Tree Genetics and Molecular Breeding 2025, Vol.15, No.3, 117-127 http://genbreedpublisher.com/index.php/tgmb 117 Review and Perspectives Open Access Functional Genomics of Root Development in Populus and Its Ecological Implications Minghua Li, Hongpeng Wang, Shiying Yu Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: shiying.yu@cuixi.org Tree Genetics and Molecular Breeding, 2025, Vol.15, No.3 doi: 10.5376/tgmb.2025.15.0014 Received: 11 May, 2025 Accepted: 14 Jun., 2025 Published: 21 Jun., 2025 Copyright © 2025 Li 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: Li M.H., Wang H.P., and Yu S.Y., 2025, Functional genomics of root development in Populus and its ecological implications, Tree Genetics and Molecular Breeding, 15(3): 117-127 (doi: 10.5376/tgmb.2025.15.0014) Abstract This study summarizes the research progress of functional genes in the development of poplar root systems, introduces some important genes and signaling pathways that control the shape, differentiation process and response to the external environment of roots, integrates many methods such as transcriptome analysis, gene editing and epigenetic research, and clarifies the response of poplar root systems to drought, nutrient deficiency and interaction with microorganisms It also explores how these root traits are regulated within the body and discusses the possible assistance they may bring in afforestation, ecological restoration and other aspects. This study aims to provide a theoretical basis and technical reference for the study of poplar root systems, and also hopes to lay the foundation for breeding new varieties that are more adapted to the environment and have better traits in the future. Keywords Populus; Root development; Functional genomics; Forestry applications; Environmental adaptation 1 Introduction The root system of poplar (Populus spp.) is very important for its growth and also plays many roles in the ecosystem. Whether the roots grow well or not is directly related to whether they can absorb sufficient water and nutrients, and these will affect whether they can survive in various environments (Zhou et al., 2020). In forestry, people often use cuttings, a method of asexual reproduction, to grow poplar trees. Whether cuttings can successfully take root is the key to promoting high-quality varieties (Bannoud and Bellini, 2021; Ahkami, 2023). In addition, the roots of poplar trees have a complex relationship with the microorganisms in the soil. They are very helpful for maintaining soil health, the carbon cycle, and ecological restoration. High-throughput sequencing, transcriptome analysis, gene editing and other technologies are widely used to understand how poplar roots form and develop, as well as how they respond to external environmental pressures (Ahkami, 2023; Shi et al., 2024b). Methods such as GWAS (genome-wide association studies), transcriptome sequencing, and gene family analysis have helped researchers identify many important genes and regulatory factors related to rooting ability, hormone signaling, and amino acid metabolism (Du et al., 2022; Han et al., 2022; Nagle et al., 2022; Li et al., 2025). These achievements have deepened the understanding of poplar root development and laid the foundation for poplar breeding and sustainable forest development. This study expounds the key genes and signaling pathways that control root formation and growth, introduces the roles of these genes in the ecological environment, summarizes the molecular mechanisms and main regulatory networks that regulate root development, and explores the significance of these research results in explaining how poplar trees adapt to the environment and resist adverse conditions. And the possible impacts of root system research on ecological restoration, forestry production and germplasm resource innovation were analyzed. This study aims to provide ideas and references for a further understanding of the molecular basis and ecological roles of poplar root development. 2 Morphological and Developmental Features of Poplar Roots 2.1 Types of roots: primary, lateral, adventitious The root system of poplar trees is generally divided into three types: main roots, lateral roots and adventite roots. adventitious roots (ARs) do not grow naturally from the roots but from places such as stems or leaves. They are
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