Tree Genetics and Molecular Breeding 2024, Vol.14, No.4, 194-205 http://genbreedpublisher.com/index.php/tgmb 194 Research Report Open Access Genetic and Molecular Mechanisms of Sex Differentiation in Eucommia ulmoides XueHuang1, Xi Chen2 , Degang Zhao1,2 1 National-local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), College of Life Sciences/Institute of Agro- Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China 2 Plant Conservation & Breeding Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology/Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China Corresponding emails: 15761626900@163.com; dgzhao@gzu.edu.cn Tree Genetics and Molecular Breeding, 2024, Vol.14, No.4 doi: 10.5376/tgmb.2024.14.0019 Received: 15 Jul., 2024 Accepted: 17 Aug., 2024 Published: 25 Aug., 2024 Copyright © 2024 Huang et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Huang X., Chen X., and Zhao D.G., 2024, Genetic and molecular mechanisms of sex differentiation in Eucommia ulmoides, Tree Genetics and Molecular Breeding, 14(4): 194-205 (doi: 10.5376/tgmb.2024.14.0019) Abstract Eucommia ulmoides, a dioecious tree species endemic to China, holds significant medicinal and economic value. This study delves into the genetic and molecular mechanisms underlying sex differentiation in E. ulmoides. Utilizing advanced genomic technologies, a high-quality chromosome-level genome assembly for both male and female E. ulmoides was achieved, revealing key insights into sex differentiation. Comparative transcriptome analyses identified differentially expressed genes (DEGs) between male and female individuals, highlighting the role of MADS-box transcription factors and specific genes such as EuAP3 and EuAGin sex determination. Additionally, molecular markers linked to sex determination were developed, facilitating early sex identification and improving breeding efficiency. The findings from this study provide a valuable genomic resource for further molecular biological studies and practical applications in the breeding and commercial production of E. ulmoides. Keywords Eucommia ulmoides; Sex differentiation; MADS-box transcription factors; Genomic assembly; Molecular markers 1 Introduction Eucommia ulmoides, also known as the hardy rubber tree, is a dioecious perennial woody plant native to China and widely distributed in subtropical and temperate regions. It is the only species in the Eucommiaceae family and is renowned for its medicinal and industrial value, particularly in rubber production and traditional Chinese medicine. However, the male and female flowers of Eucommia ulmoides grow on separate male and female trees, and its long growth cycle complicates early gender identification and breeding efforts (Du et al., 2023; Wang et al., 2023). Since it is difficult to distinguish the sex of the plant during the seedling stage based on external morphology, in-depth research into the mechanisms of sex differentiation in Eucommia ulmoides is not only important for improving breeding efficiency and utilizing the plant’s dioecious characteristics but also provides a reliable scientific basis for large-scale commercial production. Understanding the mechanisms of sex differentiation in E. ulmoides is crucial for several reasons. The dioecious nature of the plant poses challenges for breeding and economic cropping, as sex cannot be determined through morphological observation at early developmental stages. Elucidating the genetic and molecular pathways involved in sex differentiation can facilitate the development of molecular markers for early sex identification, thereby improving breeding efficiency and commercial production. Moreover, insights into sex differentiation mechanisms can contribute to the broader understanding of plant reproductive biology and may have applications in other dioecious species (Zhang et al., 2023). Recent advancements in genomic technologies have provided significant insights into the genetic and molecular mechanisms underlying sex differentiation in plants. In E. ulmoides, high-quality chromosome-level genome assemblies for both male and female individuals have been generated, revealing key genes and pathways involved in sex differentiation (Du et al., 2023). For instance, transcriptome analysis has identified EuAP3 and EuAGas potential regulators of sex differentiation in this species. Genome-wide identification and expression analysis of MADS-box transcription factors have highlighted their critical role in sex determination, with specific genes
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