Experimental Center of Tropical Forestry

This paper presents a method for predicting the above ground leafless biomass of trees in a non destructive way. We utilize terrestrial laserscan data to predict the volume of the trees. Combining volume estimates with density measurements leads to biomass predictions. Thirty-six trees of three different species are analyzed: evergreen coniferous Pinus massoniana, evergreen broadleaved Erythrophleum fordii and leafless deciduous Quercus petraea. All scans include a large number of noise points; denoising procedures are presented in detail. Density values are considered to be a minor source of error in the method if applied to stem segments, as comparison to ground truth data reveals that prediction errors for the tree volumes are in accordance with biomass prediction errors. While tree compartments with a diameter larger than 10 cm can be modeled accurately, smaller ones, especially twigs with a diameter smaller than 4 cm, are often largely overestimated. Better prediction results could be achieved by applying a biomass expansion factor to the biomass of compartments with a diameter larger than 10 cm. With this second method the average prediction error for Q. petraea could be reduced from 33.84% overestimation to 3.56%. E. fordii results could also be improved reducing the average prediction error from

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is a fast-growing evergreen conifer with high-quality timber and is an important reforestation and commercial tree species in southern China. Planting density affects the productivity of Chinese fir plantations. To study the effect of five different planting densities and soil depth on soil nutrient contents of a mature C. lanceolata plantation, the soil nutrient contents (soil depths 0–100 cm) of 36-year-old mature Chinese fir plantations under five different planting densities denoted A (1667 trees·ha−1), B (3333 trees·ha−1), C (5000 trees·ha−1), D (6667 trees·ha−1), and E (10,000 trees·ha−1) were measured in Pingxiang county, Guangxi province, China. Samples were collected from the soil surface down to a one meter depth from each of 45 soil profiles, and soil samples were obtained at 10 different soil depths of 0–10, 10–20, 20–30, 30–40, 40–50, 50–60, 60–70, 70–80, 80–90, and 90–100 cm. Twelve soil physical and chemical indicators were analyzed. The results showed that: (1) as planting density increased, the organic matter, organic carbon, total N and P, available N, effective Fe, and bulk density decreased. Soil pH, total K, and effective K increased with increasing planting density. Planting density did not significantly influence the exchangeable Ca and Mg. (2) Soil organic matter; organic carbon; total N and P; effective N, P, and K; exchangeable Ca and Mg; effective Fe content; and bulk density decreased with increasing soil depth. This pattern was particularly evident in the top 30 cm of the soil. (3) Excessively high planting density is not beneficial to the long-term maintenance of soil fertility in Chinese fir plantations, and the planting density of Chinese fir plantations should be maintained below 3333 stems·ha−1 (density A or B) to maintain soil fertility while ensuring high yields.

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Dalbergia odorifera T. Chen (Fabaceae) is a semi-deciduous tree species indigenous to Hainan Island in China. Due to its precious heartwood “Hualimu (Chinese)” and Chinese medicinal components “Jiangxiang”, D. odorifera is seriously threatened of long-term overexploitation and has been listed on the IUCN (International Union for Conservation of Nature’s) red list since 1998. Therefore, the elucidation of its genetic diversity is imperative for conservation and breeding purposes. In this study, we evaluated the genetic diversity of 42 wild D. odorifera trees from seven populations covering its whole native distribution. In total, 19 SSR (simple sequence repeat) markers harbored 54 alleles across the 42 samples, and the medium genetic diversity level was inferred by Nei’s gene diversity (0.36), observed (0.28) and expected heterozygosity (0.37). Among the seven wild populations, the expected heterozygosity (He) varied from 0.31 (HNQS) to 0.40 (HNCJ). The analysis of molecular variance (AMOVA) showed that only 3% genetic variation existed among populations. Moderate population differentiations among the investigated populations were indicated by pairwise Fst (0.042–0.115). Structure analysis suggested two clusters for the 42 samples. Moreover, the seven populations were clearly distinguished into two clusters from both the principal coordinate analysis (PCoA) and neighbor-joining (NJ) analysis. Populations from Haikou city (HNHK), Baisha autonomous county (HNBS), Ledong autonomous county (HNLD), and Dongfang city (HNDF) comprised cluster I, while cluster II comprised the populations from Wenchang city and Sansha city (HNQS), Changjiang autonomous county (HNCJ), and Wuzhisan city (HNWZS). The findings of this study provide a preliminary genetic basis for the conservation, management, and restoration of this endemic species.

