Rice Science ›› 2025, Vol. 32 ›› Issue (2): 160-176.DOI: 10.1016/j.rsci.2025.01.002
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Sanchika Snehi1, Ravi Kiran Kt2, Sanket Rathi1, Sameer Upadhyay1, Suneetha Kota3, Satish Kumar Sanwal4, Lokeshkumar Bm4, Arun Balasubramaniam1, Nitish Ranjan Prakash4(
), Pawan Kumar Singh1()
Received:2024-09-12
Accepted:2024-12-18
Online:2025-03-28
Published:2025-04-14
Contact:
Nitish Ranjan Prakash (nitishranjan240@gmail.com); Pawan Kumar Singh (pks.gpb@bhu.ac.in)
Sanchika Snehi, Ravi Kiran Kt, Sanket Rathi, Sameer Upadhyay, Suneetha Kota, Satish Kumar Sanwal, Lokeshkumar Bm, Arun Balasubramaniam, Nitish Ranjan Prakash, Pawan Kumar Singh. Discerning Genes to Deliver Varieties: Enhancing Vegetative- and Reproductive-Stage Flooding Tolerance in Rice[J]. Rice Science, 2025, 32(2): 160-176.
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Fig. 1. Overall physiological strategy for flooding stress tolerance in rice. A, Complete submergence of rice plants under flash floods for 14‒21 d at the seedling and tillering stages (vegetative stages). Rice employs one of two strategies, viz. the quiescent strategy or the escape strategy, to manage hypoxic conditions. B, Prolonged stagnant flooding (with vegetative parts submerged) during the booting to grain-filling stages. Rice can manage hypoxic conditions in submerged plant parts and enhance its survival through increased aerenchyma formation, creating barriers to radial oxygen loss, leak-proof internal transport of gases and metabolites, and the formation of gas films. C, Response of rice plants to complete submergence. The quiescent strategy reduces growth and metabolism to save energy and metabolites for post-stress recovery, while the escape strategy enhances growth by internode elongation and faster aerenchyma development to maintain metabolism. ERF, Ethylene response factor. DAS, Days after sowing.
| QTL | Chr | Trait | SD | Linked marker | LOD | PVE (%) | Parent | MP | MT | Reference |
|---|---|---|---|---|---|---|---|---|---|---|
| qSUB6.1 | 6 | Submergence tolerance | S1 | P1/M3-1‒P2/M1-11 | 4.7 | 26.5 | IR74 × FR13A | RIL | AFLP & RFLP | Nandi et al, |
| qSUB7.1 | 7 | Submergence tolerance | S1 | P2/M1-5‒P2/M8-5 | 3.6 | 21.4 | ||||
| qSUB9.1 | 9 | Submergence tolerance | S1 | RZ698 | ||||||
| qSUB11.1 | 11 | Submergence tolerance | S1 | P1/M5-2‒P1/M5-13 | 3.2 | 19.4 | ||||
| qSUB12.1 | 12 | Submergence tolerance | S1 | P3/M4-5‒P3/M1-7 | 3.2 | 21.4 | ||||
| qLNE1.1 | 1 | Internode increment | S2 | RG109‒sd-1 | 18.9 | 33.1 | IR74 × Jalmagna | RIL | RFLP & AFLP | Sripongpangkul et al, |
