SUB1A Gene Research Articles

Mechanistic Insights and Genetic Approaches for Enhancing Submergence Tolerance in Rice

Rice, a pivotal staple crop, serves as a dietary foundation for approximately half of the global population. Its cultivation, traditionally reliant on submerged conditions, faces significant challenges due to sudden flooding events. The majority of rice varieties are highly sensitive to prolonged submersion beyond a mere seven days, resulting in substantial yield losses. As global climate patterns shift, the occurrence and intensity of flooding are predictable to increase, exacerbating this issue. Therefore, development of rice varieties having enhanced submergence tolerance is critical to sustaining productivity and ensuring food security in flood-prone regions. Understanding the physiological and biochemical mechanisms underlying submergence tolerance is crucial in this context. Key physiological mechanisms include the regulation of carbohydrate reserves for energy during low oxygen availability, ethylene-responsive factors, especially the Sub1A gene to, regulate growth and stress responses, curbing excessive elongation to conserve energy and enhance survival. Additionally, specialized tissues such as aerenchyma and adventitious roots improve oxygen transport and nutrient uptake under flooded conditions. Genetic approaches, including Marker-Assisted Selection (MAS), have been instrumental in the development of submergence-tolerant rice varieties. The integration of the Sub1 QTL, especially the Sub1A gene, into high-yielding rice varieties has led to significant advancements in breeding submergence-tolerant cultivars. These genetic improvements provide a promising solution to mitigate the detrimental effects of flooding on rice production, ensuring the stability and sustainability of this essential crop in the face of changing climate conditions. This review discusses various mechanisms adapted by rice and genetic advancements aimed at enhancing submergence tolerance in rice to secure food production for future generations.

Revisiting FR13A for submergence tolerance: beyond the SUB1A gene.

Revisiting FR13A for submergence tolerance: beyond the SUB1A gene.

Marker assisted breeding of Sub1 introgressed rice (Oryza sativa L.) lines and identification of stable variety MTU 1232 suitable for flood prone ecosystem

The Development of flood-tolerant rice varieties is a prerequisite for climate resilience in flood-prone areas. The present study aimed to develop a stable, high, yielding, and tolerant rice variety against flash floods and stagnant flooding across multiple environments. Sub1A was incorporated into a popular rice variety MTU 1075 using Swarna-sub1 as a donor to generate BC3F5 families. Sub1BC2 was used as a foreground marker for selection, a proxy for the Sub1A gene. RM23865 and RM464 on Chromosome 9 were used as recombinant markers. Backcross families from the BC3F2 generation were evaluated under two weeks of flash floods 15 days after transplanting. This was followed by stagnant flooding and survived BC3F4 families were used for background selection using a 50K high-density SNP chip. The nine best families identified were included in the field trial evaluation under eight environments. Consequently, MTU Rice 1232 was identified as a high-yielding, flood-tolerant rice variety using Additive Main effects and Multiplicative Interaction stability analysis. The MTU Rice 1232 ranked first by the Best linear unbiased prediction (BLUP) based ranking parameters and 4th based on stability parameters ranking. This flood-tolerant rice variety can tolerate both flash floods and stagnant flooding and possesses an 80% survival rate. It has a yield potential of 3792 Kg ha-1 under severe floods and 6000 Kg ha-1 under normal conditions.

Creation of new rice genotypes tolerant to long-term water flooding using DNA markers

The aim of this work is to search for informative molecular markers for the identification of the Sub1A gene in rice breeding material. Studies have been carried out to identify specialized DNA marker systems that provide a clear control of the inheritance of the target locus on the basis of tolerance to prolonged flooding with water, as a factor in the fight against weeds. Of the studied set of microsatellite markers (13 SSRs), two SSR markers (RM 7481, PrC3) showed high efficiency in detecting polymorphism between donor varieties and varieties of domestic selection. Based on them, the DNA of the obtained hybrid rice plants of the F2 segregating population was analyzed for this trait and a laboratory express method was performed to evaluate the phenotype. During the statistical analysis, it was found that both SSR markers are co-heritable with the trait of tolerance to prolonged flooding under water, and on their basis, plants were selected that have the target gene in the genotype in the homozygous state, which were transferred to the breeding process for study by morphometric characteristics and economically valuable traits.

