{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T21:57:53Z","timestamp":1790114273099,"version":"4.0.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T00:00:00Z","timestamp":1732060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FOAG project \u2018Apfelzukunft dank Z\u00fcchtung\u2019","award":["2020\/17\/AZZ"],"award-info":[{"award-number":["2020\/17\/AZZ"]}]},{"name":"European Union\u2019s Horizon 2020 research and innovation program under the Marie Sk\u0142odowska-Curie","award":["847585 \u2013 RESPONSE"],"award-info":[{"award-number":["847585 \u2013 RESPONSE"]}]},{"name":"Horizon 2020 Framework Program of the European Union","award":["817970"],"award-info":[{"award-number":["817970"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Genomic prediction for multiple environments can aid the selection of genotypes suited to specific soil and climate conditions. Methodological advances allow effective integration of phenotypic, genomic (additive, nonadditive), and large-scale environmental (enviromic) data into multi-environmental genomic prediction models. These models can also account for genotype-by-environment interaction, utilize alternative relationship matrices (kernels), or substitute statistical approaches with deep learning. However, the application of multi-environmental genomic prediction in apple remained limited, likely due to the challenge of building multi-environmental datasets and structurally complex models. Here, we applied efficient statistical and deep learning models for multi-environmental genomic prediction of eleven apple traits with contrasting genetic architectures by integrating genomic- and enviromic-based model components. Incorporating genotype-by-environment interaction effects into statistical models improved predictive ability by up to 0.08 for nine traits compared to the benchmark model. This outcome, based on Gaussian and Deep kernels, shows these alternatives can effectively substitute the standard genomic best linear unbiased predictor (G-BLUP). Including nonadditive and enviromic-based effects resulted in a predictive ability very similar to the benchmark model. The deep learning approach achieved the highest predictive ability for three traits with oligogenic genetic architectures, outperforming the benchmark by up to 0.10. Our results demonstrate that the tested statistical models capture genotype-by-environment interactions particularly well, and the deep learning models efficiently integrate data from diverse sources. This study will foster the adoption of multi-environmental genomic prediction to select apple cultivars adapted to diverse environmental conditions, providing an opportunity to address climate change impacts.<\/jats:p>","DOI":"10.1093\/hr\/uhae319","type":"journal-article","created":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T03:53:32Z","timestamp":1732074812000},"source":"Crossref","is-referenced-by-count":13,"title":["Integrative multi-environmental genomic prediction in apple"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7065-6724","authenticated-orcid":false,"given":"Michaela","family":"Jung","sequence":"first","affiliation":[{"name":"Fruit Breeding, Agroscope , Mueller-Thurgau-Strasse 29, 8820 Waedenswil,","place":["Switzerland"]},{"name":"Institute of Agricultural Sciences, ETH Zurich Molecular Plant Breeding, , Universitaetstrasse 2, 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carles","family":"Quesada-Traver","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences, ETH Zurich Molecular Plant Breeding, , Universitaetstrasse 2, 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgane","family":"Roth","sequence":"additional","affiliation":[{"name":"INRAE , Research Unit for Genetics and Improvement of Fruit and Vegetable (GAFL), 67 All\u00e9e des Ch\u00eanes, 84143 Montfavet,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0240-8021","authenticated-orcid":false,"given":"Maria Jos\u00e9","family":"Aranzana","sequence":"additional","affiliation":[{"name":"Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB , Campus UAB, Bellaterra, 08193 Barcelona,","place":["Spain"]},{"name":"IRTA (Institut de Recerca i Tecnologia Agroaliment\u00e0ries) , Caldes de Montbui, 08140 Barcelona,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3956-3807","authenticated-orcid":false,"given":"H\u00e9l\u00e8ne","family":"Muranty","sequence":"additional","affiliation":[{"name":"Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV , F-49000 Angers,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marijn","family":"Rymenants","sequence":"additional","affiliation":[{"name":"Better3fruit N.V. , Steenberg 36, 3202 Rillaar,","place":["Belgium"]},{"name":"University of Leuven Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, , Willem de Croylaan 42 - bus 2427, 3001 Leuven,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Guerra","sequence":"additional","affiliation":[{"name":"Research Centre Laimburg, Institute for Fruit Growing and Viticulture , Laimburg 1, 39040 Auer,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elias","family":"Holzknecht","sequence":"additional","affiliation":[{"name":"Research Centre Laimburg, Institute for Fruit Growing and Viticulture , Laimburg 1, 39040 Auer,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Pradas","sequence":"additional","affiliation":[{"name":"Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB , Campus UAB, Bellaterra, 08193 Barcelona,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lidia","family":"Lozano","sequence":"additional","affiliation":[{"name":"IRTA (Institut de Recerca i Tecnologia Agroaliment\u00e0ries) , Caldes de Montbui, 08140 Barcelona,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9rique","family":"Didelot","sequence":"additional","affiliation":[{"name":"Unit\u00e9 exp\u00e9rimentale Horticole, INRAE , F-49000 Angers,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Laurens","sequence":"additional","affiliation":[{"name":"Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV , F-49000 Angers,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Yates","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences, ETH Zurich Molecular Plant Breeding, , Universitaetstrasse 2, 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno","family":"Studer","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences, ETH Zurich Molecular Plant Breeding, , Universitaetstrasse 2, 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni A L","family":"Broggini","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences, ETH Zurich Molecular Plant Breeding, , Universitaetstrasse 2, 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0919-2702","authenticated-orcid":false,"given":"Andrea","family":"Patocchi","sequence":"additional","affiliation":[{"name":"Fruit Breeding, Agroscope , Mueller-Thurgau-Strasse 29, 8820 Waedenswil,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,20]]},"reference":[{"key":"2025030500430929700_ref1","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/genetics\/157.4.1819","article-title":"Prediction of total genetic value using genome-wide dense marker 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