| qLNE4.1 | 4 | Internode increment | S2 | P3M1-5‒P3M5-1 | 10.7 | 36.7 | ||||
| qPPS5.1 | 5 | Survival rate, tolerance score | S3 | R1553 | 11.2 | 34.1 | IR49830 × CT6241 | DH | RFLP & SSLP | Toojinda et al, |
| qPPS9.1 | 9 | Survival rate, tolerance score | S3 | RZ698 | 17.3 | 48.3 | ||||
| qEEA12.1 | 12 | Early elongation ability | S4 | RM5479‒RM6953 | 18.2 | 41.0 | Habibganj Aman VIII × Patnai 23 | F2 | RFLP & SSR | Tang et al, |
| qTIL2.1 | 2 | Internode elongation ability | S4 | RM208 | 4.9 | 14.4 | NIL1-3-12 × C9285 | F2 | SSR | Nagai et al, |
| qSUB1.1 | 1 | Submergence tolerance | S5 | MDC17‒RM12168 | 9.4 | 41.9 | IR72 × Madabaru | F2:3 | SSR & InDel | Septiningsih et al, 2012 |
| qSUB2.1 | 2 | Submergence tolerance | S5 | RM6318‒RM2578 | 3.8 | 19.6 | ||||
| qSUB9.1 | 9 | Submergence tolerance | S5 | RM23911‒RM23966 | 3.6 | 18.6 | ||||
| qSUB12.1 | 12 | Submergence tolerance | S5 | RM511‒RM463 | 4.2 | 21.5 | ||||
| qSUB1.1 | 1 | Submergence tolerance | S1 | id1000556‒id1003559 | 5.04 | 20.2 | FR13A × IR42 | RIL | SSR & SNP | Gonzaga et al, |
| qSUB9.1 | 9 | Submergence tolerance | S1 | id9001352‒SC3 | 16.89 | 53.0 | ||||
| qSUB8.1 | 8 | Submergence tolerance | S1 | 8608433-8686009 | 10.26 | 25.7 | Ciherang-SUB1 × IR10F365 | RIL | 6kSNP chip | Gonzaga et al, |
| qDTF3.1 | 3 | Days to 50% flowering | S6 | 2499734‒2560888 | 12.5 | 26.0 | Ciherang-SUB1 × IR10F365 | RIL | 6kSNP chip | Singh et al, |
| qFLW3.1 | 3 | Flag leaf width | S6 | 2499734‒2560888 | 4.0 | 11.3 | ||||
| qGY3.1 | 3 | Grain yield | S6 | 2499734‒2560888 | 6.2 | 14.3 | ||||
| qGY5.1 | 5 | Grain yield | S6 | id5003312‒ud5000983 | 3.66 | 12.2 | ||||
| qSER5.1 | 5 | Shoot elongation rate | S6 | ud5000983‒id5013231 | 12.5 | 32.0 | ||||
| qFLL5.1 | 5 | Flag leaf length | S6 | ud5000983‒5747652 | 6.18 | 14.0 | ||||
| qPL9.1 | 9 | Panicle length | S6 | 9641863‒9869869 | 5.47 | 22.0 | ||||
| qGW10.1 | 10 | Grain weight | S6 | 10603169‒10703329 | 6.3 | 13.1 | ||||
| qSTI-EL3.1 | 3 | Stem elongation | S6 | SNP130‒SNP112 | 2.36 | 23.4 | Rashpanjor × Swarna | RIL | GBS | Chattopadhyay et al, 2021 |
| qSTI-GW10.1 | 10 | Stem elongation | S6 | SNP389‒SNP407 | 2.15 | 54.9 | ||||
| qSTI-EL12.1 | 12 | Stem elongation | S6 | SNP488‒SNP498 | 2.05 | 15.5 | ||||
| qSUB2.1 | 2 | Submergence tolerance | S1 | 10.78 | 10.8 | TOS6454 × (Each of FARO44, FARO52, and FARO60) | RIL | DArT | Akintayo et al, |
Table 1. List of major QTLs (> 10% PVE) on flooding tolerance at vegetative-stage submergence and stagnant flooding in rice.
