Toona sinensis is an important “vegetable and timber” tree species that is widely distributed in eastern and southeastern Asia. An efficient mechanism for preserving and utilizing germplasm resources is crucial for speeding up the process of genetic improvement of T. sinensis. We collected a total of 1040 germplasm resources of T. sinensis from China, Britain, and New Zealand. Using a total of 27,040 markers, we analyzed the genetic diversity, genetic structure, and core collection of these resources. Additionally, a comprehensive evaluation method for phenotypes of T. sinensis was established by principal component analysis (PCA) and the technique for order preference by similarity to ideal solution (TOPSIS). Our analysis included three main results: Firstly, the breeding population, consisting of a total of 1040 individuals, contains a diverse genetic pool and can be divided into two genetic clusters. Secondly, the best core collection was obtained from the alternative population, consisting of a total of 208 individuals and comprising 20% of the breeding population. It was screened out based on Core Hunter 3 software with the average entry-to-nearest-entry (E-NE) algorithm. Finally, a comprehensive evaluation method was established based on eight selected agronomic traits of the core collection. This method allowed us to screen the best individual plants of the core collection, including N0237, N0972, and N0409. Overall, our research findings will enable better preservation and utilization of T. sinensis germplasm resources and result in faster improvement of T. sinensis varieties.

Toona sinensis, commonly known as Chinese Toon, is a plant species that possesses noteworthy value as a tree and vegetable. Its tender young buds exhibit a diverse range of colors, primarily determined by the presence and composition of anthocyanins and flavonoids. However, the underlying mechanisms of anthocyanin biosynthesis in Toona sinensis have been rarely reported. To explore the related genes and metabolites associated with composition of leaf color, we conducted an analysis of the transcriptome and metabolome of five distinct Toona clones. The results showed that differentially expressed genes and metabolites involved in anthocyanin biosynthesis pathway were mainly enriched. A conjoint analysis of transcripts and metabolites was carried out in JFC (red) and LFC (green), resulting in the identification of 510 genes and 23 anthocyanin-related metabolites with a positive correlation coefficient greater than 0.8. Among these genes and metabolites, 23 transcription factors and phytohormone-related genes showed strong coefficients with 13 anthocyanin derivates, which mainly belonged to the stable types of delphinidin, cyanidin, peonidin. The core derivative was found to be Cyanidin-3-O-arabinoside, which was present in JFC at 520.93 times the abundance compared to LFC. Additionally, the regulatory network and relative expression levels of genes revealed that the structural genes DFR, ANS, and UFGT1 might be directly or indirectly regulated by the transcription factors SOC1 (MADS-box), CPC (MYB), and bHLH162 (bHLH) to control the accumulation of anthocyanin. The expression of these genes was significantly higher in red clones compared to green clones. Furthermore, RNA-seq results accurately reflected the true expression levels of genes. Overall, this study provides a foundation for future research aimed at manipulating anthocyanin biosynthesis to improve plant coloration or to derive human health benefits.

Somatic embryogenesis is an ideal model process for studying early plant development. Embryonic cell lines of Larix kaempferi (Lamb.) Carr overexpressing LaMIR166a were obtained in our previous study. Here, a combination of de novo transcriptomics and extensively targeted metabolomics was used to study the transcriptional profiles and metabolic changes in wild-type and LaMIR166a-overexpressed embryonic cell lines. A total of 459 metabolites were found in the wild-type and transgenic cell lines. Compared to those in the wild-type cell lines, transcripts and metabolites were significantly altered in the LaMIR166a-overexpressed cell lines. Among differentially expressed genes (DEGs), phenylalanine and flavonoid synthesis genes were significantly enriched, and among differentially accumulated metabolites (DAMs), phenolic acids and flavonoids accumulated in particularly high amounts. Thus, the flavonoid biosynthetic pathway seems to be the most abundant pathway in response to LaMIR166a overexpression. Based on the Kyoto Encyclopedia of Genes and Genomes database, the association analysis of metabolome and transcriptome data showed that flavonoid biosynthesis and plant hormone signal transduction processes were significantly changed in miR166a-overexpression lines, suggesting that miR166 might be involved in these processes. The present study identified a number of potential metabolites associated with LaMIR166a overexpression, providing a significant foundation for a better understanding of the regulatory mechanisms underlying miR166.