DEVELOPMENT OF NON-TIDAL ADAPTIVE RICE VARIETIES: MOLECULAR MARKER ASSISTED SELECTION OF BC2F1 PROGENIES

Submergence stress and drought stress are main abiotic constraints encountered in South Sumatra swampland rice cultivation area. The development of new abiotic stress tolerant varieties through the introgresion of tolerance genes, such as the Sub1 gene (submergence tolerance) by using Marker-assisted Backcrossing (MABC method) is one of an ideal solution to obtain an adaptive rice variety for those conditions. The study was carried out at Faculty of Agriculture, Sriwijaya University, Indonesia. In this study, BC2F1 used as the plant materials derived from backcross performed in BC1F1 and the recipient parent, Inpago 5. Previously, BC1F1 obtained from backcrossed progenies from Inpara 8 (inherited Sub1A gene) and Inpago 5 as recipient parent, a drought tolerant variety. The main objective of this study was to analyze the Sub1 introgressed plants in backcrossed progeny BC2F1 that closest similarity to recipient parent. The result showed that Sub1 introgression was confirmed by a tightly linked Sub1 gene marker, SUB1C173 marker. Out of 47 plants, 20 plants were selected based on foreground selection. Those plants were further analyzed on background selection by using 13 SSR markers. Based on the foreground and background selection, two plants, viz, plant no. 41 and 44, were selected and will be used for further study.

Identification of the allelic state of the flood tolerance gene (Sub-1A) in rice breeding samples

Rice is one of the most important crops in the world. Rice crops provide food for many people in Asia and the Pacific. In Russia, the production of this crop is concentrated in several regions, one of which is the Rostov region. The trend towards the greening of agriculture throughout the world and in Russia is becoming more and more stable. In order to combat weeds using an environmentally friendly herbicide-free technology, it is necessary to increase the water layer on simultaneous surviving rice plants. For such a strategy to work, it is necessary to develop varieties that are resistant to flooding. The purpose of the current study was to identify the allelic state of the Sub1A flood resistance gene in breeding rice samples. The objects of the study were 90 rice samples of the sixth generation, identified in hybrids obtained from crossing Russian varieties with gene donor varieties. The analysis was carried out by such methods as DNA extraction using the “DNA-Extran-3” commercial kit (Sintol, Russia), classical PCR with the specialized diagnostic marker Sub1A203, separation of amplicons by electrophoresis in 2 % agarose gels, analysis of electrophoregrams in the software Bio-Rad ImageLab 6.0.1. As a result of the analysis, there was identified the allelic state of the Sub1A gene in 90 rice samples. A significant number of samples carried a non-functional recessive allele, the presence of the gene was not established in 19 samples. The Sub1A gene was in the heterozygous state in 9 samples. The presence of a functional dominant allele of the target gene was identified n 5 breeding samples. There has been recommended to use these samples in breeding work aimed at developing new rice varieties resistant to prolonged flooding.

Silicon enhances the submergence tolerance of rice by regulating quiescence strategy and alleviating oxidative damage

The safety of rice production under submergence is one of the research hotspots worldwide. Although the effects of silicon (Si) on enhancing plant stress tolerance have been widely investigated, the underlying mechanisms mediated by Si under submergence remains poorly understood. In this study, wild type (WT) and Si-defective mutant (lsi1) rice were chosen to investigate the mechanisms of Si-mediated rice resistance to submergence. Our results showed that Si addition effectively mitigated oxidative damages under submergence by reducing the content of hydrogen peroxide (H2O2) and superoxide (O2.-) in WT rice plants. Moreover, Si treatment increased rice yield by 21.5% for WT rice under submergence. The application of Si significantly inhibited the elongation and internode length in WT rice under submergence, through the synergistic regulation of endogenous hormones ethylene (ET), gibberellic acid (GA) and jasmonic acid (JA). Further investigation showed that the ethylene-responsive factor (ERF) SUB1A gene was expressed under submergence in WT and lsi1 rice, but Si addition did not influence the expression of SUB1A. Interestingly, exogenous Si down-regulated the relative expression levels of Si transporter genes Lsi1 and Lsi2 in WT rice roots by 51.7% and 48.0%, respectively. However, the physiological characteristics and genes expression of lsi1 rice were not affected by Si application regardless of submergence. The present study indicated that Si enhances the submergence tolerance and reduce the adverse effects of yield loss through the removal of reactive oxygen species and the adjustment of quiescence strategy.

