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Rice Genomics and Genetics 2025, Vol.16 http://cropscipublisher.com/index.php/rgg © 2025 CropSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, foundedin British Columbia of Canada. All Rights Reserved. CropSci Publisher is an international Open Access publishing specializing in crop genome, trait-controlling, crop gene expression and regulation at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher CropSci Publisher Editedby Editorial Team of Rice Genomics and Genetics Email: edit@rgg.cropscipublisher.com Website: http://cropscipublisher.com/index.php/rgg Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Rice Genomics and Genetics (ISSN 1925-2021) is an open access, peer reviewed journal published online by CropSciPublisher. The journal publishes original research papers of Rice Genomics and Genetics should be innovative research work in field of rice research, particular in the areas of rice functional genomics, transgene, genome sequencing analysis, molecular genetics, proteomics, genetic diversity, dominance relationships, heterosis, genetic characteristics, genetic modification, genetic rule analysis, genotype-phenotype relationships, stress physiology characteristics, QTL analysis and advanced rice breeding technologies. All the articles published in Rice Genomics and Genetics are Open Access, and are distributed 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. CropSciPublisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Rice Genomics and Genetics (online), 2025, Vol. 16, No. 5 ISSN 1925-2021 http://cropscipublisher.com/index.php/rgg © 2025 CropSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher Latest Content The Role of Structural Variants in Rice Domestication and Environmental Adaptation Weijie Sun, Jiawei Li Rice Genomics and Genetics, 2025, Vol.16, No.5, 245-253 Evaluating the Application Effects of Alternate Wetting and Drying (AWD) Irrigation in Rice Cultivation Zhongxian Li, Ruchun Chen, Haiying Huang Rice Genomics and Genetics, 2025, Vol.16, No.5, 254-259 The Role and Mechanism of Integrated Rice-fish Farming in Enhancing Rice Quality Yue Zhu, Jinni Wu Rice Genomics and Genetics, 2025, Vol.16, No.5, 260-266 Enhancement Effects of Rice-Duck Co-Culture Systems on the Ecosystem Services of Paddy Fields Xingzhu Feng Rice Genomics and Genetics, 2025, Vol.16, No.5, 267-281 Climate-Resilient Rice Farming Techniques for Sustainable Production Mingliang Jin, Danyan Ding Rice Genomics and Genetics, 2025, Vol.16, No.5, 282-293
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 245 Review Article Open Access The Role of Structural Variants in Rice Domestication and Environmental Adaptation Weijie Sun, Jiawei Li Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: jiawei.li@cuixi.org Rice Genomics and Genetics, 2025, Vol.16, No.5 doi: 10.5376/rgg.2025.16.0021 Received: 12 Jul., 2025 Accepted: 28 Aug., 2025 Published: 09 Sep., 2025 Copyright © 2025 Sun and Li, 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. Preferred citation for this article: Sun W.J., and Li J.W., 2025, The role of structural variants in rice domestication and environmental adaptation, Rice Genomics and Genetics, 16(5): 245-253 (doi: 10.5376/rgg.2025.16.0021) Abstract Structural variants (SVs), as an important form of genomic genetic variation, play a key role in the domestication of rice and its adaptation to complex environments. With the development of third-generation sequencing technology and pan-genomics, an increasing number of studies have revealed the extensive functions of SV in regulating agronomic traits, environmental stress responses, and germplasm diversity. This study systematically reviewed the genetic evidence of SV during the domestication of rice, covering key structural variation events in domestication-related traits such as plant type, flowering period, and grain shedding. At the same time, it explored the functional mechanisms of SV in adaptation to adverse conditions such as drought, salt stress, and cold damage, including regulatory region reconstruction, cis-element changes, and gene replication and deletion processes. This paper further introduces the current mainstream SV detection techniques and their applications in pan-genome construction and functional annotation, with a focus on analyzing how SV regulates gene expression through chromatin accessibility changes, quantitative trait loci (eQTL) reconfiguration, and non-coding RNA networks. Through the analysis of typical cases (such as OsSPL14, OsHKT1;5), this study clarifies the application value of SV in the improvement of rice traits. This study aims to provide theoretical support for a deeper understanding of the functions of structural variations and offer new ideas and strategies for molecular design breeding and precise improvement of rice. Keywords Rice; Structural variation; Domestication; Environmental adaptation; Pan-genome 1 Introduction Rice (Oryza sativa) is almost the daily food supply for more than half of the world's population. It is not an exaggeration to say that it is related to