Feature Review

Meta-analysis of Flood Tolerance Genes in Rice: Evaluating Their Impact on Agronomic Traits  

Mingliang  Jin , Yanfu  Wang , Danyan Ding
Institute of Life Sciences, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China
Author    Correspondence author
Rice Genomics and Genetics, 2024, Vol. 15, No. 6   
Received: 27 Oct., 2024    Accepted: 26 Nov., 2024    Published: 03 Dec., 2024
© 2024 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract

Rice, as a staple crop, plays a crucial role in global food security; however, flood stress poses significant challenges to its productivity. This study conducts a comprehensive meta-analysis of flood tolerance genes in rice, aiming to understand their genetic contributions and evaluate their impact on key agronomic traits. Utilizing rigorous criteria, statistical methodologies, and bioinformatics tools, the analysis synthesizes data from diverse studies to elucidate the distribution, frequency, and functional roles of genes associated with flood tolerance, such as SUB1A. A detailed case study on the SUB1A gene highlights its discovery, molecular mechanisms, and practical applications in enhancing submergence tolerance. The findings underscore the agronomic implications of flood tolerance genes, including yield stability and economic benefits in flood-prone regions. Challenges such as gene expression variability and limited phenotypic data are addressed, and future directions emphasize genome editing, multi-omics approaches, and integrated breeding strategies. This study provides critical insights to guide the development of resilient rice varieties, contributing to sustainable agriculture and food security.

Keywords
Rice flood tolerance; SUB1A gene; Agronomic traits; Meta-analysis; Genetic breeding

1 Introduction

Rice (Oryza sativa L.) is a fundamental staple food for more than half of the world's population, playing a crucial role in global food security and economic stability (Singh et al., 2016; Entila et al., 2021). It is cultivated extensively across diverse agro-ecological zones, making it a vital crop for both subsistence and commercial agriculture (Zhang et al., 2017; Beena et al., 2021). The importance of rice extends beyond nutrition, as it also supports the livelihoods of millions of farmers and contributes significantly to the economies of many developing countries (Septiningsih and Mackill, 2018).

 

Flooding is a major abiotic stress that severely impacts rice production, leading to substantial yield losses and economic damage (Oladosu et al., 2020; Panda et al., 2021). The frequency and intensity of flooding events are expected to increase due to climate change, exacerbating the challenges faced by rice farmers (Khahani et al., 2021). Flood stress affects rice at various growth stages, from germination to maturity, and can result in complete crop failure if not managed effectively (Septiningsih and Mackill, 2018). The complexity of flood tolerance in rice involves multiple physiological and genetic factors, making it a challenging trait to breed for.

 

Genetic solutions offer a promising approach to enhancing flood tolerance in rice. Significant progress has been made in identifying and mapping quantitative trait loci (QTLs) associated with flood tolerance, such as the SUB1 QTL, which has been successfully incorporated into several high-yielding rice varieties through marker-assisted backcrossing (Singh et al., 2016; Oladosu et al., 2020). These genetic advancements have led to the development of rice varieties that can withstand submergence and other flood-related stresses, thereby improving yield stability in flood-prone areas (Septiningsih and Mackill, 2018; Panda et al., 2021). The integration of modern genomic tools and breeding techniques continues to be essential for developing rice varieties with enhanced flood tolerance (Khahani et al., 2021; Zhu et al., 2024).

 

This study attempts to comprehensively evaluate the genetic contributions of flood tolerance genes in rice and their impact on key agronomic traits, discuss the identification of stable QTLs and key genes that confer flood tolerance and their physiological mechanisms, and provide an overview of their effects on yield and other important traits. By synthesizing data from various studies, this analysis aims to generate knowledge that aids in the development of more resilient rice varieties, ultimately contributing to sustainable rice production and food security in flood-prone regions.

