Genomics and Applied Biology 2024, Vol.15, No.3, 142-152 http://bioscipublisher.com/index.php/gab 142 Research Insight Open Access Integrating Functional Genomics with Breeding inEucommia ulmoides Xiaoyan Ran 1, YingZhu2, Degang Zhao1,2 1 The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China 2 Plant Conservation & Breeding Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology/Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China Corresponding author: dgzhao@gzu.edu.cn Genomics and Applied Biology, 2024, Vol.15, No.3 doi: 10.5376/gab.2024.15.0016 Received: 02 Apr., 2024 Accepted: 11 May, 2024 Published: 27 May, 2024 Copyright © 2024 Ran 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: Ran X.Y., Zhu Y., and Zhao D.G., 2024, Integrating functional genomics with breeding in Eucommia ulmoides, Genomics and Applied Biology, 15(3): 142-152 (doi: 10.5376/gab.2024.15.0016) Abstract This involved constructing high-density genetic maps, analyzing quantitative trait loci (QTL) for growth traits, and identifying key genes involved in various biological processes. The study successfully constructed a high-density genetic map using single-nucleotide polymorphism (SNP) markers, covering 90% of the E. ulmoides genome with a total genetic distance of 4051.11 cM and an average marker distance of 0.45 cM. A total of 44 QTLs associated with growth traits were identified, along with 33 candidate genes related to energy storage, signal transmission, hormones, and metabolic pathways. Additionally, the genome of E. ulmoides was sequenced, revealing insights into sex differentiation and α-linolenic acid biosynthesis. The study also identified 71 NAC transcription factors and their potential role in rubber biosynthesis, and 119 MYB transcription factors involved in growth and development. The integration of functional genomics with breeding in Eucommia ulmoides has provided a solid foundation for future genetic improvement and breeding programs. The identification of key QTLs and candidate genes will facilitate targeted breeding strategies to enhance desirable traits, thereby improving the economic and ecological value of this important species. Keywords Eucommia ulmoides; Functional genomics; Breeding; SNP markers; QTL analysis; Genetic map; NAC transcription factors; MYB transcription factors; α-linolenic acid; Rubber biosynthesis 1 Introduction Eucommia ulmoides, commonly known as the hardy rubber tree, is a unique species renowned for its dual utility in both traditional medicine and industrial applications. The tree is the sole member of the family Eucommiaceae and is highly valued for its ability to produce rubber and various medicinal compounds. The rubber produced by E. ulmoides is distinct due to its reliance on the methylerythritol-phosphate (MEP) pathway, which is different from the mevalonate (MVA) pathway used by other rubber-producing species like Hevea brasiliensis. Additionally, the tree's leaves and bark are rich in chlorogenic acid, a compound with significant medicinal properties (Li et al., 2020). Despite its economic and medicinal importance, the cultivation and breeding of E. ulmoides face several challenges. One of the primary issues is the dioecious nature of the species, which means that male and female flowers are produced on separate trees. This characteristic complicates early sex identification, making traditional breeding methods inefficient and time-consuming (Wang et al., 2020). Furthermore, the genetic regulation of sex determination in E. ulmoides is complex, involving various MADS-box transcription factors that exhibit sex-specific expression patterns (Zhang et al., 2023b). These challenges hinder the optimization of breeding programs aimed at improving yield and quality. Integrating functional genomics into breeding programs offers a viable solution to the challenges faced in Eucommia ulmoides cultivation. High-quality genome assemblies and advanced genomic tools provide deep insights into the genetic and molecular mechanisms of important traits such as rubber biosynthesis and sex determination (Li et al., 2020; Zhang et al., 2023b). For instance, the recently acquired high-quality haploid genome assembly of Eucommia ulmoides has greatly enhanced our understanding of its genomic structure and
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