Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 106-118 http://genbreedpublisher.com/index.php/tgmb 106 Review Article Open Access From Leaves to Roots: Mapping the Full Genome of Trees and Decoding Their Functions Yeping Han , Xuelian Jiang Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding email: yeping.han@jicat.org Tree Genetics and Molecular Breeding, 2024, Vol.14, No.3 doi: 10.5376/tgmb.2024.14.0011 Received: 13 Apr., 2024 Accepted: 15 May, 2024 Published: 22 May, 2024 Copyright © 2024 Han and Jiang, 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: Han Y.P., and Jiang X.L., 2024, From leaves to roots: mapping the full genome of trees and decoding their functions, Tree Genetics and Molecular Breeding, 14(3): 106-118 (doi: 10.5376/tgmb.2024.14.0011) Abstract The advent of high-throughput sequencing technologies has revolutionized the field of tree genomics, enabling comprehensive mapping and functional analysis of tree genomes. This study synthesizes recent advancements in tree genomics, highlighting the integration of genomic, phenotypic, and environmental data to understand tree biology and improve forest health. Key findings include the development of standardized genome-wide function prediction tools, such as GOMAP, which facilitate comparative functional genomics across multiple species. Resources like PhyloGenes provide phylogenetic trees and experimentally validated gene functions, aiding in the functional inference of uncharacterized genes. This study also discusses the genomic studies of hardwood trees, which have linked genes to ecological and developmental traits, and the use of genomic prediction models for breeding. Additionally, the application of genome-wide association studies (GWAS) and joint-GWAS approaches in Eucalyptus has identified significant genetic associations with growth traits, enhancing tree breeding efforts. This study underscores the importance of integrating genomic data with environmental and phenotypic data through advanced cyberinfrastructure and databases to improve forest health and productivity. Emerging technologies and methodologies, such as RADseq and KEGG mapping tools, are also explored for their potential to uncover hidden features in tree genomes and facilitate large-scale genomic studies. This study provides a roadmap for future research in tree genomics, emphasizing the need for collaborative efforts and advanced analytical tools to decode the complex biology of trees. Keywords Tree genomics; Comparative functional genomics; GWAS; Genomic prediction; Cyberinfrastructure 1 Introduction Understanding the full genome of trees is crucial for advancing modern botany and ecology. Trees play a pivotal role in ecosystems, providing habitat, maintaining biodiversity, and influencing climate through carbon sequestration. Comprehensive genomic analysis allows researchers to uncover the genetic basis of traits that are vital for tree survival and adaptation, such as resistance to biotic and abiotic stresses, growth patterns, and reproductive strategies (Neale et al., 2017; Müller et al, 2018). This knowledge is essential for conservation efforts, especially in the face of climate change, as it can inform strategies to preserve genetic diversity and enhance the resilience of forest ecosystems (Holliday et al., 2017; Cortés et al., 2020). Recent advancements in sequencing technologies have significantly accelerated the pace of tree genomic research. High-quality reference genomes have been assembled for several tree species, revealing insights into their unique genetic features and evolutionary histories (Neale et al., 2017; Wang et al, 2023). For instance, the genome of Quercus dentata has been sequenced, providing valuable information on the genetic regulation of leaf color transition and other adaptive traits (Wang et al, 2023). Genome-wide association studies (GWAS) have identified genes linked to important growth traits in species like Eucalyptus, enhancing our understanding of genetic variation and its impact on phenotypic traits (Müller et al., 2018). However, tree genomic research faces several challenges. Trees often have large and complex genomes, long generation times, and outcrossing reproductive systems, which complicate genetic studies (Holliday et al., 2017; Cortés et al., 2020). Additionally, the number of sequenced tree genomes still lags behind those of other plant species, limiting the scope of comparative genomic analyses (Neale et al., 2017). Despite these challenges, ongoing efforts in genome sequencing and the development of new analytical methods continue to push the boundaries of our knowledge in this field (Hug et al., 2016; Osborne et al., 2022).
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