| [1] |
Harris NL, Gibbs DA, Baccini A, Birdsey RA, de Bruin S, et al. 2021. Global maps of twenty-first century forest carbon fluxes. |
| [2] |
Pan Y, Birdsey RA, Fang J, Houghton R, Kauppi PE, et al. 2011. A large and persistent carbon sink in the world's forests. |
| [3] |
Wullschleger SD, Jansson S, Taylor G. 2002. Genomics and forest biology: Populus emerges as the perennial favorite. |
| [4] |
Neale DB, Kremer A. 2011. Forest tree genomics: growing resources and applications. |
| [5] |
Isik F. 2014. Genomic selection in forest tree breeding: the concept and an outlook to the future. |
| [6] |
Stobrawa K. 2014. Poplars (Populus spp.): ecological role, applications and scientific perspectives in the 21st century. Baltic Forestry 20:204−213 |
| [7] |
Cronk QCB. 2005. Plant eco-devo: the potential of poplar as a model organism. |
| [8] |
Jansson S, Douglas CJ. 2007. Populus: a model system for plant biology. |
| [9] |
Zalesny RS, Headlee WL, Gopalakrishnan G, Bauer EO, Hall RB, et al. 2019. Ecosystem services of poplar at long‐term phytoremediation sites in the Midwest and Southeast, United States. |
| [10] |
Ruttens A, Boulet J, Weyens N, Smeets K, Adriaensen K, et al. 2011. Short rotation coppice culture of willows and poplars as energy crops on metal contaminated agricultural soils. |
| [11] |
Fuertes A, Oliveira N, Cañellas I, Sixto H, Rodríguez-Soalleiro R, et al. 2023. Assessing the potential of poplar short rotation plantations to contribute to a low-carbon bioeconomy under water-limited conditions. |
| [12] |
Plomion C, Bastien C, Bogeat-Triboulot MB, Bouffier L, Déjardin A, et al. 2016. Forest tree genomics: 10 achievements from the past 10 years and future prospects. |
| [13] |
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). |
| [14] |
Fillatti JJ, Sellmer J, McCown B, Haissig B, Comai L. 1987. Agrobacterium mediated transformation and regeneration of Populus. |
| [15] |
Guo J, Morrell-Falvey JL, Labbé JL, Muchero W, Kalluri UC, et al. 2012. Highly efficient isolation of Populus mesophyll protoplasts and its application in transient expression assays. |
| [16] |
Fan D, Liu T, Li C, Jiao B, Li S, et al. 2015. Efficient CRISPR/Cas9-mediated targeted mutagenesis in Populus in the first generation. |
| [17] |
Yao T, Yuan G, Lu H, Liu Y, Zhang J, et al. 2023. CRISPR/Cas9-based gene activation and base editing in Populus. |
| [18] |
Lin YC, Wang J, Delhomme N, Schiffthaler B, Sundström G, et al. 2018. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. |
| [19] |
Zhang B, Zhu W, Diao S, Wu X, Lu J, et al. 2019. The poplar pangenome provides insights into the evolutionary history of the genus. |
| [20] |
Shi T, Zhang X, Hou Y, Jia C, Dan X, et al. 2024. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. |
| [21] |
Yu X, Liu Z, Sun X. 2023. Single-cell and spatial multi-omics in the plant sciences: technical advances, applications, and perspectives. |
| [22] |
Raza A, Li Y, Prakash CS, Hu Z. 2025. Panomics to manage combined abiotic stresses in plants. |
| [23] |
Ming M, Liu Q, Zhang J, Zhao A, Yi M, et al. 2025. Revolutionizing poplar biotechnology: genetic transformation and CRISPR/Cas9 strategies. |
| [24] |
Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. |
| [25] |
International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. |
| [26] |
The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. |
| [27] |
Goff SA, Ricke D, Lan TH, Presting G, Wang R, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). |
| [28] |
Ellegren H. 2014. Genome sequencing and population genomics in non-model organisms. |
| [29] |
Harris L, McDonagh EM, Zhang X, Fawcett K, Foreman A, et al. 2025. Genome-wide association testing beyond SNPs. |
| [30] |
Wang J, Ding J, Tan B, Robinson KM, Michelson IH, et al. 2018. A major locus controls local adaptation and adaptive life history variation in a perennial plant. |
| [31] |
Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, et al. 2014. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. |
| [32] |
Wang J, Street NR, Scofield DG, Ingvarsson PK. 2016. Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species. |