| QTL | Chr | Trait | SD | Linked marker | LOD | PVE (%) | Parent | MP | MT | Reference |
|---|---|---|---|---|---|---|---|---|---|---|
| qSUB6.1 | 6 | Submergence tolerance | S1 | P1/M3-1‒P2/M1-11 | 4.7 | 26.5 | IR74 × FR13A | RIL | AFLP & RFLP | Nandi et al, |
| qSUB7.1 | 7 | Submergence tolerance | S1 | P2/M1-5‒P2/M8-5 | 3.6 | 21.4 | ||||
| qSUB9.1 | 9 | Submergence tolerance | S1 | RZ698 | ||||||
| qSUB11.1 | 11 | Submergence tolerance | S1 | P1/M5-2‒P1/M5-13 | 3.2 | 19.4 | ||||
| qSUB12.1 | 12 | Submergence tolerance | S1 | P3/M4-5‒P3/M1-7 | 3.2 | 21.4 | ||||
| qLNE1.1 | 1 | Internode increment | S2 | RG109‒sd-1 | 18.9 | 33.1 | IR74 × Jalmagna | RIL | RFLP & AFLP | Sripongpangkul et al, |
| qLNE4.1 | 4 | Internode increment | S2 | P3M1-5‒P3M5-1 | 10.7 | 36.7 | ||||
| qPPS5.1 | 5 | Survival rate, tolerance score | S3 | R1553 | 11.2 | 34.1 | IR49830 × CT6241 | DH | RFLP & SSLP | Toojinda et al, |
| qPPS9.1 | 9 | Survival rate, tolerance score | S3 | RZ698 | 17.3 | 48.3 | ||||
| qEEA12.1 | 12 | Early elongation ability | S4 | RM5479‒RM6953 | 18.2 | 41.0 | Habibganj Aman VIII × Patnai 23 | F2 | RFLP & SSR | Tang et al, |
| qTIL2.1 | 2 | Internode elongation ability | S4 | RM208 | 4.9 | 14.4 | NIL1-3-12 × C9285 | F2 | SSR | Nagai et al, |
| qSUB1.1 | 1 | Submergence tolerance | S5 | MDC17‒RM12168 | 9.4 | 41.9 | IR72 × Madabaru | F2:3 | SSR & InDel | Septiningsih et al, 2012 |
| qSUB2.1 | 2 | Submergence tolerance | S5 | RM6318‒RM2578 | 3.8 | 19.6 | ||||
| qSUB9.1 | 9 | Submergence tolerance | S5 | RM23911‒RM23966 | 3.6 | 18.6 | ||||
| qSUB12.1 | 12 | Submergence tolerance | S5 | RM511‒RM463 | 4.2 | 21.5 | ||||
| qSUB1.1 | 1 | Submergence tolerance | S1 | id1000556‒id1003559 | 5.04 | 20.2 | FR13A × IR42 | RIL | SSR & SNP | Gonzaga et al, |
| qSUB9.1 | 9 | Submergence tolerance | S1 | id9001352‒SC3 | 16.89 | 53.0 | ||||
| qSUB8.1 | 8 | Submergence tolerance | S1 | 8608433-8686009 | 10.26 | 25.7 | Ciherang-SUB1 × IR10F365 | RIL | 6kSNP chip | Gonzaga et al, |
| qDTF3.1 | 3 | Days to 50% flowering | S6 | 2499734‒2560888 | 12.5 | 26.0 | Ciherang-SUB1 × IR10F365 | RIL | 6kSNP chip | Singh et al, |
| qFLW3.1 | 3 | Flag leaf width | S6 | 2499734‒2560888 | 4.0 | 11.3 | ||||
| qGY3.1 | 3 | Grain yield | S6 | 2499734‒2560888 | 6.2 | 14.3 | ||||
| qGY5.1 | 5 | Grain yield | S6 | id5003312‒ud5000983 | 3.66 | 12.2 | ||||
| qSER5.1 | 5 | Shoot elongation rate | S6 | ud5000983‒id5013231 | 12.5 | 32.0 | ||||
| qFLL5.1 | 5 | Flag leaf length | S6 | ud5000983‒5747652 | 6.18 | 14.0 | ||||
| qPL9.1 | 9 | Panicle length | S6 | 9641863‒9869869 | 5.47 | 22.0 | ||||
| qGW10.1 | 10 | Grain weight | S6 | 10603169‒10703329 | 6.3 | 13.1 | ||||
| qSTI-EL3.1 | 3 | Stem elongation | S6 | SNP130‒SNP112 | 2.36 | 23.4 | Rashpanjor × Swarna | RIL | GBS | Chattopadhyay et al, 2021 |
| qSTI-GW10.1 | 10 | Stem elongation | S6 | SNP389‒SNP407 | 2.15 | 54.9 | ||||
| qSTI-EL12.1 | 12 | Stem elongation | S6 | SNP488‒SNP498 | 2.05 | 15.5 | ||||
| qSUB2.1 | 2 | Submergence tolerance | S1 | 10.78 | 10.8 | TOS6454 × (Each of FARO44, FARO52, and FARO60) | RIL | DArT | Akintayo et al, |
