Plant Gene and Trait 2025, Vol.16, No.1, 23-31 http://genbreedpublisher.com/index.php/pgt 23 Research Report Open Access Molecular Markers from Chloroplast Genomes inEucommia ulmoides Guangman Xu Traditional Chinese Medicine Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: guangman.xu@cuixi.org Plant Gene and Trait, 2025, Vol.16, No.1 doi: 10.5376/pgt.2025.16.0003 Received: 03 Jan., 2025 Accepted: 05 Feb., 2025 Published: 15 Feb., 2025 Copyright © 2025 Xu, 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: Xu G.M., 2025, Molecular markers from chloroplast genomes in Eucommia ulmoides, Plant Gene and Trait, 16(1): 23-31 (doi: 10.5376/pgt.2025.16.0003) Abstract The chloroplast genome is very helpful for understanding the genetics and evolution of Eucommia ulmoides and can also provide many useful molecular markers. This study expounds the general structure, gene content and arrangement pattern of the chloroplast genome of Eucommia ulmoides, and analyzes several types of molecular markers extracted from the chloroplast genome. The development and application of these markers can be used to study genetic diversity, population structure and evolutionary relationships, and help protect genetic resources. This study also introduced the commonly used methods for chloroplast labeling analysis, discussed some technical difficulties, summarized the current research progress and new applications, and proposed some future research directions. This study aims to provide a scientific basis for a more comprehensive understanding of the chloroplast genome and molecular markers of Eucommia ulmoides. Keywords Eucommia ulmoides; Chloroplast genome; Molecular markers; Genetic diversity; Conservation genetics 1 Introduction Eucommia ulmoides, also known as hardy rubber tree, is of great value in both industrial and medicinal fields (Wang et al., 2019). It is the sole member of the Eucommulaceae family and holds an important position in traditional Chinese medicine, especially being very common in the treatment of orthopedic diseases (Zhu et al., 2020). Eucommia ulmoides can also produce rubber, and this unique ability has attracted the attention of many scientists and enterprises (Li et al., 2020). However, Eucommia ulmoides is dioecious, that is to say, each tree is either male or female. This characteristic has brought a lot of troubles to breeding and cultivation (Wang et al., 2019). The structure of the chloroplast genome is relatively stable, which is very helpful for studying the genetic relationship and classification among plants (Yu et al., 2015). The research conducted by Zhang et al. in 2023 demonstrated that the chloroplast genome of Eucommia ulmoides has been fully sequenced, revealing a typical tetrad structure with 135 genes, containing a wealth of useful genetic information. These data can be used to develop molecular markers, which are of great value for the breeding and conservation of Eucommia ulmoides. Meng et al. in the same year, that is, in 2023, believed that the chloroplast genome is involved in photosynthesis and other important metabolic processes and is a crucial research object in plant physiology and biochemistry studies. This study analyzed the molecular markers obtained from the chloroplast genome of Eucommia ulmoides. By summarizing existing research, it understood the role of these genetic markers in breeding, species conservation, and in-depth study of the specific traits of Eucommia ulmoides. It emphasized their importance in the entire field of plant genomics and their application potential in enhancing the industrial and medicinal value of Eucommia ulmoides. This study aims to provide a foundation for the subsequent scientific research and development of Eucommia ulmoides. 2 Chloroplast Genome Structure inEucommia ulmoides 2.1 General features The chloroplast genome of Eucommia ulmoides has a typical four-segment structure, which is divided into a large single-copy (LSC) region, a small single-copy region (SSC), and two inverted repeat (IR) regions. The total length of its genome is approximately 163 586 base pairs (Wang et al., 2018). Liu et al. (2022) found that the GC content
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