Soil aggregates are the basic units of soil structure, and their stability is a key indicator of soil quality and capacity to support ecosystem functions. The impacts of various environmental factors on soil aggregates have been widely studied. However, there remains elusive knowledge on the synergistic effects of changing forest stand structure on soil aggregate stability (SAS), particularly in subtropical China where soil erosion remains a critical issue. We investigated variations in the components of soil humus (HS), including humic acids (HAs), fulvic acids (FAs), and humins (HMs), under pure Chinese fir (Cunninghamia lanceolata) plantation (PP) and multi-layered mixed plantation (MP) comprising C. lanceolata, Castanopsis hystrix, and Michelia hedyosperma. The state of soil aggregate stability, was determined by three separate methods, i.e., dry-sieving, wet-sieving, and the Le Bissonnais. High-throughput sequencing was used to determine the diversity and composition of microbial communities under PP and MP. We then built partial least squares path models (PLS-PM) for assessing the responses of SAS to the variations in soil microorganisms and HS components. The MP stands had significantly greater SAS (P < 0.05), higher content of HAs and more rapid organic matter humification within aggregates, than the PP stands. High-throughput sequencing confirmed that the Pielou and α-diversity index values (Chao1 and Shannon) for fungi were all significantly higher under MP than under PP, while no marked difference was found in bacterial α-diversity between the two plantation types. Moreover, there were markedly greater abundance of three bacterial phyla (Verrucomicrobia, Chloroflexi, and Gemmatimonadetes) and three fungal phyla (Ascomycota, Kickxellomycota, and Glomeromycota), and significantly less abundance of two bacterial phyla (Planctomycetes and Firmicutes) and four fungal phyla (Basidiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota) under MP than under PP. The Chloroflexi and Ascomycota phyla appeared to be the primary drivers of soil aggregate distribution. Our findings revealed that the promotion of SAS under MP was mainly driven by increased soil organic matter (SOM) content, which altered bacterial communities and enhanced fungal diversity, thereby increasing HAs content and the rate of organic matter humification. Considering the combined effects of enhanced soil quality, productivity, and relevant economic costs, introducing broadleaved tree species into Chinese fir plantations can be an effective strategy for stabilizing soil structure against erosion in subtropical China. Our study elucidated the controls on variations of SAS in Chinese fir-dominated plantations and demonstrated the benefit of converting pure Chinese fir plantation to multi-layered mixed plantations in increasing soil structural stability and improving site quality.

Abstract Climate change is an important driver of species distribution and biodiversity. Understanding the response of plants to climate change is helpful to understand species differentiation and formulate conservation strategies. The genus Polyspora (Theaceae) has an ancient origin and is widely distributed in subtropical evergreen broad‐leaved forests. Studies on the impacts of climate change on species geographical distribution of Chinese Polyspora can provide an important reference for exploring the responses of plant groups in subtropical evergreen broad‐leaved forests with geological events and climate change in China. Based on the environmental variables, distribution records, and chloroplast genomes, we modeled the potential distribution of Chinese Polyspora in the Last Glacial Maximum, middle Holocene, current, and future by using MaxEnt‐ArcGIS model and molecular phylogenetic method. The changes in the species distribution area, centroid shift, and ecological niche in each periods were analyzed to speculate the response modes of Chinese Polyspora to climate change in different periods. The most important environmental factor affecting the distribution of Polyspora was the precipitation of the driest month, ranging from 13 to 25 mm for the highly suitable habitats. At present, highly suitable distribution areas of Polyspora were mainly located in the south of 25°N, and had species‐specificity. The main glacial refugia of the Chinese Polyspora might be located in the Ailao, Gaoligong, and Dawei Mountains of Yunnan Province. Jinping County, Pingbian County, and the Maguan County at the border of China and Vietnam might be the species differentiation center of the Chinese Polyspora . Moderate climate warming in the future would be beneficial to the survival of P. axillaris , P. chrysandra , and P. speciosa . However, climate warming under different shared socio‐economic pathways would reduce the suitable habitats of P. hainanensis and P. longicarpa .

Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha2 in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.

More than 60% of the total area of tree plantations in China is in subtropical, and over 70% of subtropical plantations consist of pure stands of coniferous species. Because of the poor ecosystem services provided by pure coniferous plantations and the ecological instability of these stands, a movement is under way to promote indigenous broadleaf plantation cultivation as a promising alternative. However, little is known about the carbon (C) stocks in indigenous broadleaf plantations and their dependence on stand age. Thus, we studied above- and below-ground biomass and C stocks in a chronosequence of Mytilaria laosensis plantations in subtropical China; stands were 7, 10, 18, 23, 29 and 33 years old. Our assessments included tree, shrub, herb and litter layers. We used plot-level inventories and destructive tree sampling to determine vegetation C stocks. We also measured soil C stocks by analyses of soil profiles to 100 cm depth. C stocks in the tree layer dominated the above-ground ecosystem C pool across the chronosequence. C stocks increased with age from 7 to 29 years and plateaued thereafter due to a reduction in tree growth rates. Minor C stocks were found in the shrub and herb layers of all six plantations and their temporal fluctuations were relatively small. C stocks in the litter and soil layers increased with stand age. Total above-ground ecosystem C also increased with stand age. Most increases in C stocks in below-ground and total ecosystems were attributable to increases in soil C content and tree biomass. Therefore, considerations of C sequestration potential in indigenous broadleaf plantations must take stand age into account.

Abstract Understanding the effects of the demographic dynamics and environmental heterogeneity on the genomic variation of forest species is important, not only for uncovering the evolutionary history of the species, but also for predicting their ability to adapt to climate change. In this study, we combined a common garden experiment with range‐wide population genomics analyses to infer the demographic history and characterize patterns of local adaptation in a subtropical oak species, Quercus acutissima (Carruthers). We scanned approximately 8% of the oak genome using a balanced representation of both genic and non‐genic regions and identified a total of 55 361 single nucleotide polymorphisms (SNPs) in 167 trees. Genomic diversity analyses revealed an east–west split in the species distribution range. Coalescent‐based model simulations inferred a late Pleistocene divergence in Q. acutissima between the east and west groups as well as subsequent preglaciation population expansion events. Consistent with observed genetic differentiation, morphological traits also showed east–west differentiation and the biomass allocation in seedlings was significantly associated with precipitation. Environment was found to have a significant and stronger impact on the non‐neutral than the neutral SNPs, and also significantly associated with the phenotypic differentiation, suggesting that, apart from the geography, environment had played a role in determining non‐neutral and phenotypic variation. Our approach, which combined a common garden experiment with landscape genomics data, validated the hypothesis of local adaptation of this long‐lived oak tree of subtropical China. Our study joins the small number of studies that have combined genotypic and phenotypic data to detect patterns of local adaptation.

We transformed a Pinus massoniana plantation, the most important conifer plantation in southern China, with four different transformation treatments, in which Pinus massoniana was thinned to a density of 70%, and then differing richness and compositions of enrichment plantings were added. In order to examine the effects of the transformation, we compared species composition, stand structure and growth pattern in transformed stands with those in control stands. The results suggested that in the transformed stands species composition was diverse with trees both from the enrichment plantings and from natural recruitment. The size structure was changed such that the diameter at breast height (DBH) distribution tended to shift from a nearly normal distribution to an irregular multi-modal distribution. Substantial new ingrowth was found in the small DBH classes. The residual trees in the transformed stands were significantly larger than in the control treatment. However, for all trees, the control stands had the largest mean size, even though the residual tree growth was significantly smaller in the control stands. Finally, transformation treatment A4, which had the smallest overall mortality rate and simultaneously the mortality rate of each tree species was smaller than the corresponding value in other transformation treatments, was identified as the optimal transformation.