| [33] |
Ma T, Wang K, Hu Q, Xi Z, Wan D, et al. 2018. Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex. |
| [34] |
Liu S, Zhang L, Sang Y, Lai Q, Zhang X, et al. 2022. Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome. |
| [35] |
Sang Y, Long Z, Dan X, Feng J, Shi T, et al. 2022. Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. |
| [36] |
Xiang X, Zhou X, Zi H, Wei H, Cao D, et al. 2024. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. |
| [37] |
Sun J, Xu J, Qiu C, Zhai J, Zhang S, et al. 2024. The chromosome-scale genome and population genomics reveal the adaptative evolution of Populus pruinosa to desertification environment. |
| [38] |
Long Z, Sang Y, Feng J, Zhang X, Shi T, et al. 2025. Evolutionary genomics unravels the responses and adaptation to climate change in a key alpine forest tree species. |
| [39] |
Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. 2021. Nanopore sequencing technology, bioinformatics and applications. |
| [40] |
Sigurpalsdottir BD, Stefansson OA, Holley G, Beyter D, Zink F, et al. 2024. A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes. |
| [41] |
Lee H, Gurtowski J, Yoo S, Nattestad M, Marcus S, et al. 2016. Third-generation sequencing and the future of genomics. |
| [42] |
Zhang Z, Chen Y, Zhang J, Ma X, Li Y, et al. 2020. Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica). |
| [43] |
Zhang S, Wu Z, Ma D, Zhai J, Han X, et al. 2022. Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism. |
| [44] |
An X, Gao K, Chen Z, Li J, Yang X, et al. 2022. High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. |
| [45] |
Li P, Xiao L, Du Q, Quan M, Song Y, et al. 2023. Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa. |
| [46] |
Gao K, Guo T, An X. 2025. Comprehensive analysis of the multi-rings mitochondrial genome of Populus tomentosa. |
| [47] |
Melnikova NV, Pushkova EN, Dvorianinova EM, Beniaminov AD, Novakovskiy RO, et al. 2021. Genome assembly and sex-determining region of male and female Populus × sibirica. |
| [48] |
Chen S, Yu Y, Wang X, Wang S, Zhang T, et al. 2023. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. |
| [49] |
Liu YJ, Wang XR, Zeng QY. 2019. De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China. |
| [50] |
Sarfraz I, Zuccolo A, Celii M, Francini A, Wing RA, et al. 2025. High-quality PacBio genome assembly of Populus alba L. 'Villafranca'. |
| [51] |
Liu S, Wang Z, Shi T, Dan X, Zhang Y, et al. 2023. Chromosomal-level genome assembly of Populus adenopoda. |
| [52] |
Ma J, Wan D, Duan B, Bai X, Bai Q, et al. 2019. Genome sequence and genetic transformation of a widely distributed and cultivated poplar. |
| [53] |
Robinson KM, Schiffthaler B, Liu H, Rydman SM, Rendón-Anaya M, et al. 2024. An improved chromosome-scale genome assembly and population genetics resource for Populus tremula. |
| [54] |
Bae EK, Kang MJ, Lee SJ, Park EJ, Kim KT. 2023. Chromosome-level genome assembly of the Asian aspen Populus davidiana Dode. |
| [55] |
Li Y, Wang D, Wang W, Yang W, Gao J, et al. 2023. A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. |
| [56] |
Wu H, Yao D, Chen Y, Yang W, Zhao W, et al. 2020. De novo genome assembly of Populus simonii further supports that Populus simonii and Populus trichocarpa belong to different sections. |
| [57] |
Chen S, Wang X, Wei Y, Guo Q, Ren Z, et al. 2026. The complete genome sequence of a poplar, Populus davidiana. |
| [58] |
Wang Y, Zhao L, Wang D, Chen K, Luo T, et al. 2025. Four near-complete genome assemblies reveal the landscape and evolution of centromeres in Salicaceae. |
| [59] |
Shen T, Ning Y, Wang Y, Song Z, Xi M, et al. 2025. Haplotype-resolved telomere-to-telomere genome assembly of Populus lasiocarpa unveils retrotransposon-driven centromere evolution. |
| [60] |
Bi C, Sun N, Hou Z, Dai X, Wu H, et al. 2025. A gap-free reference genome of Populus deltoides provides insights into karyotype evolution of Salicaceae. |
| [61] |
Liu W, Liu C, Chen S, Wang M, Wang X, et al. 2024. A nearly gapless, highly contiguous reference genome for a doubled haploid line of Populus ussuriensis, enabling advanced genomic studies. |