food security (Fornasiero et al., 2022; Li et al., 2025). However, apart from the act of "eating", it is also widely used as a classic model for studying domestication and crop improvement. Ultimately, rice was not a crop that was obedient from the very beginning. Many of the superior traits we see today have actually been gradually domesticated through long-term artificial selection, such as those selected step by step from ancestral materials like common wild rice (Li et al., 2021; Zheng et al., 2021). Behind this, many key genes related to output, stress resistance, and even climate change response have been identified. When it comes to genetic variation, the SNP might be the most familiar to everyone. However, when studying the traits of rice, structural variation (SV) often causes more waves. SV refers to those relatively large genomic variations - some are inserted in a large segment, some are simply missing, duplicated, or even the sequence is changed, such as inversions and translocations (Kou et al., 2020; Zheng et al., 2023). Although they are not the most abundant in the genome, each one may have a domino effect. Studies have found that SV, compared with SNP, often involves larger segments of genetic material. Therefore, they play a more significant role in influencing gene expression, crop trait diversity, and even environmental adaptation (Fuentes et al., 2019; Shang et al., 2022). If it weren't for the rapid upgrading of sequencing technology in recent years, especially the development of pan-genome analysis, many of these structural variations hidden in different species or subpopulations might not have been easily discovered. Nowadays, researchers have identified tens of thousands of SVS in cultivated rice and wild rice, and many of them are linea-specific (Wang et al., 2022). These findings precisely provide a new breakthrough for us to understand the genetic structure of rice and even further guide molecular breeding.
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 246 This study will clarify its role in rice domestication, environmental adaptation, and agronomic trait diversity. By integrating high-quality genome assembly, population scale resequencing, and functional genomics, it aims to map the evolutionary patterns of SVs, identify their associations with key traits such as grain size, stress resistance, and plant type, and reveal the genetic mechanisms by which they adapt to different environments. This research not only enables an in-depth understanding of the evolutionary history of rice but also provides valuable resources for breeding programs, allowing for targeted improvement of rice varieties to address future food security challenges. 2 Genetic Evidence of Structural Variants During Rice Domestication 2.1 Key SV events revealed by genome comparisons between wild and cultivated rice The genomic differences between wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa) are far more complex than initially imagined. Especially after using long-read sequencing and whole-genome comparative analysis, researchers found that there were a large number of structural variant (SV) events between the two, and many variant types were concentrated in the regions where transposition factors were active (Shang et al., 2022; Zheng et al., 2023). Especially in wild rice, approximately nearly half (49%) of the SV is unique to it. However, many such variations have been lost during domestication, resulting in the disappearance of approximately 1.76% of the genes in cultivated rice (Kou et al., 2020). Moreover, not only insertions and deletions, but also SVS like inversions and duplications frequently occur. Some of these specific variations, such as the 824 bp deletion in japonica rice related to grain length, were directly linked to important agronomic traits by GWAS analysis. 2.2 Regulatory roles of SVs in domestication-related traits (plant architecture, flowering time, grain shattering, etc.) Domestication has changed many traits of rice, but not every trait change comes from simple mutations. In fact, many regulations that affect plant type, flowering period, grain drop and grain shape are all orchestrated by SV. Especially those SVS that appear in promoters or within genes often directly affect the expression level of genes (Fuentes et al., 2019). For instance, a 17.1 kb tandem repeat at the GL7 locus can make the grains longer. The 1.2kb missing section of qSW5 will affect the width of the grains. In addition, some SVS can cause the plants to become shorter or the shape of the grains to change. The "extent of change" of these structural variations is often much greater than that of ordinary SNPS because they can not only regulate expression but also may reconstruct the regulatory network. Incidentally, some SVS are also associated with traits such as grains being less prone to dropping and tolerance to waterlogging, which also indicates that they were not "supporting roles" in the domestication process. 