Summary Introducing N 2 ‐fixing tree species into Eucalyptus plantations could replace nitrogen (N) fertilization to maintain high levels of N consumption and productivity. However, N enrichment may exacerbate phosphorus (P) limitation as Eucalyptus robusta Smith is extensively planted in P‐poor tropical and subtropical soils. We conducted a field experiment in a pure plantation of Eucalyptus urophylla × grandis to investigate the impacts of N fertilization and introduced an N 2 ‐fixing tree of Dalbergia odorifera T. Chen on soil P transformation. Nitrogen fertilization significantly enhanced soil occluded P pool and reduced the other P pools due to acidification‐induced pH‐sensitive geochemical processes, lowering Eucalyptus leaf P concentration with higher N : P ratio. By contrast, introduced N 2 ‐fixing tree species did not change soil pH, labile inorganic P pool, and Eucalyptus leaf N : P ratio, even enhanced organic P pools and reduced occluded P pool probably due to altering microbial community composition particularly stimulating arbuscular mycorrhiza fungal abundance. Our results revealed differential responses and mechanistic controls of soil P transformation in Eucalyptus plantations with N fertilization and introduced N 2 ‐fixing tree species. The dissolution of occluded P pool along with organic P accumulation observed in the mixed plantations may represent a promising future to better manage soil P availability.

Both deterministic and stochastic processes have been linked to forest community assembly; however, their contribution to beta diversity has not been properly explored, and no studies to date have investigated their impacts on sparse depleted soils in forests that contain widespread exposed limestone karst. We found that the pairwise differences in species composition between quadrates was determined by a balanced variation in abundance, whereby the individuals of some species at one site were substituted by an equivalent number of individuals of different species at another site. Both the total beta diversity and its balanced variation in abundance declined with increasing sampling grain size. Our research indicated that environmental differences exert a strong influence on beta diversity, particularly total beta diversity and its balanced abundance variation in larger grain sizes. It was evident that deterministic and stochastic processes worked together, and that deterministic processes were more important than stochastic processes in the regulation of beta diversity in this heterogeneous tropical karst seasonal rainforest of Southern China. However, in future research a functional trait based approach will be required to tease out the relative degree of deterministic and stochastic processes toward an assessment of the temporal changes in species composition.

Summary Climate change has altered global precipitation regimes in terms of intensity and frequency of drought stress and, consequently, it is likely to affect soil moisture and soil aggregation. However, we know little about the effects of drought on soil aggregate size, distribution and stability, and how that affects carbon sequestration. A drought manipulation experiment was conducted by throughfall exclusion treatment (TET) of 50% in two planted forests ( Pinus massoniana Lamb. and Castanopsis hystrix A.DC.) in subtropical China. The aim was to investigate the effects of a reduction in throughfall on aggregate size, distribution and stability. The results from the 4‐year experiment show that the TET affected soil moisture content significantly (with 14.5 and 20.4% decreases in the P. massoniana and C. hystrix plantations, respectively) compared with the control. Soil temperature at 0–5‐cm soil depth and soil texture were not affected significantly. Soil porosity in the TET plots was greater than that of the control, whereas soil bulk density and free Al oxide content were less. The mass fractions of macroaggregates (&gt; 0.25 mm) and mean weight diameter (MWD) of aggregates, an indicator of aggregate stability, decreased in the TET compared with the control. Variation in aggregate size, distribution and stability can be caused by Fe and Al oxides, soil texture, bulk density and porosity. Our results indicated that TET reduced soil aggregate stability in subtropical plantations because of a decrease in free Al oxide and an increase in porosity. Slaking effects from variation in soil moisture were also possible for the decreased MWD. This study suggests disturbance of forest soils should be minimized in the context of a decline in precipitation. Highlights Size, distribution and stability of forest soil aggregates were evaluated under throughfall exclusion. TET reduced free Al oxide content but increased soil porosity, leading to breakdown of macroaggregates. Soil aggregate stability was reduced by TET. Fe and Al oxides and soil texture contributed more than SOC to aggregate size and stability.

