Plant Gene and Trait 2025, Vol.16, No.1, 23-31 http://genbreedpublisher.com/index.php/pgt 29 7 Advances and Future Directions 7.1 Technological innovations Zhang et al. (2016) have obtained complete chloroplast genomic data through genomic screening and next-generation sequencing (NGS), revealing its sequence differences and mutation hotspots. High-throughput sequencing platforms like Roche 454 FLX+ and PacBio are helpful for better isolation and analysis of SSRS and SNPS. This information is very important for studying the genetic diversity of Eucommia ulmoides and conducting marker-assisted breeding. Liu et al. (2022) hold that the high-density genetic maps developed using genotyping sequencing (GBS) provide an important basis for quantitative trait locus (QTL) analysis and are beneficial for identifying genetic markers related to growth traits. 7.2 Emerging applications Meng et al. demonstrated in their 2023 study that the molecular markers found in the chloroplast genome of Eucommia ulmoides are significant in conservation genomics, as they can be used to assess genetic diversity and population structure. Wang et al. (2011) also developed gender-related markers such as AFLP and SCAR in the early stage. These markers enable researchers to determine the gender of plants when they are very young and select individuals with ideal traits in advance during breeding. Qun (2004) also combined metabolomics with molecular markers to identify different chemical types and their corresponding genetic markers, which is conducive to enhancing the medicinal value and nutritional components of Eucommia ulmoides leaves. 7.3 Research opportunities There are still many aspects worthy of further in-depth research on the chloroplast genome of Eucommia ulmoides (Taberlet et al., 1991). Yu et al. (2015) believe that future research can pay more attention to expanding the genetic linkage map and refining the QTL analysis, which is helpful to identify more growth-related traits and the genetic mechanisms behind them. The molecular markers that have been discovered still need further research to see their specific roles in metabolic processes and plants' responses to external stress. With the help of new bioinformatics tools and machine learning methods, it is also possible to analyze large amounts of genomic data more effectively, helping to make more accurate predictions and discoveries. To truly exert the role of these molecular markers, collaboration among geneticists, conservation biologists and breeding experts is indispensable (Li et al., 2014b). 8 Concluding Remarks The study of the chloroplast genome of Eucommia ulmoides has provided a lot of understanding of genetic structure and brought new opportunities for the development of molecular markers. The complete chloroplast genome of Eucommia ulmoides has been sequenced. It has a typical tetrad structure, with a total length of 163 586 bp and a GC content of 38.4%. Researchers identified 71 polymorphic chloroplast DNA fragments in comparative genomic analysis, among which 20 sites were selected to be used as potential markers in population genetics studies. Eight polymorphic chloroplast SSR markers (cpSSR) were also developed, further enriching the tools for genetic analysis. The kinship between Eucommia ulmoides and Aucuba japonica in Japan has also confirmed, which makes the understanding of its evolutionary background clearer. Molecular markers developed from the chloroplast genome of Eucommia ulmoides have helped researchers understand the genetic diversity and population structure of the species. These markers can also be applied to breeding work to screen out plants with ideal traits, thereby enhancing the yield and quality of Eucommia ulmoides in both medicinal and industrial applications. The high-density genetic maps established through these markers and the growth-related QTLS identified indicate that they play an important role in understanding the genetic mechanisms of key phenotypic traits. Future research should expand the genetic resources and genomic data of Eucommia ulmoides more. Researchers can comprehensively understand the genetic variation of Eucommia ulmoides by sequencing the chloroplast genomes from different regions, or combine the chloroplast data with the nuclear genome and mitochondrial genome to gain a more complete understanding of the genetic composition of Eucommia ulmoides. The molecular markers and candidate genes that have been identified should also continue to undergo functional research to clarify their roles in plant growth, development and response to environmental stress. Moreover, these molecular
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