 

2 Methodology

2.1 Criteria for selecting studies included in the meta-analysis

The selection criteria for studies included in this meta-analysis focused on identifying research that investigated the genetic basis of flood tolerance in rice. Studies were selected based on the following criteria: (1) they must have performed quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), or transcriptomic analyses related to flood tolerance; (2) they must have evaluated agronomic traits under flood conditions; and (3) they must have provided sufficient statistical data for meta-analysis. For instance, studies like those by which examined QTLs related to adventitious root formation under submergence (Lin et al., 2022), and which performed GWAS to identify loci contributing to flooding tolerance during germination (Zhang et al., 2017), were included.

 

2.2 Statistical methods used for synthesizing genetic data

The genetic data from the selected studies were synthesized using meta-QTL analysis, which is a robust approach for consolidating QTL information across different studies and environments. This method refines the confidence intervals of QTLs, making it easier to identify stable QTLs and candidate genes. For example, the study by utilized meta-QTL analysis to identify stable QTLs for yield and root architecture traits under water deficit conditions (Khahani et al., 2021). Additionally, mixed linear models were employed in GWAS to detect significant single nucleotide polymorphisms (SNPs) associated with flood tolerance traits (Zhang et al., 2017; Thapa et al., 2022).

 

2.3 Agronomic traits considered in the analysis

The agronomic traits considered in this meta-analysis included both primary and secondary traits related to flood tolerance. Primary traits included survival rate, plant height, and yield under flood conditions. Secondary traits encompassed root architecture traits such as root length, root thickness, and the formation of adventitious roots, as well as physiological traits like coleoptile elongation and leaf greenness. For instance, focused on the development of aquatic adventitious roots, while examined traits like stem length and panicle length under stagnant flooding conditions (Sitaresmi et al., 2019; Lin et al., 2022).

 

2.4 Tools and software used for analysis

Various tools and software were employed to conduct the meta-analysis and bioinformatics pipelines. Meta-QTL analysis was performed using software like MetaQTL, which helps in refining QTL intervals and identifying candidate genes. GWAS was conducted using software such as TASSEL and GAPIT, which facilitate the identification of significant SNPs and their associations with phenotypic traits. For transcriptomic data analysis, tools like DESeq2 and edgeR were used to identify differentially expressed genes under flood conditions (De Oliveira-Busatto et al., 2022). Additionally, bioinformatics pipelines were utilized for sequence alignment, SNP calling, and haplotype analysis (Figure 1) (Zhang et al., 2017; Thapa et al., 2022).

 


Figure 1 Statistical analysis and candidate region estimation of seq-rs2699 and seq-rs2701 (Adopted from Zhang et al., 2017)

Image caption: (A) Haplotypes consist of the two significant SNPs, Numbers indicates the amounts of corresponding accessions; (B) Phenotypic effect of each haplotype; (C) Local manhattan plots and LD heatmap around the peak on chromosome 6, the candidate region estimated using r2>0.6 (Adopted from Zhang et al., 2017)

 

This section outlines the methodology used in the meta-analysis of flood tolerance genes in rice. Studies were selected based on their focus on genetic mapping and evaluation of agronomic traits under flood conditions. Statistical methods like meta-QTL analysis and mixed linear models in GWAS were employed to synthesize genetic data. The analysis considered primary and secondary agronomic traits related to flood tolerance, and various tools and software were used to perform the meta-analysis and bioinformatics pipelines. This comprehensive approach aims to identify stable QTLs and candidate genes that can enhance flood tolerance in rice (Volante et al., 2017).

 

3 Genetic Basis of Flood Tolerance in Rice

3.1 Overview of genes associated with submergence tolerance

Submergence tolerance in rice is primarily governed by the SUB1 locus, which includes the genes Sub1A, Sub1B, and Sub1C. These genes have been extensively studied for their role in enabling rice plants to survive prolonged periods of submergence. The Sub1A-1 allele, in particular, has been identified as a key player in conferring submergence tolerance, as seen in the variety FR13A (Oe et al., 2021). The SUB1 locus operates by limiting elongation growth during submergence, thereby conserving energy and enhancing survival rates (Oladosu et al., 2020). Additionally, allelic variations in these genes among different rice cultivars have been linked to varying levels of submergence tolerance, although no consistent association has been found due to low minor allele frequencies and exceptions in the genotype panel (Figure 2) (Singh et al., 2020).