| Technique used | Genotype | Stress level | DEG | Class of genes | Reference |
|---|---|---|---|---|---|
| 44k Agilent microarray | FR13A and Goda Heenati (both carrying SUB1 but differ in submergence tolerance) | 14-day-old seedlings were submerged for 3 d | FR13A (692 up-regulated and 819 down-regulated); Goda Heenati (1 281 up-regulated and 1 507 down-regulated) | Antioxidant/ROS scavenging genes are important for better performance of shoots of FR13A during submergence | Xiong et al, |
| RT-PCR | M202 (susceptible) and M202-SUB1 (tolerant) | Submergence of 14- day-old seedlings | DWARF4 (DWF4); DWARF1 (DWF1) | Brassinosteroid synthesis, transport, and responsive genes are differentially regulated and modulated gibberellic acid signaling and homeostasis | Schmitz et al, 2013 |
| qRT-PCR | FR13A (tolerant) and Tung Lu 3 (sensitive) | Submergence of 10-day-old seedlings | sucrose synthase 1 and alcohol dehydrogenase 1 | Higher expression of both genes, while expression is much higher in Tung Lu 3 | Yang et al, |
| qRT-PCR for TF gene family | IR64 (susceptible) and IR64-SUB1 (tolerant) | 75-day-old plants were submerged for 30 h | One common down-regulated in both; IR64 (27 down-regulated); IR64-SUB1 (13 up-regulated and 7 down-regulated) | DEGs belonging to NAC, MYB, TIFY, and Zn-finger TFs, are down-regulated upon submergence; DEGs in regulating hormonal pathways, i.e. gibberellins, abscisic acid, and jasmonic acid, apart from ethylene, are up-regulated | Sharma et al, |
| qRT-PCR for WRKY gene family | Nipponbare, Epagri 108, and BR IRGA 409 | 14-day-old seedlings were submerged for 6, 12, 24, and 48 h | 100-fold higher expression of OsWRKY11 and OsWRKY56 under submergence | WRKY transcription factors are known for their role in stress responses and in aerenchyma development | Viana et al, |
| RNA-seq | Oryza coarctata | Submergence up to 12 h | 15 158 DEGs | Stress-responsive transcription factors of bHLH, MYB, AP2-EREBP, WRKY, NAC, and bZIP class are differentially regulated | Garg et al, |
| RNA-seq | M202 (susceptible) and M202-SUB1 (tolerant) | 3 d submergence of 14-day-old seedlings | 703 genes up-regulated; 307 genes down-regulated | Carbohydrate metabolism, peroxisome (ROS scavenging), growth, and development are up‐regulated in M202-SUB1 | Locke et al, |
| RNA-seq | Nampyeongbyeo | Submergence at 14 d after heading and sampled after 4 d | 106 genes up-regulated; 30 genes down-regulated | Starch and sucrose synthesis, glycolysis, and carbon fixation are important in submergence response; genes for each step related to starch and d-glucose synthesis are down-regulated in the seeds and leaves but up-regulated in the stems | Lee et al, |
| RNA-seq | Yuefu (lowland) and IRAT109 (upland rice) | 28-day-old seedlings were exposed to anoxic condition at root | Yuefu (667 DEGs); IRAT109 (448 DEGs) | Phytohormone signalling (auxin, jasmonic acid, and ethylene), energy metabolism, aerenchyma formation, ROS, and cell wall modification are common among DEGs | Liu et al, |
Table 2. Transcriptomic results of flooding tolerance at the vegetative stage and stagnant flooding at the reproductive stage in rice.