The study of somatic embryogenesis can provide insight into early plant development. We previously obtained LaMIR166a-overexpressing embryonic cell lines of Larix kaempferi (Lamb.) Carr. To further elucidate the molecular mechanisms associated with miR166 in this species, the transcriptional profiles of wild-type (WT) and three LaMIR166a-overexpressing transgenic cell lines were subjected to RNA sequencing using the Illumina NovaSeq 6000 system. In total, 203,256 unigenes were generated using Trinity de novo assembly, and 2467 differentially expressed genes were obtained by comparing transgenic and WT lines. In addition, we analyzed the cleaved degree of LaMIR166a target genes LaHDZ31–34 in different transgenic cell lines by detecting the expression pattern of LaHdZ31–34, and their cleaved degree in transgenic cell lines was higher than that in WT. The downstream genes of LaHDZ31–34 were identified using Pearson correlation coefficients. Yeast one-hybrid and dual-luciferase report assays revealed that the transcription factors LaHDZ31–34 could bind to the promoters of LaPAP, LaPP1, LaZFP5, and LaPHO1. This is the first report of gene expression changes caused by LaMIR166a overexpression in Japanese larch. These findings lay a foundation for future studies on the regulatory mechanism of miR166.

Triadica sebifera, an economically and medicinally valuable tree species native to China, was investigated for its in vitro regeneration potential using leaf explants from nodal cuttings of young stems and sprouts. This study evaluated the effects of basal media, plant growth regulators (PGRs), explant sources, and incision methods on adventitious shoot induction, supplemented by histological analysis. The highest shoot regeneration frequency (98.89%) and maximum shoot number (72) were achieved via direct organogenesis using sucker-derived nodal cuttings cultured on MS medium with 2 mg/L 6- benzyladenine (6-BA), 0.3 mg/L kinetin (KT), and 0.2 mg/L α-naphthaleneacetic acid (NAA). Under identical conditions, branch-derived explants showed lower regeneration (84.44%, 64 shoots). Transverse midvein incision proved most effective, with sucker-derived leaves exhibiting superior regeneration. Shoots elongated completely (100%) on Murashige and Skoog (MS) medium containing 0.3 mg/L 6-BA, 0.03 mg/L NAA, and activated charcoal. Rooting was optimal on MS medium with 0.3 mg/L indole-3-butyric acid (IBA), yielding a 98% acclimatization survival rate. Histological analysis revealed de novo meristem formation from parenchyma cells, confirming direct organogenesis without callus intermediation, further validating the enhanced regenerative capacity of sprout-derived explants. This efficient in vitro regeneration system provides a foundation for large-scale propagation and germplasm conservation of T. sebifera, while offering insights for woody plant regeneration studies.

Environmental factors are strong drivers of local adaptation in forest tree species. Toona ciliata var. pubescens, an endangered tree species endemic to China, is widely distributed across Eastern and Southwestern China. In this study, we used 8 genomic microsatellite markers and 17 EST-SSR markers across nine populations from the Yunnan–Kweichow Plateau and Eastern China, to explore the adaptive variation and genetic structure of T. ciliata var. pubescens. Patterns of population structure were apparent using a Bayesian clustering program, STRUCTURE, which identified four distinct clusters. We identified four outlier loci that were potentially under selection using the Dirichlet-multinomial and hierarchic simulation models. Through the Mantel test, it was found that geographic and climatic factors have jointly affected the genetic structure of T. ciliata var. pubescens in the study area. Based on redundancy analysis (RDA), it was shown that the correlation between climatic variables associated with variation is stronger than that of geographic variables. It is worth mentioning that the eight alleles from outlier loci have potentially adaptive and are associated with either precipitation or temperature variables. All analyses revealed high genetic diversity and significant genetic differentiation in the populations of T. ciliata var. pubescens. This indicated that the climatic variables including precipitation and temperature are drivers of local adaptation in the populations of T. ciliata var. pubescens.