Tree Genetics and Molecular Breeding 2024, Vol.14, No.4, 194-205 http://genbreedpublisher.com/index.php/tgmb 196 regulation of sex differentiation, with EuAP3 being a male-biased gene associated with the development of male floral organs (Hussain et al., 2016; Wang et al., 2020). The use of advanced genomic technologies has provided deeper insights into the genetic basis of sex differentiation in E. ulmoides. High-quality genome assemblies for both male and female individuals have been developed, revealing significant differences in gene expression between the sexes. For example, the female genome assembly is approximately 1.01 Gb with 31 665 protein-coding genes, while the male genome assembly is larger at 1.24 Gb with an increased number of predicted genes (Du et al., 2023). These genomic resources are invaluable for understanding the molecular mechanisms underlying sex differentiation and for facilitating the breeding of superior varieties. 2.3 Sexual differentiation of Eucommia ulmoides Sex differentiation in Eucommia ulmoides is a complex process regulated by various genetic and molecular mechanisms. The species is strictly dioecious, meaning that individual trees are either male or female, and this sexual dimorphism is evident from the earliest stages of flower development. Recent genomic studies have provided significant insights into the sex differentiation mechanisms in E. ulmoides. For instance, the high-quality chromosome-level genome assemblies for both male and female trees have revealed key genes involved in sex differentiation, such as EuAP3 and EuAG (Goldberg et al., 2017; Du et al., 2023). Comparative transcriptome analyses have identified differentially expressed genes (DEGs) between male and female individuals, including sex-biased genes like the MADS-box gene APETALA3, which is likely involved in sex determination (Nakazawa et al., 2009; Zhang et al., 2023). 3 Genetic Basis of Sex Differentiation inEucommia ulmoides 3.1 Overview of sex chromosomes and sex-determining regions Eucommia ulmoides is a dioecious plant, meaning it has distinct male and female individuals. The sex chromosomes and sex-determining regions in E. ulmoides have been a focal point of recent genomic studies. The high-quality chromosome-level genome assemblies for both male and female E. ulmoides have provided significant insights into the genetic basis of sex differentiation (Hu et al., 2023). The female genome assembly is 1.01 Gb with 17 pseudochromosomes, while the reassembled male genome is 1.24 Gb, indicating notable differences in genome size and structure between the sexes (Takeno et al., 2008; Du et al., 2023). Additionally, the identification of sex-specific markers, such as a 350 bp male-specific AFLP marker and a 569 bp pistillate-specific RAPD marker, has facilitated early sex identification, which is crucial for breeding programs (Wang et al., 2018). 3.2 Key genes involved in sex differentiation Several key genes have been implicated in the sex differentiation of E. ulmoides. Transcriptome analyses have identified differentially expressed genes (DEGs) between male and female plants, including the MADS-box gene APETALA3, which is male-biased and likely involved in sex determination (Figure 1) (Zhang et al., 2023). Other studies have highlighted the role of MADS-box transcription factors, with specific genes such as EuMADS39 and EuMADS65 showing male-biased expression, suggesting their critical role in the regulation of sex differentiation (Miljković et al., 2019; Jin et al., 2020). Furthermore, genes like EuAP3 and EuAG have been identified as potential regulators of sex differentiation based on their expression patterns. 3.3 Comparative genomics with other dioecious plants Comparative genomics has revealed that E. ulmoides shares several genomic features with other dioecious plants. For instance, the presence of sex-biased gene expression and the involvement of MADS-box genes in sex determination are common themes across dioecious species (Jin et al., 2020). The study of chromatin landscapes in other dioecious systems, such as the UV sex determination system in brown algae, has provided insights into the epigenomic changes associated with sex differentiation, which may also be relevant to E. ulmoides. These comparative studies help in understanding the evolutionary conservation and divergence of sex-determining mechanisms in dioecious plants.
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