Tree Genetics and Molecular Breeding 2025, Vol.15, No.3, 117-127 http://genbreedpublisher.com/index.php/tgmb 120 Figure 1 Auxin signaling and transport is essential for PtrXB38-mediated adventitious root formation in Populus tremula × Populus alba (Adopted from Yao et al., 2023) Image caption: (a) Log-fold changes of transcript levels of auxin biosynthesis, signaling, transport, and response-related genes in 12-d-old root samples of PtrXB38-OE vs control plants, based on RNA-seq results. (b) Log-fold changes of protein abundance of auxin response factor in 12-d-old root samples of PtrXB38-OE vs control plants, based on quantitative proteomics. (c) Root formation of PtrXB38-OE plants upon auxin transport inhibitor treatment. (d) Adventitious root number of PtrXB38-OE plants with 0.2 and 1 μM NPA treatments. Bar charts represent mean ± SE (n ≥ 3 independent plants). (e) IAA contents in the roots of PtrXB38-OE plants grown in ½-strength Murashige & Skoog medium. Bar charts represent mean ± SE (n = 4 independent plants) (Adopted from Yao et al., 2023) 5.2 RNA-Seq, ATAC-Seq, and single-cell transcriptomics Whether analyzing different organs, studying a certain growth stage, or observing how poplar responds to stresses such as cold, drought, and salt, RNA-Seq is very useful. Databases like GEPSdb also integrate a lot of these RNA expression data, allowing for the review of the high or low expression level of a certain gene under what conditions at any time (Liu et al., 2021). Shi et al. (2024a) demonstrated that, in addition to traditional transcriptome techniques, ATAC-Seq and single-cell sequencing have now also begun to be applied to poplar trees, especially in the study of epigenetic and cell type specific expression of root systems. Although these techniques are still in their nascent stage in poplar trees, they have already shown great potential. 5.3 Gene editing (CRISPR/Cas9), VIGS, and transformation systems CRISPR/Cas9 is now one of the most important tools used in poplar research. The Populus VariantDB v3.2 database provides a lot of useful information, such as the differences between different genomes, which are very helpful for designing editing targets. The transgenic system of poplar is also relatively mature and can efficiently introduce target genes, which is an important means for functional verification and variety improvement (Biselli et al., 2022). Furthermore, some reverse genetics tools, such as VIGS virus-induced gene silencing, have also been used to rapidly screen which genes are useful, helping researchers shorten the experimental cycle. 6 Root-Microbe Interactions: Genetic Insights 6.1 Mycorrhizal symbiosis and gene expression patterns The roots of poplar trees and mycorrhizal fungi often establish a cooperative relationship, which is of great help to plants in absorbing nutrients and enhancing their stress resistance. Balestrini et al. ’s research in 2024 found that
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