 


Figure 2 Regeneration of rice cultivars afer two weeks of complete submergence in a concrete pond at NDUAT, Ayodhya in 2012 (Adopted from Singh et al., 2020)

Image caption: Diferential response of the cultivars (planted in single rows) is clearly visible two weeks afer de-submergence (Adopted from Singh et al., 2020)

 

3.2 Mechanisms of anaerobic germination in rice

Anaerobic germination in rice involves several genetic and physiological adaptations that allow seeds to germinate and seedlings to grow under low oxygen conditions. Key genes involved in this process include those regulating glycolysis and gluconeogenesis pathways, which are activated to generate energy under anaerobic conditions (Lin et al., 2019). The presence of transcription factors such as ERFs (Ethylene Response Factors) and WRKYs also plays a crucial role in mediating responses to anaerobic stress by regulating the expression of genes involved in energy metabolism and stress responses (Naithani et al., 2023). These mechanisms collectively enable rice seeds to germinate and seedlings to elongate their coleoptiles, facilitating survival in flooded conditions.

 

3.3 Genetic regulation of root system adaptations to flooding

The development of adventitious roots is a critical adaptation for rice plants under flooding conditions. Genetic traits associated with the formation of these roots have been linked to specific quantitative trait loci (QTLs) such as those on chromosomes 1 and 12, which promote the development of aquatic adventitious roots (AAR). These roots exhibit distinct morphological and anatomical traits that enhance their ability to function in submerged environments. For instance, the formation of thicker roots with higher elongation capacity and desiccation tolerance is a key adaptation that allows rice plants to survive prolonged submergence (Lin et al., 2022). Additionally, the regulation of root system architecture by genes such as OsLAZY1 and IL2 is crucial for maintaining root functionality under flooded conditions (Naithani et al., 2023).

 

3.4 Role of transcription factors and signaling pathways in flood response

Transcription factors and signaling pathways play pivotal roles in orchestrating the flood response in rice. A network of 57 transcription factors, including OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, and TCPs, has been identified as key regulators of seed germination, coleoptile elongation, and submergence response (Naithani et al., 2023). These transcription factors interact with each other and with other proteins to regulate the expression of target genes involved in flood tolerance. For example, the ERF66 and ERF67 transcription factors are direct targets of Sub1A-1 and are upregulated in response to submergence, mediating the expression of genes that enhance submergence tolerance (Oe et al., 2021). Additionally, signaling pathways involving ethylene, gibberellins, and abscisic acid are crucial for modulating the plant's growth and stress responses under flooded conditions (Oladosu et al., 2020).

 

The genetic basis of flood tolerance in rice involves a complex interplay of genes, transcription factors, and signaling pathways. Key genes such as those in the SUB1 locus, along with mechanisms for anaerobic germination and root system adaptations, play crucial roles in enabling rice plants to survive and thrive under submergence. Understanding these genetic and molecular mechanisms provides valuable insights for breeding and developing flood-tolerant rice varieties, which is essential for ensuring stable rice production in flood-prone regions (Gonzaga et al., 2017; Barik et al., 2020).

 

4 Meta-analysis Results

4.1 Distribution and frequency of flood tolerance genes across rice varieties

Flood tolerance genes in rice, such as Sub1A, have been widely studied and incorporated into various rice varieties to enhance their resilience to submergence. For instance, the Sub1A gene has been successfully transferred into drought-tolerant japonica rice DT3, resulting in progenies with enhanced submergence stress tolerance (Wu et al., 2021). Additionally, genome-wide association studies (GWAS) have identified significant single nucleotide polymorphisms (SNPs) associated with flood tolerance traits, such as coleoptile length during germination under flooded conditions, across diverse indica rice varieties (Zhang et al., 2017). The distribution of these genes varies significantly among different rice genotypes, with some varieties showing a higher frequency of beneficial alleles for flood tolerance (Thapa et al., 2022).

