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Comparison of predictive ability between genomic and phenomic predictions for flowering date in sweet cherry Prunus avium L.

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBERNARD, Anthony
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMIR, Alexandre
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorOKINE, Saviour
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBONNET, Hélène
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBARRENECHE, Teresa
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorWENDEN, Bénédicte
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFOUCHÉ, Mathieu
hal.structure.identifierUnité Expérimentale Arboricole [UE ARBO]
dc.contributor.authorDELMAS, Marine
hal.structure.identifierUnité Expérimentale Arboricole [UE ARBO]
dc.contributor.authorALLÉTRU, David
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDIRLEWANGER, Elisabeth
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorQUERO-GARCIA, José
dc.date.accessioned2025-05-23T02:05:46Z
dc.date.available2025-05-23T02:05:46Z
dc.date.conference2025-05-06
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/206685
dc.description.abstractEnIn plant breeding, genomic selection is a powerful tool allowing for early and accurate selection of complex traits, reducing the time and resources required for breeding cycles. However, in the quest for alternatives to genotyping, it has been proposed recently a low-cost and efficient alternative, called phenomic selection, in which genotyping is replaced by endophenotypes such as near-infrared spectra (NIRS).At INRAE Bordeaux, the PrADAM team working on Prunus aims at predict complex traits related to phenology in sweet cherry to facilitate the early selection of interesting hybrids in breeding programs. Therefore, a comparison of the predictive ability between genomic and phenomic predictions would represent a step forward in sweet cherry breeding. Using sweet cherry germplasm collection of INRAE Prunus-Juglans Biological Resources Center, we investigated both approaches: (i) genomic prediction based on 115 accessions phenotyped for beginning, full and end flowering dates, and genotyped using the 6K SNP Illumina Infinium® array, and (ii) phenomic prediction based on 98 accessions phenotyped for the same traits using Bruker® NIRS equipment.Preliminary results gave satisfying predictive ability for both approaches. Indeed, using rrBLUP model, 1,294 SNPs and BLUPs over 7 years of phenotyping, we obtained genomic predictive abilities (PA) of 0.61 to 0.66 depending on the trait, using a training set size of 80%. Using NIRS data as phenomic tool, we observed an effect of the preprocessing method on PA such as Savitzky–Golay (SG) derivatives, standard normal variate (SNV) or multiplicative scatter correction (MSC). Using rrBLUP and one single year of phenotyping, the best PA of 0.52 was obtained for full flowering date with the combination of SNV and first SG derivative, using a training set size of 80% as well. This study highlights the promising opportunity in the use of such new omics-based breeding approaches for complex traits in sweet cherry.
dc.language.isoen
dc.subject.enGenomic prediction
dc.subject.enPhenomic prediction
dc.subject.enPhenology
dc.subject.enSweet cherry
dc.title.enComparison of predictive ability between genomic and phenomic predictions for flowering date in sweet cherry Prunus avium L.
dc.typeCommunication dans un congrès
dc.subject.halSciences du Vivant [q-bio]
bordeaux.hal.laboratoriesBiologie du Fruit & Pathologie (BFP) - UMR 1332*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.conference.title12th Rosaceae Genomics Conference (RGC12)
bordeaux.countryES
bordeaux.conference.cityBarcelona
bordeaux.peerReviewedoui
hal.identifierhal-05077276
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2025-06-09
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-05077276v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=BERNARD,%20Anthony&MIR,%20Alexandre&OKINE,%20Saviour&BONNET,%20H%C3%A9l%C3%A8ne&BARRENECHE,%20Teresa&rft.genre=unknown


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