| Technique used | Genotype | Stress level | DEG | Class of genes | Reference |
|---|---|---|---|---|---|
| 44k Agilent microarray | FR13A and Goda Heenati (both carrying SUB1 but differ in submergence tolerance) | 14-day-old seedlings were submerged for 3 d | FR13A (692 up-regulated and 819 down-regulated); Goda Heenati (1 281 up-regulated and 1 507 down-regulated) | Antioxidant/ROS scavenging genes are important for better performance of shoots of FR13A during submergence | Xiong et al, |
| RT-PCR | M202 (susceptible) and M202-SUB1 (tolerant) | Submergence of 14- day-old seedlings | DWARF4 (DWF4); DWARF1 (DWF1) | Brassinosteroid synthesis, transport, and responsive genes are differentially regulated and modulated gibberellic acid signaling and homeostasis | Schmitz et al, 2013 |
| qRT-PCR | FR13A (tolerant) and Tung Lu 3 (sensitive) | Submergence of 10-day-old seedlings | sucrose synthase 1 and alcohol dehydrogenase 1 | Higher expression of both genes, while expression is much higher in Tung Lu 3 | Yang et al, |
| qRT-PCR for TF gene family | IR64 (susceptible) and IR64-SUB1 (tolerant) | 75-day-old plants were submerged for 30 h | One common down-regulated in both; IR64 (27 down-regulated); IR64-SUB1 (13 up-regulated and 7 down-regulated) | DEGs belonging to NAC, MYB, TIFY, and Zn-finger TFs, are down-regulated upon submergence; DEGs in regulating hormonal pathways, i.e. gibberellins, abscisic acid, and jasmonic acid, apart from ethylene, are up-regulated | Sharma et al, |
| qRT-PCR for WRKY gene family | Nipponbare, Epagri 108, and BR IRGA 409 | 14-day-old seedlings were submerged for 6, 12, 24, and 48 h | 100-fold higher expression of OsWRKY11 and OsWRKY56 under submergence | WRKY transcription factors are known for their role in stress responses and in aerenchyma development | Viana et al, |
| RNA-seq | Oryza coarctata | Submergence up to 12 h | 15 158 DEGs | Stress-responsive transcription factors of bHLH, MYB, AP2-EREBP, WRKY, NAC, and bZIP class are differentially regulated | Garg et al, |
| RNA-seq | M202 (susceptible) and M202-SUB1 (tolerant) | 3 d submergence of 14-day-old seedlings | 703 genes up-regulated; 307 genes down-regulated | Carbohydrate metabolism, peroxisome (ROS scavenging), growth, and development are up‐regulated in M202-SUB1 | Locke et al, |
| RNA-seq | Nampyeongbyeo | Submergence at 14 d after heading and sampled after 4 d | 106 genes up-regulated; 30 genes down-regulated | Starch and sucrose synthesis, glycolysis, and carbon fixation are important in submergence response; genes for each step related to starch and d-glucose synthesis are down-regulated in the seeds and leaves but up-regulated in the stems | Lee et al, |
| RNA-seq | Yuefu (lowland) and IRAT109 (upland rice) | 28-day-old seedlings were exposed to anoxic condition at root | Yuefu (667 DEGs); IRAT109 (448 DEGs) | Phytohormone signalling (auxin, jasmonic acid, and ethylene), energy metabolism, aerenchyma formation, ROS, and cell wall modification are common among DEGs | Liu et al, |
| Analysis performed | Genotype | Stress level | Metabolite induced/detected | Reference |
|---|---|---|---|---|
| GC-MS and NMR | M202 (sensitive); M202-SUB1 (tolerant) | Seedlings at the 3-leaf stage were submerged for 0, 1, 2, and 3 d and then de-submerged for 1 d | GC-MS analysis exclusively identifies metabolites such as amino acids phenylalanine, proline, pyroglutamate, as well as TCA cycle intermediates like citrate, malate, and succinate. It also detects organic acids including GABA, glycerate, oxalate, shikimate, and threonate | Barding et al, |
| NMR, RPIP-UPLC-MS, GC-MS | M202 (sensitive); M202-SUB1 (tolerant) | 14-day-old seedlings were submerged for 3 d | The influence of SUB1 on metabolite levels, especially free amino acids, glucose, and sucrose, during the recovery period also affects the dynamics of trehalose-6-phosphate and the expression of mRNAs that encode crucial enzymes and signaling proteins | Locke et al, |
| LC-MS | Wufengyou 286 | 8 d submergence after panicle differentiation stage | On rice spikelets, 113 differential metabolites are detected when comparing submergence and control conditions, with 55 metabolites showing an increase and 58 metabolites decrease under submergence. The stress caused by submergence disrupted the electron transfer chain, leading to a reduction in photosynthetic rate. Additionally, the plant’s antioxidant system is triggered to manage reactive oxygen species and regulate their metabolisms | Xiong et al, |
Table 3. Metabolomic studies on flooding tolerance at the vegetative stage and stagnant flooding at the reproductive stage in rice.