Identifikasi Gen Sub1A Pada Varietas Tebu Tahan Genangan

Tebu dapat tumbuh pada berbagai kondisi lingkungan yang cukup beragam termasuk pada lahan marginal seperti lahan yang sering tergenang. Lahan tergenang dapat menurunkan produksi tebu cukup signifikan. Tujuan penelitian ini adalah menemukan gen toleran kebasahan yang terdapat pada 8 varietas unggul komersial tebu yang tahan genangan yaitu PS 881, PS 862, PS 882, Kentung, PSJT 941, Bulu Lawang, PS 865 dan Kidang Kencana serta mengidentifikasi kemiripannya dengan gen Sub1A. Dengan diperolehnya gen toleran kebasahan pada varietas tebu tahan genangan di harapkan varietas tebu tersebut dapat ditanam di lahan yang sering tergenang dan dapat memberikan tambahan sumbangan produksi gula secara Nasional. Sehingga pada akhirnya dapat mengurangi impor yang secara kontinu dilakukan pemerintah setiap tahun dan sebagai solusi peningkatan produksi pangan berbasis lahan daratan dalam menghadapi perubahan iklim. Tahapan untuk memperoleh dan mengidentifikasi gen toleran kebasahan atau tahan genangan adalah pengkondisian lahan tanaman tebu tergenang, isolasi DNA dari tanaman tebu yang tergenang, penentuan konsentrasi dan kemurnian DNA yang diperoleh, konfirmasi DNA yang diisolasi dengan elektroforesis dan identifikasi gen Sub 1 A pada DNA sampel metode PCR dengan primer Sub 1 A 203 R/F dan kontrol Positif DNA tanaman padi transgenik yang mengandung gen Sub 1 A. Hasil kegiatan penelitian dapat disimpukan bahwa 8 varietas unggul komersial tebu yaitu PS 881, PS 862, PS 882, Kentung, PSJT 941, Bulu Lawang, PS 865 dan Kidang Kencana semuanya mempunyai gen yang mirip dengan gen Sub 1 A. Dengan varietas PS 881 dan Kentung menghasilkan band sekuens DNA target gen Sub 1 A paling tebal.

English

Selection done using molecular markers has spread to all types of agricultural plants and animals. Marker assisted selection (MAS) is safe for ecology and food products consumed. The purpose of the study is to develop Sub1A gene (which determines tolerance to prolonged flooding) in the Russian rice varieties using DNA-markers and Polymerase chain reaction (PCR) analysis. A large volume of pre-breeding rice material (F2-F4, BC2F2) was created with tolerance genes for prolonged flooding, to control weed in rice agrophytocenosis. The forms with 120-130-day vegetation period were selected. An analysis of the co-inheritance of simple sequence repeat (SSR) markers Sub1Aq, Sub1C173, Sub1A203 with the Sub1 gene was carried out. It revealed the codominance of the selected microsatellites. They can be used to identify and visualize the allelic state of a given target gene in the breeding material. The recurrent parental rice forms, donors of the gene Sub 1 and the hybrids of F2 and Ð’Ði2F1 population were tested on tolerance to prolonged flooding. The gene is effective in ensuring resistance to this stress factor within 2 to 3 weeks and it can be recommended for the breeding programs to develop modern genetic resources of rice tolerant to prolonged and deep flooding for weed control on rice fields. Key words: Polymerase chain reaction (PCR), rice, Sub genes, tolerance to flooding, weeds.

The rice SUB1A gene: Making adaptation to submergence and post-submergence possible.

The rice SUB1A gene: Making adaptation to submergence and post-submergence possible.

Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

BackgroundFlooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown.ResultsNineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression.ConclusionThis study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.