 

4.2 Impact of identified genes on agronomic traits such as yield, plant height, and survival rate

The incorporation of flood tolerance genes like Sub1A has shown a positive impact on several agronomic traits. For example, rice lines carrying the Sub1A gene exhibited higher survival rates (92%~96%) compared to their recurrent parent DT3 (64%) under submergence conditions (Figure 3) (Wu et al., 2021). Moreover, these lines maintained good yield and grain quality, demonstrating the gene's effectiveness in improving both survival and productivity under flood stress. Similarly, the presence of specific QTLs for stagnant flooding tolerance has been linked to better yield performance and plant height management, which are crucial for reducing lodging under prolonged waterlogged conditions (Singh et al., 2017; Kato et al., 2019).

 


Figure 3 Characterization of BC3F5 lines and its parental lines, IR96321-315-240 and DT3, at rice seedling stage under submergences (Adopted from Wu et al., 2021)

Image caption: (a) The phenotype of 21-day-old plants. (b) Phenotype of rice seedlings dewatering after 14 day submergence. (c) The phenotype of plants after 1 day of recovery from 14 day of submergence. (d) The phenotype of rice seedlings submerged for 14 day and then allowed to recover for 14 day. (e) Changes in plant height after submergence. (f) Total stem elongation rate (TSE%) of seedlings after 14 day submergence followed by 14 day recovery. (g) Survival rates of seedlings after 14 day submergence followed by 14 day recovery. Data are presented as the mean of three replications, and the bars represent the standard error of the mean (n =3). Values with the different letters are significantly different (p<0.05 by LSD test) (Adopted from Wu et al., 2021)

 

4.3 Variation in gene performance under different environmental and agronomic conditions

The performance of flood tolerance genes can vary significantly under different environmental and agronomic conditions. For instance, rice genotypes carrying the Sub1 QTL showed a 49% lower yield under stagnant flooding compared to those without the gene, highlighting the need for specific adaptations to different types of flooding stress (Kato et al., 2019). Additionally, the effectiveness of these genes can be influenced by seasonal variations, as seen in the differential yield reductions under stagnant flooding during the wet and dry seasons. This variation underscores the importance of considering environmental factors when evaluating the performance of flood tolerance genes.

 

4.4 Statistical synthesis of gene-trait associations

Meta-analyses and GWAS have provided robust statistical evidence linking specific genes to flood tolerance traits. For example, a meta-QTL analysis identified 61 stable QTLs associated with major agronomic traits under water deficit conditions, refining the confidence intervals and pinpointing functionally characterized genes (Khahani et al., 2021). Similarly, GWAS identified significant SNPs associated with coleoptile length and flooding tolerance index, with some loci showing strong haplotype effects on trait performance (Zhang et al., 2017). These statistical syntheses highlight the complex genetic architecture underlying flood tolerance and the potential for marker-assisted selection to enhance breeding programs.

 

The meta-analysis of flood tolerance genes in rice reveals a diverse distribution of these genes across different varieties, with significant impacts on agronomic traits such as yield, plant height, and survival rate. The performance of these genes varies under different environmental conditions, emphasizing the need for targeted breeding strategies. Statistical analyses have successfully identified key gene-trait associations, providing valuable insights for developing flood-resilient rice varieties (Sitaresmi et al., 2019).

 

5 Case Study: Impact of SUB1A Gene on Submergence Tolerance in Rice

5.1 Discovery and characterization of SUB1A gene

The SUB1A gene, an ethylene-responsive transcription factor, was first identified in the aus-type rice landrace FR13A, known for its remarkable submergence tolerance. This gene plays a crucial role in enabling rice plants to survive prolonged submergence by limiting underwater elongation growth, thereby conserving energy and resources during stress periods (Sharma et al., 2018; Singh et al., 2020; Alpuerto et al., 2022). The discovery of SUB1A has led to significant advancements in understanding the genetic basis of submergence tolerance in rice.

