Rice Genomics and Genetics 2025, Vol.16, No.2, 106-115 http://cropscipublisher.com/index.php/rgg 107 This review focuses on the development of rice functional genomics in recent years, including both technical and resource aspects and exploration of practical applications. At the same time, we have to mention the problems that still exist in the research, such as the unclear functions of some genes, or the limitations of high-throughput technology in certain situations. What is the future direction? I am afraid that it is inseparable from international cooperation and multidisciplinary integration. Only in this way can we further understand the "full picture" of the rice genome and face the pressure of global food security with more confidence. 2 Progress in Rice Functional Genomics 2.1 High-throughput sequencing technology and its impact In 2002, the advent of the draft of the rice genome was regarded as a major breakthrough, but that was just the beginning. Later, the addition of next-generation sequencing (NGS) technology suddenly accelerated the research progress of the rice genome. Compared with earlier methods, NGS has a wider coverage and is much faster, allowing researchers to quickly obtain genetic information of different germplasms and different strains, making it easier to analyze complex traits (Guo et al., 2014). However, the significance of this technology is not just in terms of sequencing speed. It has also greatly promoted molecular breeding, especially in terms of gene design. For example, the large number of SNP markers obtained through NGS are not only large in number, but also easy to call, suitable for high-throughput genotyping (Thomson, 2014). The relationship between genes and traits has also become clearer because of the accumulation of these data. Studies such as genome-wide association studies (GWAS) have developed rapidly relying on these marker resources. It is worth mentioning that this wave of technological innovation relies not only on sequencing platforms, but also on practical analysis tools. Friendly software such as NGSEP has lowered the threshold for data processing, and many non-professional experimenters can also analyze gene variations (Duitama et al., 2014). From this perspective, the role of NGS is far more than "sequencing" in the laboratory. Of course, even though NGS is already very mature, researchers still look to a more advanced solution - the third-generation sequencing technology. New technologies such as single-molecule real-time sequencing have longer read lengths and are more accurate. Especially when dealing with complex repetitive regions and identifying structural variations, its advantages are more obvious (Dijk et al., 2014). No PCR amplification is required, which means that there is less human interference during sequencing, making it closer to the real DNA sequence. This is a good tool for in-depth exploration of gene regulatory elements and new functional genes. 2.2 Genome databases and functional genomic resources Current research cannot be separated from data, and rice genome data is particularly large. In this case, who will organize and how to organize it is particularly important. The value of the database is clearly reflected here. For example, the RICE2020 project attempts to find functional annotations for every gene in rice. It not only relies on sequencing data, but also integrates various phenotypic information (Yang et al., 2013). This kind of integration can help researchers see more quickly what traits a gene affects, and it is also convenient for subsequent verification. As for the issue of data sharing, online platforms such as RAP-DB are very mature. It not only provides basic information about rice genes, but also expression conditions, functional predictions, and so on. Researchers do not need to look up information from scratch, they can use it by opening the webpage, which is very helpful for designing experiments. Although these platforms are already quite comprehensive, they are not static. As new data is added, they are also constantly updated. Only in this way can researchers get the latest information at any time and use it without being "outdated". 3 Discovery of Key Genes and Pathways in Rice Functional Genomics 3.1 Genes regulating stress resistance Rice is not naturally able to easily resist drought, salinity or high temperature. Stress resistance itself is a multi-gene, multi-link trait, involving many regulatory pathways. For example, OsPYL9, an ABA receptor gene,
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