{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T16:12:14Z","timestamp":1790784734493,"version":"4.1.0"},"reference-count":93,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"SPACE project","award":["C19764L01"],"award-info":[{"award-number":["C19764L01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Ganoderma boninense, a soil-borne pathogenic fungus causing basal stem rot (BSR) disease in oil palm, is the major threat to cultivation in Southeast Asia, with the potential to reduce oil production by up to 80% in severely affected plantations. With a view to marker-assisted selection (MAS) of resistant planting material, we combined genetics and transcriptomics approaches to investigate the defense mechanisms of oil palm against infection by G. boninense. We first performed quantitative trait locus (QTL) mapping of BSR resistance using a multi-locus Bayesian variable selection approach applied to more than 10 years of data collected during pre-nursery tests of Deli and La M\u00e9 breeding populations. We found 6 and 5 BSR resistance loci segregating in Deli and La M\u00e9 respectively, with no overlap between them. Then we performed an RNA-sequencing approach on libraries of roots and bole of oil palm seedlings inoculated or not with G. boninense, focusing on Deli \u00d7 La M\u00e9 crosses with contrasted BSR resistance. A Bayesian variable selection on predictors obtained by tracing the resistance loci haplotypes in profiled individuals identified 195 differentially expressed genes (DEGs) for the G. boninense inoculation \u00d7 QTL interaction, among the 551 DEGs found for inoculation effects. The DEGs were located both in cis and trans positions compared to the segregating QTL intervals, enabling the prioritization of candidate genes and resistance mechanisms associated. Focusing on a strong effect QTL region on chromosome 4 in the Deli genetic background, we identified three candidate genes in cis positions that exhibited differential expression both in response to G. boninense inoculation and between resistant and susceptible haplotypes. Our study is the first combining QTL and RNA-seq approaches in oil palm based on genetically connected experimental setup, providing valuable information on the underlying mechanisms and paving the way for MAS of BSR resistant planting material.<\/jats:p>","DOI":"10.3390\/microorganisms14081712","type":"journal-article","created":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T09:15:22Z","timestamp":1785834922000},"page":"1712","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Early Response QTLs and DEGs Underlying Oil Palm Resistance to Ganoderma\u00a0boninense in Two Breeding Populations Evaluated in Pre-Nursery Trials"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2613-0562","authenticated-orcid":false,"given":"Aur\u00e9lie","family":"Daval","sequence":"first","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Lopez","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3522-5053","authenticated-orcid":false,"given":"Teresa","family":"Cuellar","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aqdi","family":"Prasetio","sequence":"additional","affiliation":[{"name":"P.T SOCFINDO, Jl. Yos Sudarso, Medan 20115, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Denis","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Soriano","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sol\u00e8ne","family":"Puerto","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"},{"name":"PalmElit SAS, 34980 Montferrier-sur-Lez, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dadang","family":"Afandi","sequence":"additional","affiliation":[{"name":"P.T SOCFINDO, Jl. Yos Sudarso, Medan 20115, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginie","family":"Pomi\u00e8s","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeanne","family":"Danon","sequence":"additional","affiliation":[{"name":"UMR GDEC, INRAE-UCA, 63000 Clermont-Ferrand, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0759-3649","authenticated-orcid":false,"given":"Deni","family":"Arifiyanto","sequence":"additional","affiliation":[{"name":"P.T SOCFINDO, Jl. Yos Sudarso, Medan 20115, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Madec","sequence":"additional","affiliation":[{"name":"PalmElit SAS, 34980 Montferrier-sur-Lez, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-9667-5182","authenticated-orcid":false,"given":"Younes","family":"Amara","sequence":"additional","affiliation":[{"name":"PalmElit SAS, 34980 Montferrier-sur-Lez, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6569-4363","authenticated-orcid":false,"given":"Virginie","family":"Riou","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Indra","family":"Syahputra","sequence":"additional","affiliation":[{"name":"P.T SOCFINDO, Jl. Yos Sudarso, Medan 20115, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0454-1037","authenticated-orcid":false,"given":"Florence","family":"Jacob","sequence":"additional","affiliation":[{"name":"PalmElit SAS, 34980 Montferrier-sur-Lez, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0438-0966","authenticated-orcid":false,"given":"Norbert","family":"Billotte","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9838-3975","authenticated-orcid":false,"given":"S\u00e9bastien","family":"Tisn\u00e9","sequence":"additional","affiliation":[{"name":"CIRAD, UMR AGAP Institute, 34398 Montpellier, France"},{"name":"UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34398 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,4]]},"reference":[{"key":"ref_1","unstructured":"CIRAD-FRA (2024). 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