 

5.2 Mechanisms through which SUB1A enhances submergence tolerance

SUB1A enhances submergence tolerance through several mechanisms. It modulates gene regulation, metabolism, and elongation growth during submergence, promoting a quiescence strategy that conserves energy by restricting elongation of the uppermost leaves (Alpuerto et al., 2016; Locke et al., 2018). Additionally, SUB1A influences hormonal pathways, such as auxin and gibberellin, to modulate growth responses and maintain metabolic homeostasis during and after submergence (Alpuerto et al., 2016; Oe et al., 2021; Alpuerto et al., 2022). The gene also interacts with mitogen-activated protein kinase 3 (MPK3) in a positive feedback loop, further enhancing stress tolerance (Singh and Sinha, 2016).

 

5.3 Performance of SUB1A-integrated rice varieties in field conditions

Field studies have demonstrated that rice varieties integrated with the SUB1A gene, such as the M202(Sub1) line, exhibit superior submergence tolerance compared to their non-SUB1A counterparts. These varieties show rapid recovery of photosynthetic function and energy reserve metabolism upon desubmergence, leading to improved survival and yield under submergence stress (Alpuerto et al., 2016; Gonzaga et al., 2017; Locke et al., 2018). The incorporation of SUB1A into elite rice varieties through marker-assisted backcrossing has resulted in the development of several submergence-tolerant mega-varieties that perform well in flood-prone regions (Gonzaga et al., 2016; Oladosu et al., 2020).

 

5.4 Limitations and future prospects for the utilization of SUB1A in breeding programs

Despite the success of SUB1A in enhancing submergence tolerance, there are limitations to its effectiveness under severe and prolonged flooding conditions. Recent studies suggest that additional quantitative trait loci (QTLs) are needed to complement SUB1A for improved tolerance (Gonzaga et al., 2016). Future breeding programs should focus on identifying and incorporating these additional QTLs, as well as exploring genome-wide association studies (GWAS) to develop rice varieties with enhanced resilience to multiple stressors, including drought, salinity, and disease resistance (Oladosu et al., 2020).

 

6 Agronomic Implications of Flood Tolerance Genes

6.1 Enhancement of yield and stability under flood-prone environments

Flood tolerance genes, such as the SUB1A gene, have been shown to significantly enhance the yield and stability of rice crops in flood-prone environments. The incorporation of these genes into rice varieties allows the plants to survive prolonged submergence, thereby reducing yield losses that typically occur due to flooding. For instance, the SUB1A gene has been successfully integrated into various rice cultivars, resulting in improved survival rates and yield stability under submergence conditions (Oladosu et al., 2020; Wu et al., 2021; De Oliveira-Busatto et al., 2022). This genetic enhancement is crucial for maintaining productivity in regions frequently affected by flash floods and heavy rainfall.

 

6.2 Integration of flood tolerance traits into commercial breeding programs

The integration of flood tolerance traits into commercial breeding programs has been facilitated by advanced genetic techniques such as marker-assisted backcrossing (MABC). This method allows for the precise transfer of flood tolerance genes like SUB1 into elite rice varieties without compromising other desirable agronomic traits (Oladosu et al., 2020; Panda et al., 2021; Wu et al., 2021). The development of multi-stress tolerant rice varieties, which combine flood tolerance with other stress resistance traits such as drought and salinity tolerance, is a promising approach to enhance the resilience of rice crops in diverse environmental conditions (Singh et al., 2016).

