithm","volume":"33","author":"A Lomsadze","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pgen.1011669.ref134","doi-asserted-by":"crossref","first-page":"109287","DOI":"10.1016\/j.foodres.2020.109287","article-title":"Impact of maturation and growth temperature on cell-size distribution, heat-resistance, compatible solute composition and transcription profiles of Penicillium roqueforti conidia","volume":"136","author":"M Punt","year":"2020","journal-title":"Food Res Int"},{"issue":"1","key":"pgen.1011669.ref135","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"1","key":"pgen.1011669.ref136","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1186\/s12859-021-04482-0","article-title":"TSEBRA: transcript selector for BRAKER","volume":"22","author":"L Gabriel","year":"2021","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"pgen.1011669.ref137","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"M Krzywinski","year":"2009","journal-title":"Genome Res"},{"issue":"1","key":"pgen.1011669.ref138","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"C Jain","year":"2018","journal-title":"Nat Commun"},{"issue":"7","key":"pgen.1011669.ref139","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"CA Schneider","year":"2012","journal-title":"Nat Methods"},{"issue":"6","key":"pgen.1011669.ref140","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1128\/aem.46.6.1301-1310.1983","article-title":"Classification of Terverticillate Penicillia Based on Profiles of Mycotoxins and Other Secondary Metabolites","volume":"46","author":"JC Frisvad","year":"1983","journal-title":"Appl Environ Microbiol"},{"key":"pgen.1011669.ref141","unstructured":"Maechler M. diptest: Hartigan\u2019s Dip Test Statistic for Unimodality \u2013 Corrected. 2016. Available from: https:\/\/cran.r-project.org\/package=diptest"},{"key":"pgen.1011669.ref142","article-title":"Mouse-tracking: A practical guide to implementation and analysis. In: A handbook of process tracing methods [Internet]","author":"PJ Kieslich","journal-title":"PsyArXiv"},{"key":"pgen.1011669.ref143","doi-asserted-by":"crossref","first-page":"700","DOI":"10.3389\/fpsyg.2013.00700","article-title":"Good things peak in pairs: a note on the bimodality coefficient","volume":"4","author":"R Pfister","year":"2013","journal-title":"Front Psychol"},{"key":"pgen.1011669.ref144","article-title":"Package \u201cLaplacesDemon\u201d [Internet]","author":"B Hall","year":"2021"},{"key":"pgen.1011669.ref145","article-title":"vioplot: violin plot.","author":"D Adler","year":"2022"},{"key":"pgen.1011669.ref146","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2016"},{"issue":"12","key":"pgen.1011669.ref147","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v021.i12","article-title":"Reshaping Data with the {reshape} Package","volume":"21","author":"H Wickham","year":"2007","journal-title":"J Stat Softw"},{"issue":"1","key":"pgen.1011669.ref148","article-title":"FactoMineR: An R Package for Multivariate Analysis","volume":"25","author":"S L\u00ea","year":"2008","journal-title":"J Stat Softw [Internet]"},{"key":"pgen.1011669.ref149","article-title":"factoextra: Extract and Visualize the Results of Multivariate Data Analyses","author":"A Kassambara","year":"2020"},{"key":"pgen.1011669.ref150","article-title":"R package \u201ccorrplot\u201d: Visualization of a Correlation Matrix","author":"T Wei","year":"2021"},{"issue":"3","key":"pgen.1011669.ref151","doi-asserted-by":"crossref","first-page":"250","DOI":"10.3835\/plantgenome2011.08.0024","article-title":"Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP","volume":"4","author":"JB Endelman","year":"2011","journal-title":"Plant Genome"},{"issue":"7436","key":"pgen.1011669.ref152","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/nature11867","article-title":"Finding the sources of missing heritability in a yeast cross","volume":"494","author":"JS Bloom","year":"2013","journal-title":"Nature"},{"key":"pgen.1011669.ref153","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1038\/ncomms3876","article-title":"Multiple recent horizontal transfers of a large genomic region in cheese making fungi","volume":"5","author":"K Cheeseman","year":"2014","journal-title":"Nat Commun"},{"issue":"14","key":"pgen.1011669.ref154","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"pgen.1011669.ref155","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3--new capabilities and interfaces","volume":"40","author":"A Untergasser","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pgen.1011669.ref156","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/72708","article-title":"An economic method for the fluorescent labeling of PCR fragments. A poor man\u2019s approach to genotyping for research and high-throughput diagnostics","volume":"18","author":"M Schuelke","year":"2000","journal-title":"Nat Biotechnol"},{"issue":"1","key":"pgen.1011669.ref157","first-page":"72","article-title":"Plant microsatellite genotyping with 4-color fluorescent detection using multiple-tailed primers","volume":"5","author":"A Missiaggia","year":"2006","journal-title":"Genet Mol Res"},{"issue":"4","key":"pgen.1011669.ref158","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"issue":"2","key":"pgen.1011669.ref159","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"P Danecek","year":"2021","journal-title":"GigaScience"},{"issue":"9","key":"pgen.1011669.ref160","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"issue":"21","key":"pgen.1011669.ref161","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"H Li","year":"2011","journal-title":"Bioinformatics"},{"issue":"6","key":"pgen.1011669.ref162","article-title":"R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis","volume":"79","author":"J Taylor","year":"2017","journal-title":"J Stat Softw [Internet]"},{"key":"pgen.1011669.ref163","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","article-title":"R\/qtl: QTL mapping in experimental crosses","volume":"19","author":"KW Broman","year":"2003","journal-title":"Bioinformatics"},{"issue":"1","key":"pgen.1011669.ref164","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13059-014-0573-1","article-title":"ALLMAPS: robust scaffold ordering based on multiple maps","volume":"16","author":"H Tang","year":"2015","journal-title":"Genome Biol"},{"issue":"6","key":"pgen.1011669.ref165","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"18","key":"pgen.1011669.ref166","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"H Li","year":"2018","journal-title":"Birol I, Bioinformatics"},{"issue":"19","key":"pgen.1011669.ref167","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1093\/bioinformatics\/btx346","article-title":"karyoploteR: an R\/Bioconductor package to plot customizable genomes displaying arbitrary data. 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