{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T14:08:23Z","timestamp":1790690903653,"version":"4.1.0"},"reference-count":147,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"BMGF\u2014STRASA and AGGRi-I and II"},{"name":"CGIAR Accelerated Breeding Initiative"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Flooding is among the most devastating abiotic stresses limiting rice productivity. Although introgression of the gene SUB1A has conferred submergence tolerance in several mega-varieties, this single-gene approach is insufficient for the diverse flood types\u2014flash floods, stagnant floods, anaerobic germination, and deepwater inundation\u2014progressively intensifying with climate change. Here, we review the physiological mechanisms and genetic architecture underlying tolerance to each flood type, emphasizing the dual role of reactive oxygen species in signalling and damage, the management of elemental toxicities (Fe2+, Mn2+) under altered soil redox, and lessons from wetland species and lowland rice. We then examine why marker-assisted selection has failed for polygenic, multi-stress tolerance and identify persistent breeding bottlenecks. Building on this biological foundation, we outline an integrated five-dimensional framework (demand, discovery, design, development, deployment) that links gene-bank diversity, multi-omics discovery, predictive breeding, and on-farm validation through continuous feedback. We discuss how connected breeding, the transition from trait to environment strategy, and speed breeding can accelerate genetic gain, and we close with research priorities centred on the biology of multi-flood tolerance to develop climate-resilient rice.<\/jats:p>","DOI":"10.1093\/jxb\/erag452","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T11:34:47Z","timestamp":1788867287000},"source":"Crossref","is-referenced-by-count":0,"title":["Translating flood-tolerance biology into breeding: a five-dimensional framework for next-generation rice varieties"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6861-0193","authenticated-orcid":false,"given":"Waseem","family":"Hussain","sequence":"first","affiliation":[{"name":"Rice Breeding Innovation Platform, International Rice Research Institute (IRRI) , Los Ba\u00f1os, Laguna 4031 ,","place":["Philippines"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4492-4005","authenticated-orcid":false,"given":"Mahender","family":"Anumalla","sequence":"additional","affiliation":[{"name":"Rice Breeding Innovation Platform, International Rice Research Institute (IRRI) , Los Ba\u00f1os, Laguna 4031 ,","place":["Philippines"]},{"name":"International Rice Research Institute (IRRI)-South Asia Hub, ICRISAT , Patancheru, Hyderabad 502324 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoli","family":"Zhang","sequence":"additional","affiliation":[{"name":"Rice Breeding Innovation Platform, International Rice Research Institute (IRRI) , Los Ba\u00f1os, Laguna 4031 ,","place":["Philippines"]},{"name":"Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences , Nanning 530007 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1961-3072","authenticated-orcid":false,"given":"Abdelbagi M","family":"Ismail","sequence":"additional","affiliation":[{"name":"Rice Breeding Innovation Platform, International Rice Research Institute (IRRI) , Los Ba\u00f1os, Laguna 4031 ,","place":["Philippines"]},{"name":"Africa Regional Director, International Rice Research Institute (IRRI) , ILRI-Campus, Nairobi 30709 ,","place":["Kenya"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092909402713900_erag452-B1","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1002\/csc2.20941","article-title":"qSUB2: a novel QTL with positive epistasis with SUB1 locus enhances submergence tolerance in rice","volume":"63","author":"Akintayo","year":"2023","journal-title":"Crop 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waterlogging","volume":"14","author":"Anee","year":"2025","journal-title":"Antioxidants"},{"key":"2026092909402713900_erag452-B5","doi-asserted-by":"crossref","first-page":"1462981","DOI":"10.3389\/fpls.2024.1462981","article-title":"A comprehensive multivariate approach for G\u00d7E interaction analysis in early maturing rice varieties","volume":"15","author":"Anshori","year":"2024","journal-title":"Frontiers in Plant Science"},{"key":"2026092909402713900_erag452-B6","doi-asserted-by":"crossref","first-page":"e70040","DOI":"10.1002\/tpg2.70040","article-title":"Future flooding tolerant rice germplasm: resilience afforded beyond Sub1A gene","volume":"18","author":"Anumalla","year":"2025","journal-title":"The Plant Genome"},{"key":"2026092909402713900_erag452-B7","doi-asserted-by":"crossref","first-page":"kiaf029","DOI":"10.1093\/plphys\/kiaf029","article-title":"Surviving floods: escape and quiescence strategies of rice coping with 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A case study of rice in Ha Tinh province, Vietnam","volume":"9","author":"Giang","year":"2021","journal-title":"Frontiers in Environmental Science"},{"key":"2026092909402713900_erag452-B44","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1007\/s43657-022-00048-z","article-title":"A comprehensive review of high throughput phenotyping and machine learning for plant stress phenotyping","volume":"2","author":"Gill","year":"2022","journal-title":"Phenomics"},{"key":"2026092909402713900_erag452-B45","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1017\/S147926212300014X","article-title":"Mapping of QTLs for flood tolerance in rice using recombinant inbred lines of Indra and a new plant genetic resource AC 39416 A","volume":"20","author":"Girija Rani","year":"2022","journal-title":"Plant Genetic Resources"},{"key":"2026092909402713900_erag452-B46","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s11032-017-0637-5","article-title":"Mapping QTLs for submergence tolerance in rice using a population fixed for SUB1A tolerant allele","volume":"37","author":"Gonzaga","year":"2017","journal-title":"Molecular Breeding"},{"key":"2026092909402713900_erag452-B47","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1093\/plcell\/koab275","article-title":"Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems","volume":"34","author":"Groen","year":"2022","journal-title":"The Plant Cell"},{"key":"2026092909402713900_erag452-B48","doi-asserted-by":"crossref","first-page":"4644","DOI":"10.3390\/su14084644","article-title":"Research status and trends of underwater photosynthesis","volume":"14","author":"Guo","year":"2022","journal-title":"Sustainability"},{"key":"2026092909402713900_erag452-B49","doi-asserted-by":"crossref","first-page":"2795","DOI":"10.1007\/s11033-022-07853-9","article-title":"Flooding tolerance in rice: adaptive mechanism and marker-assisted selection breeding approaches","volume":"50","author":"Haque","year":"2023","journal-title":"Molecular Biology Reports"},{"key":"2026092909402713900_erag452-B50","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nature08258","article-title":"The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water","volume":"460","author":"Hattori","year":"2009","journal-title":"Nature"},{"key":"2026092909402713900_erag452-B51","doi-asserted-by":"crossref","first-page":"548","DOI":"10.3389\/fpls.2016.00548","article-title":"Tuning of redox regulatory mechanisms, reactive oxygen species and redox homeostasis under salinity stress","volume":"7","author":"Hossain","year":"2016","journal-title":"Frontiers in Plant Science"},{"key":"2026092909402713900_erag452-B52","doi-asserted-by":"crossref","first-page":"100247","DOI":"10.1016\/j.eehl.2026.100247","article-title":"Production of rhizosphere reactive oxygen species by root-surface iron plaque during rice growth","volume":"5","author":"Huang","year":"2026","journal-title":"Eco-Environment & Health"},{"key":"2026092909402713900_erag452-B53","doi-asserted-by":"crossref","first-page":"1271539","DOI":"10.3389\/fpls.2023.1271539","article-title":"High-throughput root phenotyping of crop cultivars tolerant to low N in waterlogged soils","volume":"14","author":"Huang","year":"2023","journal-title":"Frontiers in Plant Science"},{"key":"2026092909402713900_erag452-B54","doi-asserted-by":"crossref","first-page":"5477","DOI":"10.1093\/jxb\/erae299","article-title":"Revisiting FR13A for submergence tolerance: beyond the SUB1A gene","volume":"75","author":"Hussain","year":"2024","journal-title":"Journal of Experimental Botany"},{"key":"2026092909402713900_erag452-B55","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1111\/nph.15188","article-title":"Submergence tolerance in rice: resolving a pervasive quandary","volume":"218","author":"Ismail","year":"2018","journal-title":"New Phytologist"},{"key":"2026092909402713900_erag452-B56","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1093\/aob\/mcn211","article-title":"Mechanisms associated with tolerance to flooding during germination and early seedling growth in rice (Oryza sativa. 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