Variation in expression of Sub1 gene confers differential response to submergence tolerance in rice (Oryza sativa L.)

A cluster of three ethylene response factor (ERF) like genes at the Sub1 locus has been identified from rice variety FR13A that confers tolerance to submergence for about 14 days. Restriction digestion-based haplotype variations among 11 rice accessions were analyzed to generate polymorphisms at Sub1C and Sub1A loci. Considering different combinations of SNPs (haplotype), four haplotypes: A1C1, A1C2, A2C2 and A0C2 were detected. Further, using semi-quantitative RT-PCR - Sub1A and Sub1C transcripts in different haplotypes were interpreted in respect with stem elongation and survival for understanding mechanism of submergence tolerance. Expression variations in Sub1 genes in relation with duration of submergence, haplotype diversity and an interaction of loci were found. Differential expression of Sub1A and Sub1C affected the stem elongation and survival of different haplotypes differentially. In tolerant varieties (A1C1 haplotype, IR40931), the highest expressed gene was Sub1A; while expression of Sub1C was lower. Over-expression of Sub1A gene in tolerant varieties, suppressed the stem elongation under submergence, which improved the level of submergence tolerance. In susceptible cultivar (Fulkari), the highest-expressed gene was Sub1C, while the Sub1A was not expressed which showed higher susceptibility. In moderately tolerant varieties (Kottamali), both Sub1A and Sub1C gene transcripts were up-regulated by submergence and higher level of both Sub1A and Sub1C genes transcripts. The varieties in A2C2 haplotype showed moderate level of tolerance without the Sub1A1 allele and a distinct novel mechanism favored the expression of both the Sub1A and Sub1C alleles that confer higher tolerance under complete submergence.

English

Submergence is one of the major constraints to rice production in many rice growing areas in the world. The Sub1A gene has been demonstrated to dramatically improve submergence tolerance in rice. Here, we report the identification of a novel submergence response (RS1) gene that is specifically induced in the Sub1A-mediated submergence tolerance response. Under submergence, RS1 was upregulated in M202 (Sub1A) but downregulated in M202 in RNA-seq and microarray assays. Expression analyses of various tissues and developmental stages show that RS1 mRNA levels are high in leaves and sheaths, but low in roots, stems, and panicles. Our results also show that RS1 is highly expressed under submergence, drought, and NaCl stresses, but not under cold or dehydration stress. Hormone ABA treatment induces, whereas GA treatment decreases, RS1 expression. The RS1 and Sub1A genes are co-regulated under submergence. Overexpression of RS1 in transgenic Kitaake (without Sub1A) and M202(Sub1A)×Kitaake do not result in enhanced submergence tolerance. Conversely, down-regulation of RS1 in M202(Sub1A)×Kitaake lead to weaken submergence tolerance. We hypothesize that RS1 may play a role in the Sub1A-mediated submergence tolerance pathway. Key word: Rice (Oryza sativa L.), submergence, RNA-seq, Sub1A, abiotic stress.

Marker-assisted breeding of the rice restorer line Wanhui 6725 for disease resistance, submergence tolerance and aromatic fragrance.

BackgroundRice is a staple food crop in the world. With the increase in world population and economic development, farmers need to produce more rice in limited field. However, the rice production is frequently affected by biotic and abiotic stresses. The use of natural disease resistance and stress tolerance through genetic breeding is the most efficient and economical way to combat or acclimate to these stresses. In addition, rice with aromatic fragrance can significantly increase market value for its good grain quality. Mianhui 725 (MH725) is an elite restorer line that has been widely used to produce three-line hybrid rice in China. We previously introduced rice bacterial blight resistance genes Xa4 and Xa21 into MH725 and obtained an introgression rice line Wanhui 421 (WH421), which theoretically possesses 96.9% genetic background of MH725.ResultsHere we report the introduction and pyramiding of disease resistance genes Xa27 and Pi9, submergence tolerance gene Sub1A and aromatic fragrance gene badh2.1 in WH421 through backcrossing and marker-assisted selection. The newly developed introgression rice line was designated as Wanhui 6725 (WH6725), which theoretically possesses 95.0% genetic background of MH725. WH6725 and its hybrid rice conferred disease resistance to both blast and bacterial blight diseases and showed tolerance to submergence for over 14 days without significant loss of viability. Compared with non-aromatic rice MH725, WH6725 has strong aromatic fragrance. The major important agronomic traits and grain quality of WH6725 and its hybrid rice obtained in field trials were similar to those of MH725 and the control hybrid rice, indicating that WH6725 is as good as MH725 when it is used as a restorer line for three-line hybrid rice production.ConclusionWe have successfully developed a new restorer line WH6725 with disease resistance to rice blast and bacterial blight, tolerance to submergence and aromatic fragrance, which can be used to replace MH725 for hybrid rice production.