2.3 Differentiation of major SV loci between the two major Asian rice subspecies (indica andjaponica) Although indica rice and japonica rice, these two subspecies seem to belong to the same genus of rice, when comparing their SV differences, it becomes clear why their ecological adaptations and trait manifestations are so distinct. Many studies have found that there are large inversions, copy number variations and differences in the presence or absence of a certain sequence in their genomes. An inversion of 4.3 Mb in size can almost directly distinguish indica rice fromjaponica rice (Kou et al., 2020). What's more interesting is that these SVS are often concentrated in regions related to domestication, that is, near the genes that regulate yield, quality and stress resistance. Some variations almost only occur in a certain subspecies or are more common in that subspecies, and it is precisely these differences that define the adaptability of indica and japonica to different environments and typical agronomic manifestations. 3 Mechanisms Linking Structural Variants and Environmental Adaptation 3.1 Functional roles of SVs in rice responses to drought, salinity, and cold stresses Often, whether rice can survive drought, saline-alkali conditions or cold is not only determined by the strength of a certain gene, but also by whether there is a structural variation (SV) "working in the dark" behind this gene. In the analysis of a large number of rice genomes, SV often appears in those regions related to adverse conditions, and the density is not low. Sometimes, these SVS can cause regulatory sites to "shift", and sometimes they simply affect the dose of genes or disrupt the coding sequence. Transcription factors such as OsNAC6 and OsMYB6,
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 247 which are involved in regulating root development and antioxidant defense, are related to these variations. Studies have shown that they can actually enhance drought and salt resistance (Lee et al., 2017). However, not all SVS are positive. Some allelic variations, such as those found on OsWRKY45 or OsDIRP1, may also play a negative role in certain contexts (Tao et al., 2011; Cui et al., 2018). The "adaptability" of different SVS to environmental stresses is likely to depend on the context and the timing of expression. 3.2 Cis-regulatory SVs and their impact on gene expression via regulatory element remodeling The expression level of a gene sometimes does not depend on the gene itself, but rather on whether the cis-type element at its "front gate" has changed. SVS in the promoter region are particularly fond of "tamping", as they reconstruct the original regulatory map. As a result, the expression volume changes, and so do the spatiotemporal patterns (Ding et al., 2021). For instance, a single nucleotide variation in the promoter of the Ghd8 gene can enhance its expression, thereby improving the cold resistance of japonica rice (Figure 1) (Wang et al., 2019). Figure 1 Altered expression of Ghd8affects rice heading date (Adopted from Wang et al., 2019) Image caption: (a–d) Phenotype performances of wild type (WT) and Ghd8 overexpression line (OE) under LD conditions (14.5 h light: 9.5 h dark) (a) and SD conditions (9 h light: 15 h dark) (b). Arrows indicate the first emerging panicle. Heading date of WT and OE in LD (c) and SD (d) conditions. (e,f) The expression of Ghd8 (e) and Hd3a (f). (g–j) Performances of WT and artificial microRNA line (AMI) of Ghd8 in LD (g) and SD (h) conditions. Heading date of WT and AMI plants under LD (i) and SD (j) conditions. (k,1) The expression of Ghd8 (k) and Hd3a (l) in WT and AMI plants. Asterisks ** and * represent significant difference compared to WT by t-test at p < 0.01 and p < 0.05 levels, respectively. Error bars indicate the mean ± SD, with three to five replicates (Adopted from Wang et al., 2019)
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 248 For genes like OsSTOMAGEN that control stomatal density, once the cis-element is rewritten, not only will drought tolerance be affected, but water use efficiency will also change accordingly (Karavolias et al., 2024). These variations are often targeted by natural selection, which is why they are always given priority in breeding. 3.3 SV-driven gene loss and duplication in ecological adaptation processes Some SVS do not immediately change the function of a gene, but they quietly "replicate" a few copies or simply "delete" the original, which can also have a considerable impact on environmental adaptation. Gene duplication can double the expression levels of some stress response genes, while the loss of certain negative regulatory factors is sometimes beneficial to plants (Fuentes et al., 2019). In the high-frequency SV region, such "variant burdens" not only failed to become a burden but also gave rise to many new alleles, some of which were even used for agronomic improvement. What is more complex is that behind many SVS, transpositional factors are also involved, and even serial repetitions occur. This dynamic change in structure enables the regulatory network of rice to evolve particularly rapidly and be more adaptable to various extreme climates (Lou et al., 2017; Li, 2024). 