 

6.3 Economic benefits of deploying flood-tolerant rice varieties in vulnerable regions

Deploying flood-tolerant rice varieties in regions vulnerable to flooding can lead to significant economic benefits. These varieties reduce the risk of crop failure and ensure stable rice production, which is vital for food security and the livelihoods of farmers in flood-prone areas. The economic advantages include reduced costs associated with replanting and crop loss mitigation, as well as increased income stability for farmers (Oladosu et al., 2020; Panda et al., 2021; Wu et al., 2021). The successful implementation of flood-tolerant rice varieties can also contribute to the overall economic development of rural communities by enhancing agricultural productivity and sustainability.

 

6.4 Synergistic effects of flood tolerance genes with other stress-resistance traits

Flood tolerance genes can have synergistic effects when combined with other stress-resistance traits, leading to the development of rice varieties that are resilient to multiple environmental stresses. For example, the combination of flood tolerance with drought resistance traits has been shown to improve the overall adaptability and yield of rice under varying stress conditions (Beena et al., 2021; Wu et al., 2021; Sankarapillai et al., 2023). This multi-trait approach not only enhances the survival and productivity of rice crops but also provides a comprehensive solution to the challenges posed by climate change and extreme weather events. The integration of multiple stress-resistance traits into a single variety can significantly improve the robustness and reliability of rice production systems.

 

7 Challenges in Utilizing Flood Tolerance Genes

7.1 Variability in gene expression under different environmental conditions

One of the primary challenges in utilizing flood tolerance genes in rice is the variability in gene expression under different environmental conditions. For instance, the expression of the OsCBL10 gene, which is associated with flood tolerance during seed germination, varies significantly between upland and lowland rice cultivars. This variability can lead to inconsistent performance of flood-tolerant traits across different environments, making it difficult to develop universally effective flood-tolerant rice varieties (Ye et al., 2018).

 

7.2 Limited research on the role of wild rice species in flood tolerance

Another challenge is the limited research on the role of wild rice species in flood tolerance. While significant progress has been made in understanding the genetic mechanisms of flood tolerance in cultivated rice, the potential contributions of wild rice species remain underexplored. Wild rice species may possess unique genetic traits that could enhance flood tolerance, but their integration into breeding programs has been minimal (Septiningsih and Mackill, 2018; Panda et al., 2021).

 

7.3 Challenges in phenotyping for flood tolerance under field conditions

Phenotyping for flood tolerance under field conditions presents several challenges. Accurate phenotyping requires controlled and consistent flooding conditions, which are difficult to achieve in field settings. Additionally, the complex nature of flood tolerance, which involves multiple physiological and morphological traits, complicates the phenotyping process. This makes it challenging to identify and select for flood-tolerant traits effectively (Zhang et al., 2017; Lin et al., 2022).

 

7.4 Gaps in integrating molecular and traditional breeding approaches

There are significant gaps in integrating molecular and traditional breeding approaches for developing flood-tolerant rice varieties. While molecular breeding techniques, such as marker-assisted selection, have advanced the development of flood-tolerant varieties, traditional breeding methods still play a crucial role. However, the integration of these approaches is often hindered by a lack of comprehensive understanding of the genetic and physiological mechanisms underlying flood tolerance (Kurokawa et al., 2018; De Oliveira-Busatto et al., 2022).

 

The utilization of flood tolerance genes in rice faces several challenges, including variability in gene expression under different environmental conditions, limited research on the role of wild rice species, difficulties in phenotyping for flood tolerance under field conditions, and gaps in integrating molecular and traditional breeding approaches. Addressing these challenges requires a multifaceted approach that combines advanced genetic research with practical breeding strategies to develop robust flood-tolerant rice varieties.

 

8 Future Directions

8.1 Advancing genome editing tools for targeted improvements in flood tolerance

The application of advanced genome editing tools, such as CRISPR/Cas9, holds significant promise for enhancing flood tolerance in rice. Recent studies have demonstrated the potential of CRISPR/Cas9 to target specific genes associated with abiotic stress tolerance, including submergence tolerance genes like SUB1A (Barrero et al., 2021; Nascimento et al., 2023). By precisely editing these genes, researchers can develop rice varieties that are better equipped to withstand flooding conditions, thereby improving crop resilience and productivity in flood-prone areas.