| [62] |
Zhou X, Zhang L, Zhang M, Wei H, Bai Y, et al. 2025. Genomic selection for growth and wood properties in multi-generation hybrid populations of Populus deltoides. |
| [63] |
Gao W, Wang S, Jiang T, Hu H, Gao R, et al. 2025. Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa. |
| [64] |
Shi TL, Jia KH, Bao YT, Nie S, Tian XC, et al. 2024. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. |
| [65] |
Schreiber M, Jayakodi M, Stein N, Mascher M. 2024. Plant pangenomes for crop improvement, biodiversity and evolution. |
| [66] |
Jayakodi M, Shim H, Mascher M. 2025. What are we learning from plant pangenomes? |
| [67] |
Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, et al. 2016. Characterization of the poplar pan-genome by genome-wide identification of structural variation. |
| [68] |
Li R, Wang Z, Wang JW, Li L. 2023. Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees. |
| [69] |
Tung CC, Kuo SC, Yang CL, Yu JH, Huang CE, et al. 2023. Single-cell transcriptomics unveils xylem cell development and evolution. |
| [70] |
Dai X, Zhai R, Lin J, Wang Z, Meng D, et al. 2023. Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa. |
| [71] |
Liu S, Fu X, Wang Y, Du X, Luo L, et al. 2025. The auxin–PLETHORA 5 module regulates wood fibre development in Populus tomentosa. |
| [72] |
Zhang Y, Chen S, Xu L, Chu S, Yan X, et al. 2024. Transcription factor PagMYB31 positively regulates cambium activity and negatively regulates xylem development in poplar. |
| [73] |
Zhao J, Chen Y, Dai X, Su L, Zhai R, et al. 2026. PtrSHR1 coordinates vascular cambium proliferation and xylem lignin biosynthesis to regulate wood formation in Populus trichocarpa. |
| [74] |
Li Q, Meng S, Zhou Y, Pi H, Yun Q, et al. 2025. The miR169z-NF-YA5-GPDHc1 module improves drought tolerance by increasing NAD+ levels to inhibit ROS production in Populus. |
| [75] |
Liu X, Bao Y, Zhang MY, Zhang H, Niu MX, et al. 2025. SC35-mediated bZIP49 splicing regulates K+ channel AKT1 for salt stress adaptation in poplar. |
| [76] |
Li Y, Xu X, Wang K, Hu Z, Deng L, et al. 2026. Epigenetic reprogramming drives the annual growth–dormancy cycle in Populus. |
| [77] |
Li L, Huang R, Jin Z, Zhang D, Zhang M, et al. 2025. Natural variants of AGL80.5 and FPA. 3 contribute to bud break timing in poplar by controlling auxin biosynthesis. |
| [78] |
Liao X, Su Y, Klintenäs M, Li Y, Sane S, et al. 2023. Age-dependent seasonal growth cessation in Populus. |
| [79] |
Wang J, Liao X, Wu Z, Sane S, Han S, et al. 2025. Genetic control of seasonal meristem arrest in trees. |
| [80] |
Müller NA, Kersten B, Leite Montalvão AP, Mähler N, Bernhardsson C, et al. 2020. A single gene underlies the dynamic evolution of poplar sex determination. |
| [81] |
Xue L, Wu H, Chen Y, Li X, Hou J, et al. 2020. Evidences for a role of two Y-specific genes in sex determination in Populus deltoides. |
| [82] |
Lu J, Yang Y, Yin T. 2025. Poplar sex-determining gene directly affects tree growth through regulating cytokinin signalling pathway. |
| [83] |
Lu J, Yang Y, Yin T. 2025. Expression of poplar sex-determining gene affects plant drought tolerance and the underlying molecular mechanism. |
| [84] |
Alves FC, Balmant KM, Resende MFR Jr, Kirst M, de Los Campos G. 2020. Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping. |
| [85] |
Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, et al. 2013. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. |
| [86] |
Chhetri HB, Furches A, Macaya-Sanz D, Walker AR, Kainer D, et al. 2020. Genome-wide association study of wood anatomical and morphological traits in Populus trichocarpa. |
| [87] |
Macaya-Sanz D, Heuertz M, Lindtke D, Vendramin GG, Lexer C, et al. 2016. Causes and consequences of large clonal assemblies in a poplar hybrid zone. |
| [88] |
Hord AM, Fischer DG, Schweitzer JA, LeRoy CJ, Whitham TG, et al. 2025. Hybrid introgression as a mechanism of rapid evolution and resilience to climate change in a riparian tree species. |
| [89] |
Ma T, Wang J, Zhou G, Yue Z, Hu Q, et al. 2013. Genomic insights into salt adaptation in a desert poplar. |
| [90] |
Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, et al. 2017. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. |
| [91] |
Cortés AJ, Restrepo-Montoya M, Bedoya-Canas LE. 2020. Modern strategies to assess and breed forest tree adaptation to changing climate. |
| [92] |
Chen Y, Tong S, Jiang Y, Ai F, Feng Y, et al. 2021. Transcriptional landscape of highly lignified poplar stems at single-cell resolution. |
| [93] |
Schmidt HW, Conde D, Pereira WJ, Triozzi PM, Balmant KM, et al. 2025. Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks. |
| [94] |
Wei M, Hsieh JWA, Dang JF, Tong B, Li H, et al. 2026. Integrating scRNA-seq and snRNA-seq with spatial transcriptomics to unlock the xylem puzzle. |
| [95] |
Li Y, Kong L, Guo X, Chen Y, Shao W, et al. 2026. A single-nucleus and spatial transcriptomic atlas of poplar leaves reveals the regulation of leaf polarity and cuticle deposition. |
| [96] |
Li H, Dai X, Huang X, Xu M, Wang Q, et al. 2021. Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus. |
| [97] |
Xie J, Li M, Zeng J, Li X, Zhang D. 2022. Single-cell RNA sequencing profiles of stem-differentiating xylem in poplar. |
| [98] |
Shi T, Long T, Wu J, Zeng X, Zhu Y, et al. 2026. Dynamic reorganization of three-dimensional genome architecture during Populus diversification. |
| [99] |
Gaj T, Gersbach CA, Barbas CF. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. |
| [100] |
Bruegmann T, Fendel A, Zahn V, Fladung M. 2024. Genome editing in forest trees. In A Roadmap for Plant Genome Editing, eds. Ricroch A, Eriksson D, Miladinović D, Sweet J, Van Laere K, et al. Cham: Springer Nature Switzerland. pp. 347−372 doi: 10.1007/978-3-031-46150-7_20 |
| [101] |
Kaur N, Pati PK. 2024. Retron library recombineering: next powerful tool for genome editing after CRISPR/cas. |
| [102] |
Arimura SI, Nakazato I. 2024. Genome editing of plant mitochondrial and chloroplast genomes. |
| [103] |
Zong Y, Liu Y, Xue C, Li B, Li X, et al. 2022. An engineered prime editor with enhanced editing efficiency in plants. |
| [104] |
Pak S, Li C. 2022. Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees. |
| [105] |
Ma C, Duan C, Jiang Y, Nagle M, Peremyslova E, et al. 2022. Factors affecting in vitro regeneration in the model tree Populus trichocarpa: II. Heritability estimates, correlations among explant types, and genetic interactions with treatments among wild genotypes. |
| [106] |
Hoengenaert L, Anders C, Van Doorsselaere J, Vanholme R, Boerjan W. 2025. Transgene-free genome editing in poplar. |
| [107] |
Zhang J, Tang X, Sun M, Liu C, Yu H. 2026. A genotype-independent transformation and gene-editing system for Populus. |
| [108] |
Farooq MA, Gao S, Hassan MA, Huang Z, Rasheed A, et al. 2024. Artificial intelligence in plant breeding. |
| [109] |
Yan J, Wang X. 2023. Machine learning bridges omics sciences and plant breeding. |
| [110] |
Wang H, Cimen E, Singh N, Buckler E. 2020. Deep learning for plant genomics and crop improvement. |
| [111] |
Wang H, Chen M, Wei X, Xia R, Pei D, et al. 2024. Computational tools for plant genomics and breeding. |
| [112] |
Fan X, Zhang H, Zhou L, Bian L, Jin X, et al. 2024. Evaluating drought stress response of poplar seedlings using a proximal sensing platform via multi-parameter phenotyping and two-stage machine learning. |
| [113] |
Gilbertson L, Puchta H, Slotkin RK. 2025. The future of genome editing in plants. |
| [114] |
Chen YH, Sharma S, Bewg WP, Xue LJ, Gizelbach CR, et al. 2023. Multiplex editing of the Nucleoredoxin1 tandem array in poplar: from small indels to translocations and complex inversions. |
| [115] |
Gong Z, Yang S. 2026. NRT1. 1B: a dual receptor integrating ABA and nitrate signals for plant adaptation to compound stresses. |
| [116] |
Feng J, Dan X, Cui Y, Gong Y, Peng M, et al. 2024. Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change. |
| [117] |
Xu Y, Zhang X, Li H, Zheng H, Zhang J, et al. 2022. Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction. |
| [118] |
Syeda A. 2025. Harnessing multi-omics and genome-editing technologies for climate-resilient agriculture: bridging AI-driven insights with sustainable crop improvement. |