Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv

Molecular identification of F1 hybrids of Fraxinus mandshurica × Fraxinus chinensis using SSR markers

To breed new Fraxinus varieties with superior traits including rapid growth, drought tolerance, and salinity resistance, this study established 480 F1 interspecific hybrid progeny through controlled pollination, using Fraxinus mandshurica Rupr. as the female parent and Fraxinus chinensis Roxb. as the male parent. Early-stage hybrid identification was performed using SSR (simple sequence repeat) markers. From 37 candidate SSR primers, two highly polymorphic pairs were selected for hybrid verification via polyacrylamide gel electrophoresis. Of the 480 offspring, 280 were confirmed as true hybrids, yielding a hybrid purity of 58.33 %. Primer pair Fm19 detected 62.29 % of hybrids, with partial overlap (shared detection) with primer pair Fc1. The polymorphism information content (PIC) ranged from 0.93 to 0.97 (mean: 0.95). Polymorphic alleles from both primers were converted into binary data (1 = present, 0 = absent) to generate unique molecular IDs for 144 hybrid offspring. This work established an efficient SSR-based method for early hybrid identification in F. mandshurica and F. chinensis, facilitating accelerated breeding and variety development.

Population genetic diversity and structure of the endangered species Tetracentron sinense Oliver (Tetracentraceae) with SNPs based on RAD sequencing

Tetracentron sinense Oliv. (T. sinense), as a tertiary living fossil, has experienced a significant decline in population numbers. Currently, genetic resources depletion and human activities have led to habitat fragmentation of relict and endangered plants, despite the abundant evidence of its medicinal, economic, and ecological value. Conservation strategies were clarified and evaluated based on the genetic structure characteristics and diversity patterns among 25 wild populations using Restriction site-associated DNA sequencing (RAD-seq) technology. Through SNP calling, filtering, genetic diversity analysis, discriminant analysis of principal components (DAPC), maximum-likelihood phylogenetic tree, and ADMIXTURE clustering, significant population structure and differentiation were identified. The results revealed a total of 2,169 single nucleotide polymorphisms (SNPs), indicating lower genetic variation but higher genetic differentiation (He: 0.10, I: 0.16, Fst: 0.33). Analysis of molecular variance (AMOVA) showed that genetic variation within populations accounted for 77% of the total variance. DAPC, maximum-likelihood phylogenetic tree, and ADMIXTURE clustering analysis grouped the 25 populations into five distinct clades influenced by isolation, restricted gene flow, and complex topography. To preserve the genetic integrity of T. sinense, it is recommended to establish conservation units corresponding to different geographic clades, with a focus on populations with low/high genetic diversity by implementing artificial reproduction and germplasm resource nurseries. Given the species' vulnerable conservation status, urgent implementation of the aforementioned conservation strategies is necessary to safeguard the remaining genetic resources.

Population genetic assessment of Viburnum japonicum in China using ddRAD-seq

Viburnum japonicum is a rare plant species and endemic to the coastal region of Eastern Asia with extremely small populations. Within mainland China, this species can be only found in narrow habitats of the northeast coastal islands of Zhejiang Province. However, there are scarce conservation genetic studies on V. japonicum, which has limited the effective conservation and management of this rare species. Here, 51 individuals in four natural populations covering the Chinese geographic range of the species were sampled to assess the genetic diversity and population structure. A total of 445,060 high-quality single nucleotide polymorphisms (SNPs) were identified using double digest restriction-site associated sequencing (ddRAD-seq). The overall average values of observed heterozygosity (Ho), expected heterozygosity (He), and average nucleotide diversity (π), were 0.2207, 0.2595, and 0.2741, respectively. The DFS-2 population exhibited the highest level of genetic diversity among all the populations. Genetic differentiation between populations was moderate (F _ST = 0.1425), and there was selfing between populations (F _IS = 0.1390, S = 24.52%). Of the total genetic variation, 52.9% was found among populations through AMOVA analysis. The Mantel test (r = 0.982, p = 0.030) combined with analyses of the Maximum Likelihood (ML) phylogenetic tree, ADMIXTURE, and principal component analysis (PCA), revealed that populations of V. japonicum were genetically segregated and significantly correlated with their geographical distribution. Our study demonstrated that V. japonicum maintained a medium level of genetic diversity and differentiation with a strong population structure, and the results were mainly affected by its island distribution pattern and self-crossing characteristics. These results provide insights into the genetic diversity and population history of V. japonicum, critical information for conserving and sustainably developing its genetic resources.