 

8.2 Application of multi-omics approaches to identify novel flood tolerance genes

Multi-omics approaches, which integrate genomics, transcriptomics, proteomics, and metabolomics, offer a comprehensive strategy for identifying novel genes associated with flood tolerance. For instance, the use of advanced omics studies has been suggested to unveil the physiological and molecular mechanisms underlying flood tolerance in new genetic resources like AC39416A (Rani et al., 2023). By leveraging these technologies, researchers can gain deeper insights into the complex genetic networks and pathways involved in flood tolerance, leading to the discovery of new candidate genes for breeding programs.

 

8.3 Strategies for gene pyramiding to enhance multiple stress resistances

Gene pyramiding, which involves combining multiple genes that confer resistance to different stresses, is a promising strategy for developing rice varieties with enhanced resilience. Studies have shown that combining genes for submergence tolerance (e.g., SUB1) with other stress resistance genes can lead to the development of rice lines that are tolerant to various abiotic stresses, including drought and salinity (Pradhan et al., 2019; Shailani et al., 2020; Panda et al., 2021). This approach ensures that rice plants can survive and thrive under multiple adverse environmental conditions, thereby securing food production in challenging climates.

 

8.4 Policy recommendations for supporting flood-tolerant rice research and deployment

To effectively support the research and deployment of flood-tolerant rice varieties, it is crucial to implement supportive policies and funding mechanisms. Governments and international organizations should prioritize investments in research programs focused on developing flood-tolerant rice through advanced breeding techniques and genome editing tools. Additionally, policies should facilitate the dissemination and adoption of these improved varieties by farmers, particularly in regions that are highly susceptible to flooding. By creating an enabling environment for innovation and adoption, policymakers can help ensure food security and resilience in the face of climate change.

 

Advancing genome editing tools, applying multi-omics approaches, and implementing gene pyramiding strategies are essential for improving flood tolerance in rice. Supportive policies and funding are also critical to facilitate research and the widespread adoption of flood-tolerant rice varieties. These future directions collectively aim to enhance the resilience of rice crops, ensuring sustainable production in flood-prone areas.

 

9 Concluding Remarks

The meta-analysis of flood tolerance genes in rice has revealed significant insights into the genetic and physiological mechanisms underlying flood tolerance. Key findings include the identification of quantitative trait loci (QTLs) and specific genes such as Sub1A, which confer submergence tolerance by promoting traits like adventitious root formation and rapid coleoptile elongation under flooded conditions. Additionally, the study highlighted the role of anaerobic germination (AG) tolerance, which is crucial for seedling establishment in flooded environments, with genes like Rc and various transcription factors playing pivotal roles.

 

Flood tolerance genes are of paramount agronomic importance as they directly contribute to the resilience and productivity of rice in flood-prone regions. The ability to develop adventitious roots and elongate coleoptiles rapidly under submergence conditions enables rice plants to survive and maintain yield stability during and after flooding events. Moreover, the integration of these genes into breeding programs has led to the development of rice varieties that can withstand both drought and submergence, thereby ensuring food security in the face of climate change.

 

To further advance the development of flood-tolerant rice varieties, there is a need for integrated research efforts that combine genomics, phenomics, and advanced breeding techniques. Collaborative studies focusing on the identification and functional characterization of novel flood tolerance genes, as well as the development of high-throughput phenotyping methods, are essential. Additionally, leveraging biotechnological tools such as genome editing and transcriptome analysis can accelerate the breeding of rice varieties with enhanced flood tolerance and other desirable agronomic traits.

 

Acknowledgments

We are grateful to Dr. Chen for critically reading the manuscript and providing valuable feedback that improved the clarity of the text. We express our heartfelt gratitude to the two anonymous reviewers for their valuable comments on the manuscript.

