Rice Genomics and Genetics 2024, Vol.15, No.2, 48-57 http://cropscipublisher.com/index.php/rgg 55 association analysis (TWAS) on three key panicle traits, namely the number of spikelets in the panicle (SPP), the number of primary branches and panicle length, and their gene expression levels, and found 4 results respectively. 1 755 844 and 6 839 genes significantly associated with these traits. These significant genes discovered through TWAS include not only many key genes known to be involved in panicle development, but also a large number of new regulatory factors that may play an important role in panicle development (Figure 3). Figure 3 Transcriptome data of the panicle stage during the differentiation stage of rice branch stems and spikelet primordia (Adopted from Mao et al., 2023) 5.3 The role of GWAS in promoting rice yield and quality improvement Genome-wide association studies (GWAS) play a crucial role in improving rice yield and quality, providing an efficient method to unlock the genetic potential of rice. Through this method, researchers can identify key genetic markers and genes related to yield and quality, accelerate the process of rice breeding, and improve the accuracy and efficiency of breeding. In terms of rice yield improvement, GWAS allows breeders to accurately identify genetic variations related to yield, including genes that control traits such as plant height, tiller number, and grains per panicle. For example, through GWAS, researchers have successfully identified multiple key genes that affect rice yield, such as Gn1a, GS3, DEP1, etc. The discovery of these genes has directly promoted the breeding of high-yielding rice varieties. In addition, GWAS also reveals the complex genetic network behind yield traits, providing scientific basis for precise manipulation of genetic resources, allowing breeding work to be carried out in a more targeted manner (Song et al., 2015). In terms of quality improvement, GWAS has helped breeders gain a deeper understanding of the genetic basis that controls rice quality, including rice grain shape, endosperm texture, protein content, and disease resistance. By identifying the genes associated with these traits, breeders can more precisely select for favorable alleles, thereby creating rice varieties that are both high-yielding and of good quality. For example, different allelic variations of the Waxy gene have an important impact on amylose content, which is directly related to the stickiness and taste of rice. The application of GWAS makes it possible to improve the quality of rice based on specific consumer needs. Through GWAS, researchers can not only identify the impact of a single gene on rice traits, but also reveal the interactions and regulatory networks between multiple genes, providing new strategies for comprehensive trait improvement in rice. For example, by comprehensively considering multiple genes that affect yield and quality, breeders can improve varieties more effectively and achieve balanced selection of multiple traits. The application of GWAS in rice breeding has greatly improved the scientific nature and efficiency of breeding, not only accelerated the development of high-yield and high-quality rice varieties, but also provided powerful molecular tools for rice genetic improvement. With the continuous advancement of genome sequencing technology and the continuous optimization of data analysis methods, the role of GWAS in improving rice yield and quality will be
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