4 Technologies and Analytical Methods for SV Detection 4.1 Advantages of long-read sequencing technologies (PacBio, ONT) in SV identification Some structural variations (SVS) are hidden in large areas of repetition, and conventional short-read techniques can easily "overlook" them. This problem has been precisely solved by long-read sequencing platforms such as PacBio and ONT. PacBio HiFi read length not only has a wide coverage but also high base accuracy, capable of identifying insertions and deletions as small as a few dozen bases. Although ONT has a slightly lower single-base accuracy rate, it can pull out continuous read lengths of 2 Mb or even longer, and shows more advantages when dealing with large areas of repetition or complex regions (Lang et al., 2020; Harvey et al., 2023). Of course, both platforms have their own shortcomings. However, when used in combination, they are highly complementary, not only enhancing the completeness of genome assembly but also making SV annotations more accurate. 4.2 Genome-wide SV reconstruction and pan-genome construction in diverse populations The construction of a pan-genome is no longer as simple as "piecing together a set of reference genomes". Especially in crops with extremely strong germplasm diversity such as rice, conducting long-read sequencing based on different populations can more comprehensively explore different types of SVS such as insertions, deletions, duplications, and PAVs (presence/deletion variations). The emergence of map-based pan-genomes and super pan-genomes gives us the opportunity to concatenate linaly-specific SVS and construct a dynamically changing whole-genome structure map, which is not only convenient for GWAS localization (Shang et al., 2022), It also provides a new perspective for studying the evolutionary paths and trait effects of these variations in the population. To truly understand the relationship between SV and phenotypes, this step is inevitable. 4.3 Advances in bioinformatics tools for SV annotation, visualization, and functional prediction There are more and more tools and their functions are becoming increasingly detailed. Nowadays, in order to accurately detect SV, many research teams have begun to use software specifically optimized for long reads such as SVIM-asm, Sniffles, cuteSV, pbsv or DeBreak to handle complex or multiallelic events (Chen et al., 2023). If it is a group-level analysis, a tool like PanPop can significantly enhance the integration efficiency of SV data. As for subsequent annotations and visualization, some databases and platforms are also being continuously updated. For example, the Rice Super Pan-Genome resource integrates rich SV annotation information and browsing interfaces (Shang et al., 2022). It is worth noting that the latest functional prediction methods are no longer confined to coding regions but have also begun to attempt to analyze non-coding regulatory regions, which is crucial for understanding how SV affects gene expression and even phenotypic traits. 5 Epigenetic and Transcriptomic Regulation Mediated by SVs 5.1 Impact of SVs on chromatin accessibility and histone modifications In rice, the active state of chromatin is not always static, and changes in histone modifications are often accompanied by the emergence of structural variations (SV). Histone markers like H3K4me3 and H3K27me3 have long been regarded as key markers for regulating transcription. Studies have found that the distribution and
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 249 function of these markers can be interfered with or remodeled by SV, thereby affecting gene accessibility and expression activity (Osakabe et al., 2018; Probst, 2022; Sokolova et al., 2022). It is worth noting that regions rich in active markers, such as sequences carrying H3K4me3, tend to be less "tolerant" of structural disturbances. However, SV is more common in heterochromatin (Lyu, 2024). In other words, not all regions are equally "welcoming" to variations. Some places change frequently, while others tend to be more conservative. The way this variation affects chromatin accessibility, nucleosome stability and even participates in the regulation of stress responses cannot be ignored. 5.2 SV-mediated reconstruction of expression quantitative trait loci (eQTLs) Expressing quantitative trait loci (eQTL) has always been an important entry point in the study of expression regulation. But when SV gets involved, things will become a little more complicated. An SV may directly interrupt a control element or make it function again in a different position. This leads to the emergence of new EQtls or the reconfiguration of the original EQtls. In the transcriptome studies of rice, this situation is not uncommon - some genes are jointly regulated by multiple local and remote EQtls, and the complexity of the network far exceeds expectations (Liu et al., 2022). The influence of SV on gene expression is sometimes more intense than that of SNP, especially more obvious in non-coding regions (Chiang et al., 2016). Analyzing eQTL together with phenotypic QTL often enables the identification of those genes that truly "cut" in the regulation of agronomic traits. 