Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F₁ hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

With the birth of classical genetics, forest genetic breeding has laid a foundation in the formation of the basic theories of population genetics, quantitative genetics, cytogenetics, and molecular genetics. Driven by the rapid growth of social demand for wood and other forest products, modern genetics, biotechnology, biostatistics, crop and animal husbandry breeding theories, and technical achievements have been continuously introduced for innovation, thus forming a close combination of genetic basic research and breeding practice. Forest tree breeding research in the world has a history of more than 200 years. By the middle of the 20th century, the forest tree genetic breeding system was gradually formed. After entering the 21st century, the in-depth development stage of molecular design breeding was opened. With the continuous improvement of traditional genetic breeding methods, emerging modern bioengineering technology has also continuously promoted the development of forest genetic breeding. This study mainly summarizes the research history of forest tree genetics and breeding, as well as discusses the application of modern bioengineering technology represented by genome selection and gene editing in forest tree breeding, so as to provide better reference for forest tree breeding research.

Hibiscus (Hibiscus syriacus L.) is known as a horticultural plant of great ornamental and medicinal value. However, the effect of NaCl stress on hibiscus seedlings is unclear. Little is known about H. syriacus ‘Duede Brabaul’ (DB) and H. syriacus ‘Blueberry Smoothie’ (BS). Here, the effects of solutions with different concentrations of NaCl on the organic osmolytes, ion accumulation, and antioxidant enzyme activity of hibiscus seedling leaves were determined. The results showed that the Na⁺/K⁺ ratio was imbalanced with increasing NaCl concentration, especially in BS (range 34% to 121%), which was more sensitive than DB (range 32% to 187%) under NaCl concentrations of 50 to 200 mM. To cope with the osmotic stress, the content of organic osmolytes increased significantly. Additionally, NaCl stress caused a large increase in O₂·⁻ and H₂O₂, and other reactive oxygen species (ROS), and antioxidant enzyme activity was significantly increased to remove excess ROS. The expression level of genes related to salt tolerance was significantly higher in DB than that in BS under different NaCl concentrations. Taken together, DB possessed a stronger tolerance to salt stress and the results suggest membrane stability, Na⁺/K⁺, H₂O₂, catalase and ascorbate peroxidase as salt tolerance biomarkers that can be used for gene transformation and breeding in future hibiscus research.

Salt stress constrains poplar growth. The mitogen-activated protein kinase (MAPK) cascade and phytohormones are key regulators of plant salt tolerance. However, the mechanisms by which MAPK cascades orchestrate hormone homeostasis under salt stress in poplar are still poorly understood. This study shows that overexpressing PeMPK7 improved poplar salt tolerance. After 12 h of NaCl treatment, salicylic acid and abscisic acid (ABA) contents in PeMPK7-overexpressing poplars were significantly higher than in wild-type plants (P < 0.05). Transcriptomic profiling revealed that PeMPK7 reprogrammed phytohormone metabolism and signaling pathways, notably up-regulating ethylene (ET) biosynthesis genes (ACS1, ACO1) together with genes associated with indole-3-acetic acid, cytokinin, ABA, gibberellic acid, and jasmonic acid. Weighted gene co-expression network analysis suggested that PeMPK7 may act upstream of NAC072, NAC002, and TGA7, which are associated with ABA metabolism and signaling under salt stress. Among differentially expressed transcription factor genes, PagERF114 expression was induced by salt in PeMPK7-overexpressing plants and could be boosted by exogenous ET. Transgenic poplars overexpressing PagERF114 displayed enhanced salt tolerance, lower MDA content, and higher SOD/POD activities, demonstrating that PagERF114 enhances salt tolerance. Taken together, our findings suggest that PeMPK7 fine-tunes phytohormone homeostasis and partially enhances salt tolerance through an ethylene-associated pathway involving PagERF114.