Development of High-Yielding Rice Varieties Suitable for Swampy Lands in Indonesia

Productivity of swampy land rice varieties in Indonesia remains low due to abiotic and biotic stresses. Iron toxicity, submergence and long-term flooding are common problems that affect plant growth, sometimes leading to total crop loss. Meanwhile, rice blast, rice tungro virus (RTV), and bacterial leaf blight (BLB) can also lead to severe yield loss. These stresses could be overcome by an integrative approach of cultural practices and planting multi-stress tolerant rice. Here we describe the development of new high-yielding varieties that are adapted to the swampy land environments in Indonesia with multi-stress tolerance to diverse abiotic and biotic stresses. Multi-environmental trials were performed in nine locations to screen for several abiotic and biotic stresses in the field and greenhouse in 2012 and 2013. This study identified promising rice lines that had high grain yield as well as tolerance to iron toxicity and submergence, resistance to BLB and RTV, and good grain quality. The best line was B11377F-MR-34-2, derived from a double cross among Cinglonik, IRBB7, Mamberamo and IR64. It was confirmed that this advanced breeding line carries the submergence tolerance gene, SUB1, through expression analysis of the SUB1A gene. Another promising line was B11586F-MR-11-2-2, having iron toxicity tolerance, resistance to RTV, and high milling recovery. Moreover, these lines have passed the Indonesian national variety release committee and have been named as Inpara8 and Inpara9, and are targeted for dissemination and adoption in the swampy areas.

English

Submergence is one of the major constraints to rice production. Bioinformatics approach has been widely used to identify candidate genes on many biological aspects. In the present study, a novel gene involved in submergence stress in rice, Os07g47670 was identified by in silico approach. The amino acid sequence of Os07g47670 is highly homologous to hypoxia-responsive family proteins. No disordered regions are found in the Os07g47670 protein. In the Os07g47670 gene promoter, there are two ARE cis-regulatory elements, indicating that Os07g47670 is associated with submergence responsiveness. The Os07g47670 transcript levels are higher in roots of one or two-week old plants than in other tissues. Without the Sub1A gene, the expression level of Os07g47670 in M202 is low under submergence, ACC treatment, and normal condition. However, in the Sub1A genetic background, the Os07g47670 transcript level is strongly induced during submergence, and peaked at day 1 during submergence. The mRNA level of Os07g47670 in M202(Sub1A) was also significantly increased by ACC treatment. High expression level of Os07g47670 is correlated with the existence of the Sub1A gene. Os07g47670 shares similar expression patterns with Sub1A, ADH1, SLR1, and SLRL1 and are co-induced under submergence. Thus, we have documented Os07g47670 as a novel gene associated with submergence stress response. The identification of Os07g47670 will facilitate the understanding of the molecular mechanism of submergence tolerance in rice.   Key words: Rice (Oryza sativa L.), in silico approach, submergence, waterlogging.&nbsp

Ethylene is not involved in adaptive responses to flooding in the Amazonian wild rice species Oryza grandiglumis

