The C-Repeat Binding Factor (CBF) gene family has been identified and characterized in multiple plant species, and it plays a crucial role in responding to low temperatures. Presently, only a few studies on tree species demonstrate the mechanisms and potential functions of CBFs associated with cold resistance, while our study is a novel report on the multi-aspect differences of CBFs among three tree species, compared to previous studies. In this study, genome-wide identification and analysis of the CBF gene family in Acer truncatum, Acer pseudosieboldianum, and Acer yangbiense were performed. The results revealed that 16 CBF genes (five ApseCBFs, four AcyanCBFs, and seven AtruCBFs) were unevenly distributed across the chromosomes, and most CBF genes were mapped on chromosome 2 (Chr2) and chromosome 11 (Chr11). The analysis of phylogenetic relationships, gene structure, and conserved motif showed that 16 CBF genes could be clustered into three subgroups; they all contained Motif 1 and Motif 5, and most of them only spanned one exon. The cis-acting elements analysis showed that some CBF genes might be involved in hormone and abiotic stress responsiveness. In addition, CBF genes exhibited tissue expression specificity. High expressions of ApseCBF1, ApseCBF3, AtruCBF1, AtruCBF4, AtruCBF6, AtruCBF7, and ApseCBF3, ApseCBF4, ApseCBF5 were detected on exposure to low temperature for 3 h and 24 h. Low expressions of AtruCBF2, AtruCBF6, AtruCBF7 were detected under cold stress for 24 h, and AtruCBF3 and AtruCBF5 were always down-regulated under cold conditions. Taken together, comprehensive analysis will enhance our understanding of the potential functions of the CBF genes on cold resistance, thereby providing a reference for the introduction of Acer species in our country.

Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.

Populus alba × Populus glandulosa (84K poplar) is model material with excellent genetic engineering resource and ornamental value. In our study, AmRosea1 (Antirrhinum majus) was overexpressed in 84K poplar, and the transgenic 84K (AM) poplar with high content of anthocyanin exhibited red pigmentation leaves. The transcriptome analysis between wild type (WT) and AM showed that 170 differentially expressed genes (DEGs) (86 up-regulated and 84 down-regulated) were found, and some DEGs were involved in flavone and flavonol biosynthesis, flavonoid biosynthesis and anthocyanin biosynthesis. The metabolome analysis showed that 13 anthocyanins-related differentially accumulated metabolites (DAMs) were detected in AM. The correlation analysis between DEGs and DAMs were performed, and the results revealed that 18 DEGs, including 11 MYB genes, two BZ1 genes, one FG2 gene, one ANS gene, and three IF7MAT genes, were negatively or positively correlated with 13 DAMs. The phylogenetic analysis demonstrated that there was high homology between AmRosea1 and PagMYB113, and MYB113 co-expressed with BZ1, ANS and DFR directly. Our results elucidated the molecular mechanism of plant color change mediated by anthocyanin biosynthesis pathway, which laid the foundation for the development and utilization of colorful woody plant.

The MADS-box gene family plays a crucial role in multiple developmental processes of plants, especially in floral organ specification and the regulation of fruit development and ripening. Juglans mandshurica is a precious fruit material whose quality and yield are determined by floral organ development. The molecular mechanism of J. mandshurica female and male flower development depending on MADS-box genes remains unclear. In our study, 67 JmMADS genes were identified and unevenly distributed on 15 of 16 J. mandshurica chromosomes. These genes were divided into two types [type I (Mα, Mγ, Mδ) and type II (MIKC)]. The gene structure and motif analyses showed that most genes belonging to the same type had similar gene structures and conserved motifs. The analysis of syntenic relationships showed that MADS-box genes in J. mandshurica, J. sigillata, and J. regia exhibited the highest homology and great collinearity. Analysis of cis-acting elements showed that JmMADS gene promoter regions contained light, stress and hormone response cis-acting elements. The gene expression patterns demonstrated that 30 and 26 JmMADS genes were specifically expressed in the female and male flowers, respectively. In addition, 12 selected genes common to J. mandshurica female and male flowers were significantly upregulated at the mature stage and were used to validate the reliability of the transcriptome data using quantitative real-time PCR. This comprehensive and systematic analysis of J. mandshurica MADS-box genes lays a foundation for future studies on MADS-box gene family functions.

Lipid-rich Pinus koraiensis seed kernels are highly regarded for their nutritional and health benefits. To ascertain the molecular mechanism of lipid synthesis, we conducted widely targeted metabolomic profiling together with a transcriptome analysis of the kernels in P. koraiensis cones at various developmental stages. The findings reveal that 148 different types of lipid metabolites, or 29.6% of total metabolites, are present in kernels. Among those metabolites, the concentrations of linoleic acid, palmitic acid, and α-linolenic acid were higher, and they steadily rose as the kernels developed. An additional 10 hub genes implicated in kernel lipid synthesis were discovered using weighted gene co-expression network analysis (WGCNA), gene interaction network analysis, oil body biosynthesis, and transcriptome analysis. This study used lipid metabolome and transcriptome analyses to investigate the mechanisms of key regulatory genes and lipid synthesis molecules during kernel development, which served as a solid foundation for future research on lipid metabolism and the creation of P. koraiensis kernel food.

To evaluate differences among 19 different ploidy hybrid poplar clones grown in northeast China, 21 traits related to growth traits and photosynthetic characteristics were detected and analyzed. Abundant phenotypic variations exist among and within populations, and these variations are the basis of forest tree genetic improvements. In this research, variance analysis showed that the traits except the net photosynthesis rate among the different ploidies and all the other traits exhibited significant differences among the ploidies or clones (p < 0.01). Estimation of phenotypic coefficients of variation, genotypic coefficients of variation, and repeatability is important for selecting superior materials. The larger the value, the greater the potential for material selection improvement. The repeatability of the different traits ranged from 0.88 to 0.99. The phenotypic and genotypic coefficients of variation of all the investigated traits ranged from 6.88% to 57.40% and from 4.85% to 42.89%, respectively. Correlation analysis showed that there were significant positive correlations between tree height, diameter, and volume. Transpiration rate, intercellular carbon dioxide concentration, and stomatal conductance were significantly positively correlated with each other but negatively correlated with instantaneous water use efficiency. Growth traits were weakly correlated with photosynthetic indexes. The rank correlation coefficient showed that most of the growth indicators reached a significant correlation level among different years (0.40–0.98), except 1-year-old tree height with 4-year-old tree height and 1-year-old ground diameter with 3-year-old tree height, which indicated the potential possibility for early selection of elite clones. Principal analysis results showed that the contribution rate of the first principal component was 46.606%, and 2-year-old tree height, 2-year-old ground diameter, 3-year-old tree height, 3-year-old ground diameter, 3-year-old diameter at breast height, 3-year-old volume, 4-year-old tree height, 4-year-old ground diameter, 4-year-old diameter at breast height, and 4-year-old volume showed higher vector values than other traits. With the method of multiple-trait comprehensive evaluation to evaluate clones, SX3.1, SY3.1, and XY4.2 were selected as elite clones, and the genetic gains of height, basal diameter, diameter at breast height, and volume of selected clones ranged from 12.85% to 64.87% in the fourth growth year. The results showed fundamental information for selecting superior poplar clones, which might provide new materials for the regeneration and improvement of forests in Northeast China.