5.3 Interactions between SVs and non-coding RNAs (lncRNAs, miRNAs) Non-coding Rnas, such as lncrnas and mirnas, are not simply "non-coding" entities; they are highly active in regulatory networks. However, the expression of these RNA molecules themselves may also be affected by SV. Although direct research in this regard in rice is still advancing, existing evidence suggests that SV may indirectly affect the expression and function of these non-coding Rnas by rewriting chromatin structure or altering regulatory regions (Nunez-Vazquez et al., 2022; Jiang and Berger, 2023). The presence of SV in a gene segment may lead to an earlier or delayed transcriptional initiation of adjacent lncrnas, and may also interfere with miRNA binding sites. This "chain reaction" forms a dynamic regulatory relationship among SV, apparent state and non-coding RNA. It is not merely a one-way regulatory channel but more like a feedback network. Especially in the process of crop adaptation and domestication, this network relationship becomes increasingly important. 6 Case Studies: Representative Applications of SVs in Trait Improvement and Environmental Adaptation 6.1 Structural variation in the OsSPL14 gene and its role in plant architecture improvement The OsSPL14 (also known as IPA1) gene is often mentioned in the regulation of rice plant type. Not every mutation attracts widespread attention, but the point mutation in it unexpectedly disrupted the regulation of OsmiR156, leading to the amplification of OsSPL14 expression. The result is: fewer tillers, thicker stems, larger ears, not only increased yield but also enhanced lodging resistance (Jiao et al., 2010; Wang et al., 2017; Yan et al., 2021). Of course, this kind of variation is essentially a structural variation (SV), but its impact goes far beyond the structural level. Later, researchers attempted to overexpress this favorable allele or introduce it into different background materials through targeted introduction. The results all indicated that this type of SV could directly affect plant type, hormone levels, and even rice quality (Lian et al., 2020). The role of SV in breeding is very directly demonstrated in this case. 6.2 Copy number variation of OsHKT1;5 and its contribution to salt stress tolerance Not all salt tolerance comes from a certain "magic gene", but OsHKT1; 5 is undoubtedly one of the sodium transporters that have been studied more thoroughly at present. Natural variations of this gene, especially changes in copy number, have been found to help plants excrete sodium more effectively, particularly in the aboveground parts (Negrao et al., 2013; Liu et al., 2021). In salt-tolerant varieties like "Nona Bokra", amino acid substitutions at some key sites, along with an increase in gene dosage, ultimately improved the transport capacity of sodium ions. These SVS were not locked at the very beginning but gradually emerged during the actual screening process. For this very reason, they have become important targets in salt-tolerant breeding (Kobayashi et al., 2017).
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 250 6.3 Transcriptomic regulation by SVs in cold tolerance of japonica rice at high latitudes Whether japonica rice can withstand the cold and achieve stable production in the north is actually influenced by multiple factors, but the variations in the regulated areas are particularly worth mentioning. For example, structural variations in the promoter and coding region of the CTB5 gene have been found to enhance its expression activity under cold stress, thereby improving the cold tolerance level during the seedling stage and reproductive stage (Figure 2) (Guo et al., 2025). This is not an isolated case. In the joint study of pan-transcriptome and eQTL, cold response genes such as OsMAPK3, OsLEA9, and OsWRKY61 also showed significant SV-driven expression differences, including splicing variations and changes at the regulatory level (Lou et al., 2022). These genes seem to have been selectively strengthened during the domestication process of high-latitude japonica rice varieties, which also indicates that the "behind-the-scenes role" of SV in adaptive evolution should not be underestimated. Figure 2CTB5is essential for cold tolerance at the booting stage (Adopted from Guo et al., 2025)
