Tree Genetics and Molecular Breeding 2024, Vol.14, No.4, 194-205 http://genbreedpublisher.com/index.php/tgmb 197 Figure 1 DEGs were involved in IAA biosynthesis pathway and signaling pathway in CK vs. T1 on day 4 (Adopted from Zhang et al., 2023) Image caption: A: DEGs participated in IAA biosynthesis and metabolism pathway; B: DEGs participated in IAA signaling pathway; The different font color represents the genes that are regulated in CK vs. T1 (red indicated upregulation; green indicated downregulation) (Adopted from Zhang et al., 2023) 3.4 Recent advances in genomic studies of Eucommia ulmoides Recent advances in genomic technologies have significantly enhanced our understanding of the genetic and molecular mechanisms underlying sex differentiation in E. ulmoides. The use of PacBio and Hi-C technologies has led to the development of high-quality genome assemblies, which have been instrumental in identifying sex-specific regions and genes. Additionally, the application of de novo transcriptome sequencing has provided a comprehensive view of the sex-biased gene expression landscape in E. ulmoides (Li et al., 2020). These genomic resources are invaluable for further studies on sex differentiation and for the genetic improvement of E. ulmoides through breeding and biotechnological approaches. 4 Molecular Pathways and Mechanisms 4.1 Hormonal regulation of sex differentiation Hormonal regulation plays a crucial role in the sex differentiation of Eucommia ulmoides. The involvement of phytohormones in the differentiation process is evident from the presence of phytohormone-response cis-elements in the MADS-box transcription factors, which are key regulators of floral organ development. These transcription factors exhibit differential expression patterns between male and female flowers, suggesting that hormonal signals may influence the expression of these genes, thereby contributing to sex differentiation (Zhang et al., 2023). Additionally, the high expression of certain genes, such as the ω-3 fatty acid desaturase coding gene EU0103017, has been linked to specific metabolic pathways that may be hormonally regulated, further underscoring the importance of hormonal control in sex differentiation (Du et al., 2023). Cucumber sex differentiation is primarily determined by the F, M, and A genes. Both the F (CsACS1G) andM (CsACS2) genes encode two ACC synthases (key enzymes in the ethylene biosynthesis pathway) that regulate the expression of female sex traits in cucumbers. The F gene promotes the development of female flowers, while the
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