Plant Gene and Trait 2024, Vol.15, No.2, 73-84 http://genbreedpublisher.com/index.php/pgt 78 5.2 Use of CRISPR/Cas9 for precise DEP1 modification CRISPR/Cas9 technology has emerged as a powerful tool for precise genetic modifications, including those at the DEP1 locus. This technology has been employed to create erect panicle mutants by editing the DEP1 gene, resulting in improved canopy structure and increased yield. For example, a CRISPR/Cas9-edited DEP1 mutant exhibited a more efficient canopy structure, allowing more light to reach the leaves under the panicle, which in turn enhanced biomass and yield under low fertilization conditions (Fei et al., 2019). Furthermore, CRISPR/Cas9 has been used to develop near-isogenic lines (NILs) with modified grain shape genes in the background of erect-panicle geng/japonica rice, demonstrating the potential of this technology to improve both yield and grain quality (Mao et al., 2021). 5.3 Integrating genomic data for enhanced breeding strategies The integration of genomic data into breeding strategies has significantly enhanced the efficiency and effectiveness of rice breeding programs. By combining genomic information with traditional breeding techniques, researchers have been able to develop high-yielding rice varieties with desirable traits (Grenier et al., 2015; Cui et al., 2019). For instance, the identification of a dominant allele at the DEP1 locus, which enhances meristematic activity and increases grain yield, has been instrumental in breeding high-yielding rice varieties in China (Huang et al., 2009). Additionally, the integration of genomic data has facilitated the development of new plant types with improved yield potential, such as the pyramiding of high-yielding npt1 and DEP1-1 alleles (Wang et al., 2017). This approach not only improves individual plant yield but also optimizes population structure for better light penetration and resource use efficiency (Fei et al., 2019). In summary, advances in genomic technologies, including NGS and CRISPR/Cas9, have significantly contributed to the understanding and manipulation of the DEP1 locus. These technologies have enabled precise genetic modifications and the integration of genomic data into breeding strategies, leading to the development of high-yielding rice varieties with improved panicle architecture and overall yield. 6 Breeding Strategies Incorporating DEP1 6.1 From gene to field: translating DEP1 research into practical applications The dense and erect panicle 1 (DEP1) gene has been a focal point in rice breeding due to its significant impact on grain yield and panicle architecture. The DEP1 gene, which encodes a phosphatidylethanolamine-binding protein-like domain protein, enhances meristematic activity, leading to a reduced length of the inflorescence internode and an increased number of grains per panicle (Huang et al., 2009). This gene has been widely utilized in Chinese high-yielding rice varieties, demonstrating its practical application in breeding programs aimed at increasing rice yield. The application of DEP1 in breeding programs has also been explored through the creation of near-isogenic lines (NILs) using CRISPR/Cas9 technology. These NILs have shown improvements in grain appearance and yield components, indicating that pyramiding DEP1 with other major-effect grain shape alleles can enhance both yield and quality (Mao et al., 2021). Additionally, the integration of DEP1 with other yield-related genes, such as IPA1, has been studied to develop hybrid japonica rice with ideal plant types, further demonstrating the practical applications of DEP1 in breeding programs (Xu et al., 2014). 6.2 Challenges inDEP1-based breeding programs Despite the promising results, there are several challenges associated with DEP1-based breeding programs. One major challenge is the narrow genetic diversity of DEP1, which limits the potential for further improvements in panicle traits. Studies have shown that the genetic diversity of DEP1 in high-yielding japonica rice varieties is limited, necessitating efforts to broaden the genetic base for more flexible applications in breeding (Zhao et al., 2016). Another challenge is the trade-off between yield and grain quality. While the DEP1 gene contributes to higher yield, it can also negatively impact grain quality, such as grain shape and taste. For instance, the introgression of the qPE9-1 allele, which confers panicle erectness, has been associated with a decrease in grain yield per plant,
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