The Amazonian wild rice Oryza grandiglumis has two contrasting adaptation mechanisms to flooding submergence: a quiescence response to complete submergence at the seedling stage and an escape response based on internodal elongation to partial submergence at the mature stage. We investigated possible factors that trigger these responses. In stem segments excised from mature O. grandiglumis plants, complete submergence only slightly promoted internodal elongation with increased ethylene levels in the internodes, while partial submergence substantially promoted internodal elongation without increased ethylene levels in the internodes. Incubation of non-submerged stem segments under a continuous flow of humidified ethylene-free air promoted internodal elongation to the same extent as that observed for partially submerged segments. Applied ethylene had little effect on the internodal elongation of non-submerged segments irrespective of humidity conditions. These results indicate that the enhanced internodal elongation of submerged O. grandiglumis plants is not triggered by ethylene accumulated during submergence but by the moist surroundings provided by submergence. The growth of shoots in O. grandiglumis seedlings was not promoted by ethylene or complete submergence, as is the case in O. sativa cultivars possessing the submergence-tolerant gene SUB1A. However, because the genome of O. grandiglumis lacks the SUB1A gene, the quiescence response of O. grandiglumis seedlings to complete submergence may be regulated by a mechanism distinct from that involved in the response of submergence-tolerant O. sativa cultivars.

Quiescence in rice submergence tolerance: an evolutionary hypothesis

Rice (Oryza sativa) varieties differ considerably in their tolerance to submergence, a trait that has been associated with the SUB1A gene. Recently, this gene was found in some wild rice species and landraces, which along with O. sativa, belong to the AA genome type group. On the basis of geographical and historical data, we hypothesize that SUB1A-1 from wild species may have been introgressed into domesticated rice. This introgression probably occurred in the Ganges Basin, with the subsequent spread of the SUB1A-1 to other areas of South Asia due to human migration. The lack of the SUB1A gene in diploid CC genome type wild rice showing submergence-tolerant traits suggests the presence of a different survival mechanism in this genetic group.

SUB1A‐dependent and ‐independent mechanisms are involved in the flooding tolerance of wild rice species

Crop tolerance to flooding is an important agronomic trait. Although rice (Oryza sativa) is considered a flood-tolerant crop, only limited cultivars display tolerance to prolonged submergence, which is largely attributed to the presence of the SUB1A gene. Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits. In this study, we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance. Oryza nivara and Oryza rufipogon accessions, belonging to the A-genome group, together with Oryza sativa, showed a wide range of submergence responses, and the tolerance-related SUB1A-1 and the intolerance-related SUB1A-2 alleles were found in tolerant and sensitive accessions, respectively. Flooding-tolerant accessions of Oryza rhizomatis and Oryza eichingeri, belonging to the C-genome group, were also identified. Interestingly, SUB1A was absent in these species, which possess a SUB1 orthologue with high similarity to O. sativa SUB1C. The expression patterns of submergence-induced genes in these rice genotypes indicated limited induction of anaerobic genes, with classical anaerobic proteins poorly induced in O. rhizomatis under submergence. The results indicated that SUB1A-1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C-genome group, which show instead a SUB1A-independent response to submergence.

Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru

Short-term submergence is a recurring problem in many rice production areas. The SUB1 gene, derived from the tolerant variety FR13A, has been transferred to a number of widely grown varieties, allowing them to withstand complete submergence for up to 2weeks. However, in areas where longer-term submergence occurs, improved varieties having higher tolerance levels are needed. To search for novel quantitative trait loci (QTLs) from other donors, an F(2:3) population between IR72 and Madabaru, both moderately tolerant varieties, was investigated. After a repeated phenotyping of 466 families under submergence stress, a subset of 80 families selected from the two extreme phenotypic tails was used for the QTL analysis. Phenotypic data showed transgressive segregation, with several families having an even higher survival rate than the FR13A-derived tolerant check (IR40931). Four QTLs were identified on chromosomes 1, 2, 9, and 12; the largest QTL on chromosome 1 had a LOD score of 11.2 and R (2) of 52.3%. A QTL mapping to the SUB1 region on chromosome 9, with a LOD score of 3.6 and R (2) of 18.6%, had the tolerant allele from Madabaru, while the other three QTLs had tolerant alleles from IR72. The identification of three non-SUB1 QTLs from IR72 suggests that an alternative pathway may be present in this variety that is independent of the ethylene-dependent pathway mediated by the SUB1A gene. These novel QTLs can be combined with SUB1 using marker assisted backcrossing in an effort to enhance the level of submergence tolerance for flood-prone areas.