The Prunus mume species has undergone a long process of domestication and introduction in China, resulting in marked differences in freezing tolerance among populations across a latitudinal gradient of approximately 1,000 km. However, the introduction and domestication process is time-consuming, constraining the efficiency of species introduction. In this study, P. mume samples with the same genetic background spanning over 1,000 km from north to south were selected as experimental materials. The molecular mechanisms underlying cold-acclimation-mediated freeze tolerance in P. mume were investigated using multiomics high-throughput sequencing and molecular biology techniques. The cold-acclimated plant material exhibited enhanced freezing tolerance. Cold acclimation substantially enhanced transcriptional reprogramming under cold stress, accompanied by the remodeling of chromatin states in the promoter region. A variety of cis-regulatory elements were identified in the open chromatin regions of cold-acclimated plant materials, including G-box, ABRE, and other stress-responsive elements. The bZIP transcription factor PmGBF1, as a key regulatory node, directly regulates the expression of the cold shock protein gene PmCSL by binding to G-box elements to regulate freezing tolerance. This study reveals the molecular mechanism underlying cold acclimation mediated by the PmGBF1-PmCSL pathway in regulating P. mume freezing tolerance, providing an epigenetic theoretical basis and genetic resources for cold-acclimation breeding of freezing tolerance in woody plants.

Innovation in plant-breeding technology relies on precise, targeted genetic manipulation, which depends on the efficient delivery of genetic elements and robust plant cell regeneration systems. Agrobacterium tumefaciens, a traditional medium for genetic material delivery, is well established and has become widely adopted, but it faces limitations such as species specificity, transformation chimerism, and the requirement for two-step processes of transformation and regeneration. In contrast, Rhizobium rhizogenes can deliver genetic material with efficiency comparable to that of A. tumefaciens while excelling in producing transgenic homozygotes in a single step. This article summarizes the molecular mechanisms underlying R. rhizogenes-mediated hairy-root induction in plants, discusses the development of genetic material delivery systems, details the construction of hairy-root induction and regeneration platforms, explores molecular mechanisms in hairy roots and their applications in genetic breeding, and highlights the use of hairy roots for extracting secondary metabolites. The hairy-root genetic transformation system provides efficient, simplified, and broadly adaptable tools for genetic manipulation in breeding, accelerating the advancement of cutting-edge technologies such as gene editing, rapid domestication, and synthetic biology-driven breeding.