Performance comparison of RGB and multispectral vegetation indices based on machine learning for estimating Hopea hainanensis SPAD values under different shade conditions

Reasonable cultivation is an important part of the protection work of endangered species. The timely and nondestructive monitoring of chlorophyll can provide a basis for the accurate management and intelligent development of cultivation. The image analysis method has been applied in the nutrient estimation of many economic crops, but information on endangered tree species is seldom reported. Moreover, shade control, as the common seedling management measure, has a significant impact on chlorophyll, but shade levels are rarely discussed in chlorophyll estimation and are used as variables to improve model accuracy. In this study, 2-year-old seedlings of tropical and endangered Hopea hainanensis were taken as the research object, and the SPAD value was used to represent the relative chlorophyll content. Based on the performance comparison of RGB and multispectral (MS) images using different algorithms, a low-cost SPAD estimation method combined with a machine learning algorithm that is adaptable to different shade conditions was proposed. The SPAD values changed significantly at different shade levels (p < 0.01), and 50% shade in the orthographic direction was conducive to chlorophyll accumulation in seedling leaves. The coefficient of determination (R ²), root mean square error (RMSE), and average absolute percent error (MAPE) were used as indicators, and the models with dummy variables or random effects of shade greatly improved the goodness of fit, allowing better adaption to monitoring under different shade conditions. Most of the RGB and MS vegetation indices (VIs) were significantly correlated with the SPAD values, but some VIs exhibited multicollinearity (variance inflation factor (VIF) > 10). Among RGB VIs, RGRI had the strongest correlation, but multiple VIs filtered by the Lasso algorithm had a stronger ability to interpret the SPAD data, and there was no multicollinearity (VIF < 10). A comparison of the use of multiple VIs to estimate SPAD indicated that Random forest (RF) had the highest fitting ability, followed by Support vector regression (SVR), linear mixed effect model (LMM), and ordinary least squares regression (OLR). In addition, the performance of MS VIs was superior to that of RGB VIs. The R ² of the optimal model reached 0.9389 for the modeling samples and 0.8013 for the test samples. These findings reinforce the effectiveness of using VIs to estimate the SPAD value of H. hainanensis under different shade conditions based on machine learning and provide a reference for the selection of image data sources.

Full-Length Transcriptome Characterization and Comparative Analysis of Chosenia arbutifolia

As a unique tree species in the Salicaceae family, Chosenia arbutifolia is used primarily for construction materials and landscape planting in China. Compared with other Salicaceae species members, the genomic resources of C. arbutifolia are extremely scarce. Thus, in the present study, the full-length transcriptome of C. arbutifolia was sequenced by single-molecular real-time sequencing (SMRT) technology based on the PacBio platform. Then, it was compared against those of other Salicaceae species. We generated 17,397,064 subreads and 95,940 polished reads with an average length of 1812 bp, which were acquired through calibration, clustering, and polishing. In total, 50,073 genes were reconstructed, of which 48,174 open reading frames, 4281 long non-coding RNAs, and 3121 transcription factors were discovered. Functional annotation revealed that 47,717 genes had a hit in at least one of five reference databases. Moreover, a set of 12,332 putative SSR markers were screened among the reconstructed genes. Single-copy and special orthogroups, and divergent and conserved genes, were identified and analyzed to find divergence among C. arbutifolia and the five Salicaceae species. To reveal genes involved in a specific function and pathway, enrichment analyses for GO and KEGG were also performed. In conclusion, the present study empirically confirmed that SMRT sequencing realistically depicted the C. arbutifolia transcriptome and provided a comprehensive reference for functional genomic research on Salicaceae species.