{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T12:24:01Z","timestamp":1780489441182,"version":"3.54.1"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T00:00:00Z","timestamp":1755216000000},"content-version":"vor","delay-in-days":45,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012421","name":"Agricultural Science and Technology Innovation Program","doi-asserted-by":"publisher","award":["CAAS-CSIAF-202303"],"award-info":[{"award-number":["CAAS-CSIAF-202303"]}],"id":[{"id":"10.13039\/501100012421","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-030574"],"award-info":[{"award-number":["INV-030574"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Nanfan special project, Chinese Academy of Agricultural Sciences","award":["YBXM2506"],"award-info":[{"award-number":["YBXM2506"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32361143514"],"award-info":[{"award-number":["32361143514"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Phenotypic variation results from the combination of genotype, the environment, and their interaction. The ability to quantify the relative contributions of genetic and environmental factors to complex traits can help in breeding crops with superior adaptability for growth in varied environments. Here, we developed and extensively evaluated the performance of an explainable machine-learning framework named explainable genotype-by-environment interactions prediction (EXGEP) to accurately predict the grain yield in crops. To assess the performance of EXGEP, we applied it to a dataset comprising 70\u00a0693 phenotypic records of grain yield traits for 3793 hybrids (also including both genotype and environmental condition data). When used with four different combinations of genotypes and environmental data, EXGEP exceeded the yield prediction performance of the classic model Bayesian ridge regression model by 17.37%\u201342.35%. Moreover, EXGEP incorporates SHapley Additive exPlanations values that can uncover complex nonlinear relationships between genotype and environment and identify key features, and their interactions, that provide the main contributions to model performance, thus enhancing our understanding of genotype-by-environment interactions. Additionally, data from a series of tests support that EXGEP exhibits superior performance in terms of prediction accuracy and explainability. Our development of EXGEP and comparisons of it against alternative models provides valuable insights into methods for accurately predicting complex traits in multiple environments.<\/jats:p>","DOI":"10.1093\/bib\/bbaf414","type":"journal-article","created":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T11:37:57Z","timestamp":1753961877000},"source":"Crossref","is-referenced-by-count":9,"title":["EXGEP: a framework for predicting genotype-by-environment interactions using ensembles of explainable machine-learning models"],"prefix":"10.1093","volume":"26","author":[{"given":"Tingxi","family":"Yu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Maize and Wheat Improvement Center (CIMMYT)-China Office , No. 12 Zhongguancun South Street, Haidian District, Beijing 100081 ,","place":["China"]},{"name":"Nanfan Research Institute, Chinese Academy of Agricultural Sciences , Sanya 572024, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2179-7720","authenticated-orcid":false,"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Maize and Wheat Improvement Center (CIMMYT)-China Office , No. 12 Zhongguancun South Street, Haidian District, Beijing 100081 ,","place":["China"]},{"name":"Nanfan Research Institute, Chinese Academy of Agricultural Sciences , Sanya 572024, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shoukun","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Maize and Wheat Improvement Center (CIMMYT)-China Office , No. 12 Zhongguancun South Street, Haidian District, Beijing 100081 ,","place":["China"]},{"name":"Nanfan Research Institute, Chinese Academy of Agricultural Sciences , Sanya 572024, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shang","family":"Gao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Maize and Wheat Improvement Center (CIMMYT)-China Office , No. 12 Zhongguancun South Street, Haidian District, Beijing 100081 ,","place":["China"]},{"name":"Nanfan Research Institute, Chinese Academy of Agricultural Sciences , Sanya 572024, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ze","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Maize and Wheat Improvement Center (CIMMYT)-China Office , No. 12 Zhongguancun South Street, Haidian District, Beijing 100081 ,","place":["China"]},{"name":"Nanfan Research Institute, Chinese Academy of Agricultural Sciences , Sanya 572024, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiankang","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Maize and Wheat Improvement Center (CIMMYT)-China Office , No. 12 Zhongguancun South Street, Haidian District, Beijing 100081 ,","place":["China"]},{"name":"Nanfan Research Institute, Chinese Academy of Agricultural Sciences , Sanya 572024, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose","family":"Crossa","sequence":"additional","affiliation":[{"name":"International Maize and Wheat Improvement Center (CIMMYT) , Apdo. Postal 6-641, Texcoco, D. F. 06600 ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osval A","family":"Montesinos-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Facultad de Telem\u00e1tica, Universidad de Colima , C. P. 28040, Colima, Estado de Colima ,","place":["M\u00e9xico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Hearne","sequence":"additional","affiliation":[{"name":"International Maize and Wheat Improvement Center (CIMMYT) , Apdo. Postal 6-641, Texcoco, D. 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