The stem height–diameter allometric relationship is fundamental in determining forest and ecosystem structures as well as in estimating tree volume, biomass, and carbon stocks. Understanding the effects of silvicultural practices on tree height–diameter allometry is necessary for sustainable forest management, though the impact of measures such as thinning on the allometric relationship remain understudied. In the present study, the effects of thinning on tree height–diameter allometry were evaluated using Masson pine height and diameter growth data from a plantation experiment that included unthinned and thinned treatments with different intensities. To determine whether thinning altered the height–diameter allometry rhythm, the optimal height–diameter model was identified and dummy variable methods were used to investigate the differences among model parameters for different thinning treatments. Periodic (annual) allometric coefficients were calculated based on height and diameter increment data and were modeled using the generalized additive mixed model (GAMM) to further illustrate the response of tree height–diameter allometry to different thinning treatments over time. Significant differences were detected among the parameters of the optimal height–diameter model (power function) for different thinning treatments, which indicated that the pattern of the height–diameter allometry relationship of Masson pine was indeed altered by thinning treatments. Results also indicated a nonlinear trend in the allometric relationship through time which was significantly affected by thinning. The height–diameter allometric coefficient exhibited a unimodal convex bell curve with time in unthinned plots, and thinning significantly interfered with the original trend of the height–diameter allometric coefficient. Thinning caused trees to increase diameter growth at the expense of height growth, resulting in a decrease of the ratio of tree height to diameter, and this trend was more obvious as the thinning intensity increased.

Tree species can substantially impact the structure and functioning of soil microbial communities. However, how tree species mixing affects soil microbial communities along different soil compartment niches remains unknown, despite the theoretical (e.g., plant-soil feedback) and practical (e.g., rhizosphere engineering) importance of such knowledge in understanding and managing forest ecosystems. In this study, we analyzed soil samples taken from three microhabitats (bulk soil, rhizosphere soil, and root tissue) of pure conifer species (Pinus massoniana) plantations (PP), pure broadleaf species (Castanopsis hystrix) plantations (PC), and mixed plantation forest of the two species (MF) to understand the effects of tree species mixing on core soil microbial communities. We found that the diversity of soil bacterial and fungal communities was not affected by tree species mixing in most cases, but community composition (relative abundance and functional composition) was largely shaped by tree species mixing. Non-metric multidimensional scaling (NMDS) analysis revealed that the core bacterial and fungal communities of MF were between those of PP and PC. This suggests that tree species mixing can lead to a combination of soil microbial communities associated with each of the two tree species, potentially resulting in higher nutrient contents in the bulk soil of MF and lower phosphorus and carbon limitations in both the bulk and rhizosphere soils of MF compared to those of PP and PC. The Mantel test and redundancy analysis (RDA) showed that pH and NO3–-N content were the main environmental variables influencing soil microbial communities. Overall, the effects of tree species mixing varied markedly with microhabitat and season, with rhizosphere soil having the highest microbial diversity and network complexity and root tissue having the lowest. These results suggest that the mixing effects of tree species are more pronounced in the rhizosphere and dry season, on which silvicultural practices should focus.

The essential oil were extracted from the leaf of Phoebe bournei (Hemsl.) Yang by a hydrothermal method and then analyzed by gas chromatography–mass spectrometry. The leaf oil mainly included α-copaene (5.44%), α-muurolene (7.32%), δ-cadinene (11.44%), 1s-calamenene (5.18%). Phoebe bournei (Hemsl.) Yang leaf essential oil had significant inhibitory activity against Epidermophyton floccosum and Microsporum gypseum, the potential antitumor activity towards leukemia, breast, and colon cancer cell lines was good. Phoebe bournei (Hemsl.) Yang leaf essential oil had weaker activity on the four tested bacteria, it exhibited a certain role in promoting glucose uptake by adipocytes.

