{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T03:48:33Z","timestamp":1791776913665,"version":"4.3.4"},"reference-count":71,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T00:00:00Z","timestamp":1791676800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T00:00:00Z","timestamp":1791676800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Cacao (\n                    <jats:italic>Theobroma cacao<\/jats:italic>\n                    L.) production is severely constrained by black pod rot (BPR) and frosty pod rot (FPR), two major diseases that cause substantial yield losses across the tropics. Breeding for disease resistance remains challenging due to long generation intervals and the complex genetic control of disease responses. Here, we used genome\u2010wide association studies (GWASs) and genomic prediction (GP) to dissect the genetic basis of BPR and FPR resistance in an interrelated multi\u2010parent F\n                    <jats:sub>1<\/jats:sub>\n                    panel comprising 495 individuals derived from eight bi\u2010parental crosses. Whole\u2010genome sequencing of 495 F1 cacao plants yielded 103,479 high\u2010quality single\u2010nucleotide polymorphisms used for association mapping. GWAS identified 45 quantitative trait loci (QTLs) associated with BPR or FPR resistance, including a shared hotspot on chromosome 7 involved in both diseases. Disease resistance loci exhibited small individual effects (0%\u20138% variance explained), consistent with a highly polygenic architecture. Genomic prediction showed encouraging predictive abilities ranging from 0.36 to 0.64 for FPR and BPR. Multi\u2010trait GP models that incorporated secondary traits increased predictive ability between 1.3\u2010 and 2\u2010folds for frosty pod rot traits. Marker subset and training population analyses demonstrated that predictive ability plateaued at \u223c1000 markers and \u223c450 training individuals, respectively, with little improvements on accuracy after that. Our results highlight the polygenic nature of resistance to BPR and FPR and demonstrate the strong potential of incorporating secondary traits into a multi\u2010trait analyses for increasing accuracies for primary traits.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70322","type":"journal-article","created":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T03:42:17Z","timestamp":1791776537000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (\n                    <i>Theobroma cacao<\/i>\n                    L.) populations"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-0779-1452","authenticated-orcid":false,"given":"Elisa","family":"Jacquotte","sequence":"first","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2018-2112","authenticated-orcid":false,"given":"James A.","family":"Holzwarth","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Zotta","family":"Mota","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6153-8662","authenticated-orcid":false,"given":"Mariela E.","family":"Leandro\u2010Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"CATIE (Centro Agron\u00f3mico Tropical de Investigacion y Ense\u00f1anza) Turrialba  Cartago Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4198-622X","authenticated-orcid":false,"given":"B\u00e9n\u00e9dicte","family":"Rhon\u00e9","sequence":"additional","affiliation":[{"name":"CATIE (Centro Agron\u00f3mico Tropical de Investigacion y Ense\u00f1anza) Turrialba  Cartago Costa Rica"},{"name":"CIRAD, UMR AGAP Institut  Montpellier France"},{"name":"AGAP Institut, Universit\u00e9 Montpellier, CIRAD, INRAE, Institut Agro  Montpellier France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5885-754X","authenticated-orcid":false,"given":"Evelyn T.","family":"Todd","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7577-2839","authenticated-orcid":false,"given":"Maud","family":"Lepelley","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Bellanger","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1274-247X","authenticated-orcid":false,"given":"Patrick","family":"Descombes","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrizio","family":"Arigoni","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Fillodeau","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2318-3615","authenticated-orcid":false,"given":"Eduardo","family":"Beche","sequence":"additional","affiliation":[{"name":"Soci\u00e9t\u00e9 des Produits Nestl\u00e9 SA, Nestl\u00e9 Research  Tours France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,11]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad445"},{"key":"e_1_2_11_3_1","unstructured":"Andrews S.(2010).FastQC: A quality control tool for high throughput sequence data.https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/"},{"key":"e_1_2_11_4_1","doi-asserted-by":"crossref","unstructured":"Argout X. 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