 

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

 

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Locke A., Barding G., Sathnur S., Larive C., and Bailey-Serres J., 2018, Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery.., Plant cell and Environment, 4(14): 721-736.

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Naithani S., Mohanty B., Elser J., D’Eustachio P., and Jaiswal P., 2023, Biocuration of a transcription factors network involved in submergence tolerance during seed germination and coleoptile elongation in rice Oryza sativa, Plants, 12(11): 2146.

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Nascimento F., Rocha A., Soares J., Mascarenhas M., Ferreira M., Lino L., De Souza Ramos A., Diniz L., Mendes T., Ferreira C., Santos-Serejo J., and Amorim E., 2023, Gene editing for plant resistance to abiotic factors: a systematic review, Plants, 12(2): 305.

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Oe S., Sasayama D., Luo Q., Fukayama H., Hatanaka T., and Azuma T., 2021, Growth responses of seedlings under complete submergence in rice cultivars carrying both the submergence-tolerance gene SUB1A-1 and the floating genes SNORKELs, Plant Production Science, 25: 70-77.

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Oladosu Y., Rafii M., Arolu F., Chukwu S., Muhammad I., Kareem I., Salisu M., and Arolu I., 2020, Submergence tolerance in rice: review of mechanism breeding and future prospects, Sustainability, 12: 1632.

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Panda D., Barik J., and Sarkar R., 2021, Recent advances of genetic resources genes and genetic approaches for flooding tolerance in rice, Current Genomics, 22: 41-58.

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Pradhan S., Pandit E., Pawar S., Baksh S., Mukherjee A., and Mohanty S., 2019, Development of flash-flood tolerant and durable bacterial blight resistant versions of mega rice variety ‘Swarna’ through marker-assisted backcross breeding., Scientific Reports, 9(1): 12810.

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Rani G., Satyanarayana P., Chamundeswari N., Rao P., Prabhakar M., Ravikumar B., Nagakumari P., and Kalpana K., 2023, Mapping of QTLs for flood tolerance in rice using recombinant inbred lines of Indra and a new plant genetic resource AC 39416 A, Plant Genetic Resources: Characterization and Utilization, 20(4): 270-276.

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Sankarapillai L., Vijayaraghavareddy P., Nanaiah K., Arpitha G., Chaitanya P., Sathishraj R., Shindhe D., Vemanna R., Yin X., Struik P., and Sreeman S., 2023, Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice, Physiologia plantarum, 1755: e13992.

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Volante A., Desiderio F., Tondelli A., Perrini R., Orasen G., Biselli C., Riccardi P., Vattari A., Cavalluzzo D., Urso S., Hassen B., Fricano A., Piffanelli P., Cozzi P., Biscarini F., Sacchi G., Cattivelli L., and Valè G., 2017, Genome-wide analysis of japonica rice performance under limited water and permanent flooding conditions, Frontiers in Plant Science, 8: 1862.

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Ye N., Wang F., Shi L., Chen M., Cao Y., Zhu F., Wu Y., Xie L., Liu T., Su Z., Xiao S., Zhang H., Yang J., Gu H., Hou X., Hu Q., Yi H., Zhu C., Zhang J., and Liu Y., 2018, Natural variation in the promoter of rice calcineurin B-like protein10 OsCBL10) affects flooding tolerance during seed germination among rice subspecies, The Plant Journal, 94: 612-625.

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Zhang M., Lu Q., Wu W., Niu X., Wang C., Feng Y., Xu Q., Wang S., Yuan X., Yu H., Wang Y., and Wei X., 2017, Association mapping reveals novel genetic loci contributing to flooding tolerance during germination in indica rice, Frontiers in Plant Science, .8: 678.

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Zhu Q., Zhang X.L., Ni Naing N.N.Z., Li J.Q., Chen L.J., and Lee D.S., 2024, Strategies for rice improvement: utilizing genetic resources from wild and cultivated Oryza species, Rice Genomics and Genetics, 15: 106-120.

 

Rice Genomics and Genetics
• Volume 15
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