Molecular Plant Breeding 2024, Vol.15, No.5, 317-327 http://genbreedpublisher.com/index.php/mpb 320 3.3 Transcriptome analysis Transcriptome analysis involves the comprehensive study of RNA transcripts produced by the genome under specific conditions or developmental stages. This approach provides valuable insights into gene expression patterns and regulatory networks influencing various traits, including wood quality. In Eucalyptus, transcriptome studies have been instrumental in uncovering the molecular mechanisms underlying wood formation and quality. Transcriptome analysis has provided valuable insights into the genes influencing wood quality in Eucalyptus. In a study on Eucalyptus urophylla × E. tereticornis hybrids, transcriptome analysis combined with QTL mapping identified 1 052 candidate genes associated with wood formation, including transcription factor families like TALE, which play a crucial role in secondary growth and wood formation (Zhu et al., 2023). These findings underscore the importance of integrating transcriptome data with QTL mapping to elucidate the regulatory mechanisms underlying wood quality traits. This approach can significantly enhance the understanding of genetic control over wood properties and inform targeted genome editing strategies for wood quality improvement. 4 Applications of Genome Editing inEucalyptus 4.1 Improving lignin content and composition Lignin is a complex polymer that provides structural integrity to plant cell walls but can pose challenges in industrial processing, particularly in pulp and paper production (Chanoca et al., 2019). High lignin content and certain lignin compositions make wood harder to process and less desirable for these applications. Genome editing technologies, particularly CRISPR/Cas9, have been utilized to target and modify genes involved in lignin biosynthesis to improve wood quality. Genome editing has shown significant potential in modifying lignin content and composition in Eucalyptus, which is crucial for improving wood quality. The CRISPR/Cas9 technology has been effectively used to target key lignin biosynthetic genes such as Cinnamoyl-CoA Reductase1 (CCR1). Editing these genes has resulted in decreased lignification and altered lignin composition, which are beneficial for reducing biomass recalcitrance and enhancing wood processing efficiency (Chanoca et al., 2019; Dai et al., 2020). Additionally, the overexpression of specific transcription factors like EgNAC141 has been found to positively regulate lignin biosynthesis, leading to increased lignin deposition and improved wood properties (Sun et al., 2021). 4.2 Enhancing cellulose content and fiber quality Cellulose is a primary component of plant cell walls and a critical determinant of wood quality, particularly for its applications in paper, textiles, and biofuels. Enhancing cellulose content and improving fiber quality can significantly boost the economic value of Eucalyptus wood. Genome editing tools offer precise methods to modify genes involved in cellulose biosynthesis and regulation. Enhancing cellulose content and fiber quality in Eucalyptus through genome editing involves targeting genes that regulate cellulose biosynthesis. Studies have shown that perturbing the expression of genes involved in the lignin biosynthetic pathway can also impact cellulose content and fiber quality. For instance, a multi-omics integrative analysis has demonstrated that modifying the expression of specific monolignol genes can lead to improvements in cellulose content and other wood traits (Wang et al., 2018). Furthermore, the use of advanced genetic transformation methods, such as the fluorescence labelling method with CRISPR/Cas9, has facilitated the efficient selection of genetically modified progenies with enhanced cellulose content and fiber quality (Wang et al., 2021). 4.3 Optimizing wood density and pulp yield Optimizing wood density and pulp yield in Eucalyptus is another critical application of genome editing. Genetic parameters for wood density and other wood properties have been extensively studied, revealing that these traits have strong genetic control and can be effectively targeted through genome editing (Lima et al., 2019). The study found that the EgNAC141 transcription factor fromEucalyptus can significantly increase lignin deposition and wood density. Overexpression of EgNAC141 in Arabidopsis resulted in stronger lignification, larger xylem, and higher lignin content (Figure 2). Dual-luciferase reporter gene analysis showed that EgNAC141 could activate the expression of lignin biosynthesis genes in Arabidopsis. These results indicate that EgNAC141 is a positive
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