Genomics and Applied Biology 2024, Vol.15, No.3, 142-152 http://bioscipublisher.com/index.php/gab 148 6.3 Solutions and future directions: multi-omics integration, collaborative research efforts To overcome these challenges, several solutions and future directions can be considered. One promising approach is to integrate multi-omics data, including genomics, transcriptomics, and metabolomics, to gain a comprehensive understanding of the genetic and molecular mechanisms of key traits in Eucommia ulmoides (Li et al., 2020; Du et al., 2023; Hu et al., 2023). Collaborative research at both national and international levels can help pool resources and expertise, making advanced genomic technologies more accessible and cost-effective (Wang et al., 2018; Zhang et al., 2023a). Additionally, the development of molecular markers such as sex-specific AFLP and SCAR markers can facilitate early identification of important traits, thereby accelerating breeding cycles (Wang et al., 2011). Investments in bioinformatics infrastructure and training can also effectively enhance data analysis and interpretation capabilities, ensuring that the large volumes of genomic data generated are effectively utilized in breeding programs (Jin et al., 2020; Liu et al., 2022; Du et al., 2023). 7 Future Prospects of Functional Genomics inE. ulmoides Breeding 7.1 Potential breakthroughs in crop improvement Integrating functional genomics into the breeding of Eucommia ulmoides holds great promise for significant breakthroughs in crop improvement. Advances in genome editing technologies, especially CRISPR/Cas9, have revolutionized this field by offering an efficient and flexible method for precise gene editing, making it possible to modify plant genomes with accuracy. This technology allows for the deletion of detrimental traits and the addition of beneficial characteristics, thereby accelerating the development of novel plant varieties with improved traits such as disease resistance, drought tolerance, and enhanced nutritional profiles (Bortesi and Fischer, 2015; Arora and Narula, 2017; Rao and Wang, 2021). Additionally, the ability to generate diverse cis-regulatory alleles through CRISPR/Cas9-mediated editing of promoters can provide beneficial quantitative variation for breeding, which is crucial for improving complex traits like yield and plant architecture (Rodriguez-Leal et al., 2017). 7.2 Exploring the role of CRISPR-Cas9 and other gene-editing technologies in accelerating breeding CRISPR-Cas9 and its variants have emerged as powerful tools for accelerating the breeding process in E. ulmoides. The technology's ability to introduce site-specific double-stranded DNA breaks and facilitate precise genome modifications has made it a cornerstone of modern plant breeding (Bortesi and Fischer, 2015; Zhang et al., 2017). Base editing, a derivative of CRISPR/Cas9, allows for precise single-nucleotide changes without the need for double-strand breaks, offering a new avenue for creating desirable traits in crops (Li et al., 2023). The development of delivery systems, such as DNA-free methods and CRISPR ribonucleoproteins (RNPs), has further enhanced the efficiency and specificity of genome editing, making it a more viable option for practical breeding applications (Arora and Narula, 2017; Chen et al., 2019) (Figure 3). These advancements are expected to significantly reduce the time required to develop newE. ulmoides varieties with improved traits. 7.3 Collaborative efforts between academia and industry in genomics-based breeding initiatives The successful integration of functional genomics into E. ulmoides breeding will require robust collaboration between academic institutions and industry stakeholders. Academia can contribute cutting-edge research and technological innovations, while industry can provide the resources and infrastructure necessary for large-scale breeding programs. Collaborative efforts have already shown promise in other crops, where partnerships have led to the development of genome-edited varieties with enhanced traits (Wang et al., 2019; Ahmad et al., 2020). By leveraging the strengths of both sectors, it is possible to accelerate the translation of genomic research into practical breeding solutions. Such collaborations can also facilitate the sharing of genomic data, the development of standardized protocols, and the establishment of regulatory frameworks to ensure the safe and effective use of genome editing technologies in crop improvement (Wan et al., 2021). 8 Concluding Remarks Functional genomics holds great potential for revolutionizing Eucommia ulmoides breeding. The availability of high-quality male and female plant genome assemblies provides a solid foundation for understanding the genetic basis of key traits, including sex differentiation and α-linolenic acid biosynthesis. The identification of sex-specific markers, such as SCAR markers for early sex identification, can significantly improve breeding
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