Near-natural forest management is an important way to change the soil fertility decline and productivity reduction of pure Chinese fir plantations. At present, many detailed studies have been carried out on the impact of near-natural forest management on Chinese fir plantations at home and abroad. However, there are still few studies on the response of rhizosphere bacterial communities to near-natural forest management. Our study determined absolute quantities of Chinese fir rhizosphere bacterial communities in different mixed patterns. The results underscore the importance of near-natural forest management for Chinese fir plantation rhizosphere bacterial communities and provide new information on soil factors that affect rhizosphere bacterial communities in South China.

Greenhouse gases are the main cause of global warming, and forest soil plays an important role in greenhouse gas flux. Near natural forest management is one of the most promising options for improving the function of forests as carbon sinks. However, its effects on greenhouse gas emissions are not yet clear. It is therefore necessary to characterise the effects of near natural forest management on greenhouse gas emissions and soil carbon management in plantation ecosystems. We analysed the influence of near natural management on the flux of three major greenhouse gases (carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O)) in Pinus massoniana Lamb. and Cunninghamia lanceolata (Lamb.) Hook. plantations. The average emission rates of CO2 and N2O in the near natural plantations were higher than those in the corresponding unimproved pure plantations of P. massoniana and C. lanceolata, and the average absorption rate of CH4 in the pure plantations was lower than that in the near natural plantations. The differences in the CO2 emission rates between plantations could be explained by differences in the C:N ratio of the fine roots. The differences in the N2O emission rates could be attributed to differences in soil available N content and the C:N ratio of leaf litter, while the differences in CH4 uptake rate could be explained by differences in the C:N ratio of leaf litter only. Near natural forest management negatively affected the soil greenhouse gas emissions in P. massoniana and C. lanceolata plantations. The potential impact of greenhouse gas flux should be considered when selecting tree species for enrichment planting.

Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3–13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.

Heartwood has a high economic value because of its natural durability, beautiful color, special aroma, and richness in active ingredients used in traditional Chinese medicine. However, the mechanism of heartwood formation remains unclear. Dalbergia odorifera was selected as the object of research to analyze this variation in the chemical composition of sapwood, transition zone, and heartwood as well as to elucidate the relationship between this variation and the formation of heartwood. The variation of secondary metabolites was analyzed using gas chromatography-mass spectrometry and ultra-high performance liquid chromatography–mass spectrometry, the variation of lignin was analyzed using Fourier transform infrared spectroscopy and ultraviolet visible spectrophotometry, and the variation law of mineral elements was analyzed using atomic absorption spectrophotometry. The results demonstrated that contents of characteristic secondary metabolites in Dalbergia odorifera were mainly distributed in heartwood (84.3–96.8%), increased from the outer to inner layers of the xylem, and sudden changes occurred in the transition zone (the fourth growth ring). The Dalbergia odorifera lignin can be identified as typical “syringyl–guaiacyl (S–G)” lignin, and the color darkened from the outside to the inside. The results demonstrated that there were more benzene rings and conjugated C=O structures in the heartwood. Additionally, the variation of minerals in the xylem was related to elemental types; the average concentrations of Mg, Ca, Fe and Sr were higher in the heartwood than in the sapwood, whereas the concentrations of K and Zn were higher in the sapwood than in the heartwood owing to the reabsorption of elements. The concentrations of Na and Cu were similar in the heartwood and sapwood. The composition and structural characteristics of secondary metabolites, lignin, and mineral elements in the three typical xylem regions (sapwood, transition zone and heartwood) of Dalbergia odorifera changed. The most abrupt change occurred in the narrow xylem transition zone, which is the key location involved in heartwood formation in Dalbergia odorifera.