| Analysis performed | Genotype | Stress level | Metabolite induced/detected | Reference |
|---|---|---|---|---|
| GC-MS and NMR | M202 (sensitive); M202-SUB1 (tolerant) | Seedlings at the 3-leaf stage were submerged for 0, 1, 2, and 3 d and then de-submerged for 1 d | GC-MS analysis exclusively identifies metabolites such as amino acids phenylalanine, proline, pyroglutamate, as well as TCA cycle intermediates like citrate, malate, and succinate. It also detects organic acids including GABA, glycerate, oxalate, shikimate, and threonate | Barding et al, |
| NMR, RPIP-UPLC-MS, GC-MS | M202 (sensitive); M202-SUB1 (tolerant) | 14-day-old seedlings were submerged for 3 d | The influence of SUB1 on metabolite levels, especially free amino acids, glucose, and sucrose, during the recovery period also affects the dynamics of trehalose-6-phosphate and the expression of mRNAs that encode crucial enzymes and signaling proteins | Locke et al, |
| LC-MS | Wufengyou 286 | 8 d submergence after panicle differentiation stage | On rice spikelets, 113 differential metabolites are detected when comparing submergence and control conditions, with 55 metabolites showing an increase and 58 metabolites decrease under submergence. The stress caused by submergence disrupted the electron transfer chain, leading to a reduction in photosynthetic rate. Additionally, the plant’s antioxidant system is triggered to manage reactive oxygen species and regulate their metabolisms | Xiong et al, |
Fig. 2. Germplasm bases include landraces native to submergence- prone regions, deep-water rice landraces (donors for stagnant flooding tolerance traits), released varieties (for submergence, semi- deep-water, and deep-water ecologies), wild relatives, and respective donors for component traits. A, Overall breeding strategy to develop vegetative-stage submergence and reproductive-stage stagnant flooding tolerant rice varieties involves the physiological, morphological, and molecular characterization of traits to identify component traits (easy to track across generations and simple to score) governing flooding responses. A high-throughput phenotyping platform can dissect component traits and use hyperspectral signatures to monitor stress and post-stress recovery. SUB1-dependent and -independent pathways can be explored to identify candidate genes/QTLs, which can then be used in marker-assisted backcross breeding (e.g., transferring SUB1A-1 alleles), gene pyramiding, haplotype-based selection, and marker- assisted introgression of alleles/genes from wild species. Reproductive-stage stagnant flood tolerance is influenced by multiple physiological traits; hence, a genomic selection (GS)- based breeding strategy (augmented with haplotype-assisted selection and environmental characterization) is deemed suitable. B, Proposed breeding strategy includes the evaluation of the germplasm base and the identification of donors for traits governing vegetative-stage sub- mergence tolerance and reproductive- stage stagnant flooding tolerance. Elite lines can be crossed with donors, and the accumulation of beneficial alleles can be achieved using a haplotype-based GS strategy (targeting Sub1-dependent and -independent pathways) for vegetative-stage sub- mergence and a multi-trait GS approach for reproductive-stage stagnant flooding tolerance. The identified elite lines can be used for field evaluation under stress in multi- location trials. GA, Gibberellic acid; GWAS, Genome- wide association study; ROS, Reactive oxygen species.