Rice Genomics and Genetics 2025, Vol.16, No.5, 245-253 http://cropscipublisher.com/index.php/rgg 251 7 Conclusions and Future Perspectives In recent years, a number of large-scale rice genome studies have been carried out one after another under the impetus of technology, uncovering an astonishing amount of variant information - often in the millions. These variations, especially their enrichment in regulatory regions and stress-resistant related genes, have attracted the attention of researchers. But strangely enough, those effects that have a significant impact on traits are often hard to detect in traditional SNP analysis. For instance, behind key agronomic traits such as grain shape, plant height and drought tolerance, there may be some structural variations (SVS) rather than single-point mutations. The causes behind these structural variations are actually not simple. Some are caused by recombination between non-allelic genes, while others result from the insertion of transposable factors. In other words, they are not merely "abnormal events" in the genome, but may also be involved in the process of species evolution and adaptation (especially changes in population structure). So, from a theoretical perspective, studying SV is not merely for breeding, but more importantly, to figure out how plants "adapt" and "shape" themselves. But from another perspective, SV is not only a scientific research material but is also increasingly becoming a "tool". They reveal some previously overlooked new alleles with breeding potential, and it is not difficult to directly apply them to molecular design breeding. Methods like GWAS and genomic prediction, when SV is taken into account, have significantly enhanced explanatory power for complex traits. This also enables some truly "useful" variations to surface, thereby serving tag selection and precise editing. Now, resources including the pan-genome and SV maps have begun to play a role in rice breeding, with the goal of achieving high yields, stable yields, stress resistance and high quality. Looking ahead, multi-omics integration is likely to be the next key direction in SV research. Not only the genome, but also the transcriptome, epigenome and even phenome must be combined to clearly understand what a certain SV is doing, how it regulates and what traits it affects. And how should these priorities be ranked? It all depends on the data. Fortunately, deep learning and bioinformatics tools are also developing rapidly nowadays. Not only has the annotation efficiency improved, but the functional prediction of rare SVS has also become reliable. When big data is combined with these tools, it is really worth looking forward to whether the SV mechanism behind complex traits can be clarified in the future. This might be a brand-new breakthrough for rice breeding. Acknowledgments We would like to express our gratitude to the reviewers for their valuable feedback, which helped improve 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. References Chen Y., Wang A., Barkley C., Zhang Y., Zhao X., Gao M., Edmonds M., and Chong Z., 2023, Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak, Nature Communications, 14: 283. https://doi.org/10.1038/s41467-023-35996-1 Chiang C., Scott A., Davis J., Tsang E., Li X., Kim Y., Hadzic T., Damani F., Ganel L., Montgomery S., Battle A., Conrad D., and Hall I., 2016, The impact of structural variation on human gene expression, Nature genetics, 49: 692-699. https://doi.org/10.1038/ng.3834 Cui L., Min H., Byun M., Oh H., and Kim W., 2018, OsDIRP1, a putative RING E3 ligase, plays an opposite role in drought and cold stress responses as a negative and positive factor, respectively, in rice (Oryza sativa L.), Frontiers in Plant Science, 9: 1797. https://doi.org/10.3389/fpls.2018.01797 Ding Y., Zhu J., Zhao D., Liu Q., Yang Q., and Zhang T., 2021, Targeting cis-regulatory elements for rice grain quality improvement, Frontiers in Plant Science, 12: 705834. https://doi.org/10.3389/fpls.2021.705834 Fornasiero A., Wing R., and Ronald P., 2022, Rice domestication, Current Biology, 32: R20-R24. https://doi.org/10.1016/j.cub.2021.11.025 Fuentes R., Chebotarov D., Duitama J., Smith S., De La Hoz J., Mohiyuddin M., Wing R., McNally K., Tatarinova T., Grigoriev A., Mauleon R., and Alexandrov N., 2019, Structural variants in 3000 rice genomes, Genome Research, 29: 870-880. https://doi.org/10.1101/gr.241240.118
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Rice Genomics and Genetics 2025, Vol.16, No.5, 254-259 http://cropscipublisher.com/index.php/rgg 254 Case Study Open Access Evaluating the Application Effects of Alternate Wetting and Drying (AWD) Irrigation in Rice Cultivation Zhongxian Li, Ruchun Chen, Haiying Huang Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: haiying.huang@hitar.org Rice Genomics and Genetics, 2025, Vol.16, No.5 doi: 10.5376/rgg.2025.16.0022 Received: 27 Jul., 2025 Accepted: 06 Sep., 2025 Published: 20 Sep., 2025 Copyright © 2025 Li et al., 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. Preferred citation for this article: Li Z.X., Chen R.C., and Huang H.Y., 2025, Evaluating the application effects of alternate wetting and drying (AWD) irrigation in rice cultivation, Rice Genomics and Genetics, 16(5): 254-259 (doi: 10.5376/rgg.2025.16.0022) Abstract This study systematically evaluated the application effects of alternate wetting and drying (AWD) irrigation technology in rice cultivation, with a focus on its role in improving water use efficiency, maintaining yield stability, enhancing grain quality, and reducing environmental impacts. Field experiments were conducted in two representative rice-growing regions in China-Xinghua in Jiangsu Province and Guanghan in Sichuan Province-to compare the performance of AWD and conventional continuous flooding under varying ecological and