| Gene | RAP-DB ID | Function | Reference |
|---|---|---|---|
| OsRboh1 | Os01g0360200 | NADPH oxidase | Wu and Yang, |
| OsFLZ2 | Os01g0593200 | FCS-like zinc finger protein 2 | Ma et al, |
| OsACS5 | Os01g0192900 | 1-Aminocyclopropane-1-carboxylic acid synthase 5 | Zhou et al, |
| ALDH2a | Os02g0730000 | Mitochondrial aldehyde dehydrogenase | Nakazono et al, |
| OsCTP | Os02g0465900 | Vacuolar antiporter-regulating protein | Qi et al, |
| OsMPK3 | Os02g0148100 | TEY-type mitogen-activated protein kinase | Singh and Sinha, |
| OsABA8ox1 | Os02g0703600 | Similar to abscisic acid 8ʹ-hydroxylase 1; Response to submergence | Saika et al, |
| OsDWF4 | Os03g0227700 | Cytochrome P450 90B2, brassinosteroid C-22 hydroxylase | Schmitz et al, |
| OsERF66 | Os03g0341000 | ETHYLENE RESPONSE FACTOR 66 | Hsiao et al, |
| OsGAPDH | Os04g0486600 | Cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 | Arumugam Pillai et al, |
| OsGID1 | Os05g0407500 | GIBBERELLIN-INSENSITIVE DWARF 1 (GID1) | Du et al, |
| OsERF67 | Os07g0674800 | ETHYLENE RESPONSE FACTOR 67 | Hsiao et al, |
| OsGGT | Os10g0555100 | Glycogenin glucosyltransferase | Qi et al, |
| OsARD1 | Os10g0419400 | Acireductone dioxygenase; SUBMERGENCE-INDUCED PROTEIN 2 | Liang et al, |
| OsDWF1 | Os10g0397400 | BRASSINOSTEROID DEFICIENT DWARF 2 | Schmitz et al, |
| OsMT1a | Os11g0704500 | Down-regulation promotes aerenchyma formation | Yamauchi et al, |
| OsSUB1A-1 | Absent in Reference ‘Nipponbare’ | Group VII ethylene response factors | Xu et al, |
Table 4. Cloned and characterized genes that can be targeted for haplotype-based selection and gene editing to generate vegetative-stage submergence tolerance in rice.
| Gene | RAP-DB ID | Function | Reference |
|---|---|---|---|
| OsRboh1 | Os01g0360200 | NADPH oxidase | Wu and Yang, |
| OsFLZ2 | Os01g0593200 | FCS-like zinc finger protein 2 | Ma et al, |
| OsACS5 | Os01g0192900 | 1-Aminocyclopropane-1-carboxylic acid synthase 5 | Zhou et al, |
| ALDH2a | Os02g0730000 | Mitochondrial aldehyde dehydrogenase | Nakazono et al, |
| OsCTP | Os02g0465900 | Vacuolar antiporter-regulating protein | Qi et al, |
| OsMPK3 | Os02g0148100 | TEY-type mitogen-activated protein kinase | Singh and Sinha, |
| OsABA8ox1 | Os02g0703600 | Similar to abscisic acid 8ʹ-hydroxylase 1; Response to submergence | Saika et al, |
| OsDWF4 | Os03g0227700 | Cytochrome P450 90B2, brassinosteroid C-22 hydroxylase | Schmitz et al, |
| OsERF66 | Os03g0341000 | ETHYLENE RESPONSE FACTOR 66 | Hsiao et al, |
| OsGAPDH | Os04g0486600 | Cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 | Arumugam Pillai et al, |
| OsGID1 | Os05g0407500 | GIBBERELLIN-INSENSITIVE DWARF 1 (GID1) | Du et al, |
| OsERF67 | Os07g0674800 | ETHYLENE RESPONSE FACTOR 67 | Hsiao et al, |
| OsGGT | Os10g0555100 | Glycogenin glucosyltransferase | Qi et al, |
| OsARD1 | Os10g0419400 | Acireductone dioxygenase; SUBMERGENCE-INDUCED PROTEIN 2 | Liang et al, |
| OsDWF1 | Os10g0397400 | BRASSINOSTEROID DEFICIENT DWARF 2 | Schmitz et al, |
| OsMT1a | Os11g0704500 | Down-regulation promotes aerenchyma formation | Yamauchi et al, |
| OsSUB1A-1 | Absent in Reference ‘Nipponbare’ | Group VII ethylene response factors | Xu et al, |
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