agronomic conditions. The results showed that AWD significantly reduced irrigation water consumption while maintaining or slightly increasing yield, and effectively mitigated greenhouse gas emissions, demonstrating a strong synergy between water saving and emission reduction. By integrating agronomic performance with ecological benefits, this study clarified the practical value and strategic significance of AWD technology in building a climate-resilient and resource-efficient rice production system. The findings aim to provide theoretical guidance and technical support for advancing sustainable and efficient rice farming, and promoting the development of water-saving agriculture. Keywords Rice cultivation; Alternate wetting and drying (AWD); Water use efficiency; Greenhouse gas mitigation; Sustainable agriculture 1 Introduction Rice cultivation is a critical agricultural activity, providing a staple food source for over half of the global population. However, traditional irrigation practices in rice farming, such as continuous flooding (CF), pose significant challenges, particularly concerning water use efficiency and environmental sustainability. Rice fields are among the largest consumers of freshwater resources and are significant contributors to greenhouse gas emissions, particularly methane (CH4) and nitrous oxide (N2O) (Carrijo et al., 2017; Sriphirom et al., 2019; Gao et al., 2024). These challenges necessitate the exploration of alternative irrigation methods that can conserve water and reduce emissions without compromising rice yields. Alternate wetting and drying (AWD) irrigation has emerged as a promising water-saving technique in rice cultivation. This method involves periodic drying of the rice fields, allowing the water level to drop below the soil surface before re-irrigation. The theoretical basis of AWD is rooted in its potential to enhance water use efficiency and reduce methane emissions by introducing aerobic soil conditions intermittently during the growing season (Carrijo et al., 2017; Song et al., 2019; Zhang et al., 2023). Over the years, AWD has evolved with varying thresholds and management practices to optimize its benefits, such as maintaining soil water potential above certain levels to prevent yield loss (Zhao et al., 2024). This study will evaluate the effectiveness of AWD irrigation in specific regions, focusing on its impact on water use, rice yield, and greenhouse gas emissions, and gain insight into the feasibility and benefits of adopting AWD as a standard practice for rice cultivation, thereby providing a reference for policies and practices in similar agricultural settings.
Rice Genomics and Genetics 2025, Vol.16, No.5, 254-259 http://cropscipublisher.com/index.php/rgg 255 2 AWD Irrigation Technology: Principles and Implementation 2.1 Definition and water depth control methods Alternate wetting and drying (AWD) is an irrigation practice designed to reduce water usage in rice cultivation by allowing the soil to dry out to a certain extent before re-irrigation. This method contrasts with continuous flooding, where fields are kept submerged throughout the growing season. AWD involves monitoring the water depth and allowing it to drop below the soil surface to a predetermined level before reapplying water. The water depth control is crucial, as it determines the frequency and amount of irrigation needed. For instance, in some studies, water levels are allowed to drop 10, 20, or 30 cm below the ground before re-irrigation. The optimal water potential for AWD is often maintained at pressures greater than -15 kPa, with water depths less than 18.5 cm during the rice growing season (Figure 1) (Zhang et al., 2023). Figure 1 Alternate wetting and drying irrigation (AWD) (Adopted from Zhang et al., 2023) 2.2 Implementation requirements and field infrastructure Implementing AWD requires specific field infrastructure and management practices. Fields must be equipped with tools to measure water depth accurately, such as field water tubes or simple observation wells. These tools help farmers determine when to irrigate based on the water level. Additionally, the field must be leveled properly to ensure uniform water distribution and prevent waterlogging in certain areas. The infrastructure should also support efficient water delivery and drainage systems to facilitate the alternate wetting and drying cycles (Gilardi et al., 2023; Wijesundara, 2024). In regions with shallow aquifers, the interaction between irrigation and groundwater recharge must be considered to maintain overall irrigation efficiency (Gilardi et al., 2023). 2.3 Irrigation scheduling across rice growth stages AWD irrigation scheduling is tailored to the different growth stages of rice, ensuring that water is applied when it is most needed. During the early stages of rice growth, fields may be kept flooded to suppress weeds and support seedling establishment. As the rice plants mature, the AWD method is employed, allowing the soil to dry to the specified depth before re-irrigation. This cycle is repeated throughout the growing season, with adjustments made based on weather conditions, soil type, and crop needs (Carrijo et al., 2017; Cheng et al., 2022). The scheduling must be flexible to accommodate variations in environmental conditions and to optimize water use efficiency without compromising yield (Gao et al., 2024). 3 Case Study Region and Field Application 3.1 Xinghua, Jiangsu—AWD in a rice-wheat rotation system In Xinghua, Jiangsu, the application of alternate wetting and drying (AWD) irrigation in a rice-wheat rotation system has shown promising results. The AWD technique is particularly beneficial in regions with water scarcity, as it reduces water consumption while maintaining rice yields. Studies have demonstrated that AWD can decrease water use by 25%-70% compared to traditional continuous flooding methods, without significantly impacting rice
Rice Genomics and Genetics 2025, Vol.16, No.5, 254-259 http://cropscipublisher.com/index.php/rgg 256 yield (Ishfaq et al., 2020; Martínez-Eixarch et al., 2021). This makes AWD a viable option for sustainable rice cultivation in Jiangsu, where water resources are limited. 3.2 Guanghan, Sichuan—AWD ecological benefits in a double rice cropping system In Guanghan, Sichuan, the implementation of AWD in a double rice cropping system has highlighted several ecological benefits. The technique not only conserves water but also reduces methane emissions, a significant contributor to greenhouse gases from rice fields (Malumpong et al., 2020; Martínez-Eixarch et al., 2021). The reduction in methane emissions is particularly important in addressing climate change impacts. Additionally, AWD has been shown to improve water productivity, making it an eco-friendly alternative to continuous flooding (Patikorn et al., 2018; Ishfaq et al., 2020). These ecological benefits make AWD a suitable irrigation strategy for the double rice cropping systems prevalent in Sichuan. 3.3 Comparative insights and practical implications Comparing the application of AWD in Xinghua and Guanghan reveals several insights. Both regions benefit from reduced water usage and improved water productivity, which are crucial in areas facing water scarcity (Patikorn et al., 2018; Wijesundara, 2024). However, the ecological benefits, such as reduced methane emissions, are more pronounced in Guanghan due to the double cropping system (Malumpong et al., 2020). Practically, the adoption of AWD requires careful management to ensure water levels are maintained appropriately, as variations can impact yield and environmental benefits (Martínez-Eixarch et al., 2021; Duong et al., 2024). The successful implementation of AWD in these regions underscores its potential as a sustainable irrigation practice that balances water conservation with agricultural productivity. 4 Effects on Water Use and Irrigation Efficiency 4.1 Change in total irrigation volume Alternate wetting and drying (AWD) irrigation significantly reduces the total volume of water used in rice cultivation compared to continuous flooding (CF). Studies have shown that AWD can decrease irrigation water usage by approximately 33.88% globally, highlighting its potential as a water-saving technique (Gao et al., 2024). In Nepal, AWD plots received 57% less irrigation water than CF plots without a significant difference in yield, indicating a substantial reduction in water use (Howell et al., 2015). Similarly, in Italy, AWD was found to require less water from June onwards compared to continuous flooding, while still maintaining groundwater recharge (Gilardi et al., 2023). 4.2 Field seepage and evaporation comparisons AWD irrigation affects field seepage and evaporation differently than continuous flooding. In the Mid-South United States, AWD did not result in decreased gross primary production (GPP), evapotranspiration (ET), or transpiration (T), suggesting that the periodic drying associated with AWD does not negatively impact these processes (Reavis et al., 2024). This indicates that AWD can maintain similar levels of field seepage and evaporation as CF, while using less water overall. 4.3 Improvement in water use efficiency (WUE) AWD irrigation has been shown to improve water use efficiency (WUE) in rice cultivation. In China, AWD increased WUE by 25.3% to 28.9% across different rice cultivars, primarily due to enhanced root and shoot growth and development (Chu et al., 2016). A global meta-analysis also reported that AWD enhances WUE by 20.27% and irrigation water use efficiency by 47.58% (Gao et al., 2024). In Bangladesh, AWD treatments demonstrated higher WUE compared to continuous flooding, with treatment T1 achieving a WUE of 41.86 kg/ha/cm, compared to 38.64 kg/ha/cm for the control. 5 Impact on Rice Growth and Yield 5.1 Tiller number and plant height trends Alternate wetting and drying (AWD) irrigation has shown varied effects on tiller number and plant height in rice cultivation. In a study conducted in Nepal, it was observed that tillering was significantly higher under AWD compared to continuous flooding (CF), although leaf elongation rates did not differ between treatments (Howell et
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