Search

Japanese larch (Larix kaempferi) is an important plantation species in Japan as well as in Europe. The inheritance of wood color (L*, a* and b*), mass loss by a white-rot fungus (Trametes versicolor) and a brown-rot fungus (Fomitopsis palustris), and polyphenol content (as the taxifolin equivalent) in heartwood were examined for 75 trees in 15 full-sib families of L. kaempferi. The mean values of all trees were 74.5 in L*, 8.4 in a*, 23.0 in b*, 18.3 and 26.0% in mass loss by T. versicolor and F. palustris, and 0.045 µmol/mg in polyphenol content. The narrow-sense heritability (h 2) showed higher values in heartwood color (h 2 = 0.70–0.87), but mass loss and polyphenol content showed relatively lower values (h 2 = 0.00–0.33). Significant negative correlations were found between polyphenol content and mass loss by white-rot and brown-rot fungi. In addition, the polyphenol content of heartwood was significantly correlated with the color of heartwood. Similar results were obtained in genetic correlations. Thus, it is concluded that parents with lower L* and higher a* and b* in heartwood could produce progenies with higher polyphenol content in heartwood, thereby leading to higher decay resistance.

Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we optimized the DNA library preparation protocols and employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species,Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, andCunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb inC. obtusato 16.0 Mb inL. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.

Pine wilt disease is one of the most serious tree diseases occurring worldwide. Clones of Pinus densiflora Siebold et Zucc with pine wood nematode resistance were selected. In addition to resistance, wood quality is also an important criterion in the breeding program of P. densiflora because of its use as construction lumber. However, little information is available on the wood qualities of the progenies of resistant clones. The repeatabilities of the wood properties were investigated for 11 open-pollinated families of P. densiflora selected for their pine wood nematode resistance. Oven-dry density, latewood tracheid length, the microfibril angle (MFA) of the S2 layer in latewood tracheids, modulus of elasticity (MOE), and modulus of rupture (MOR) were measured in the third or fourth annual ring from the pith. No significant correlations were found between the wood properties and the stem diameter or tree height. However, significant correlations were found between oven-dry density and MOE or MOR, which suggests that oven-dry density is a good indicator for selecting wood with higher bending properties. Among the measured wood properties, oven-dry density had the highest repeatability (R=0.47), followed by MOR (R=0.33), tracheid length (R=0.21), and MFA (R=0.14). MOE had the lowest value (R=0.01). The 11 families examined were classified into three groups according to their growth characteristics, wood properties, and resistance to pine wilt disease. On the basis of the results, we conclude that genetic improvement of wood properties especially for wood density and MOR is possible for the resistant P. densiflora.

To clarify inheritance of static bending properties in relation to elastic and plastic regions, air-dry density, microfibril angle of the S2 layer in latewood tracheid (MFA), and static bending properties (modulus of elasticity [MOE], modulus of rupture [MOR] and bending work) were examined for juvenile wood of 18 full-sib families in 20-year-old Cryptomeria japonica. Heritability of all traits ranged from 0.12 (bending work) to 0.51 (air-dry density). Based on the results from principal component analysis (PCA) and cluster analysis, the families were classified into four groups with different types of load-deflection curves, suggesting that both elastic properties and deflection in plastic region differed among families. Furthermore, families included in a group were produced from specific parents, suggesting that deflection in plastic region as well as elastic property is inheritable. It can be concluded that mating parents may affect elasticity and plasticity of offspring.

Wood properties, including Young’s modulus, differ among clones in Larix kaempferi; however, available information is still limited on among-clonal variations of lumber qualities in L. kaempferi. T...

In order to promote plantation establishment of Larix gmelinii var. olgensis (syn. L. olgensis A. Henry), a ‘near threatened’ species, the wood and lumber properties were preliminary investigated for five trees from two clones of 57-year-old trees planted in Japan. The mean value of dynamic Young’s modulus of logs was 10.16 GPa. The mean values of annual ring width, latewood percentage, basic density, MOE, and MOR of five sample trees were 2.1 mm, 29.3%, 0.47 g•cm-3, 8.06 GPa, and 60.4 MPa, respectively. In addition, the MOE and MOR of 2 by 4 lumber were 10.43 GPa and 42.4 MPa, respectively. These values were similar to those obtained from other Larix species. Thus, construction lumber could be produced from the wood from plantation grown L. gmelinii var. olgensis.

Preventive plantation of resistant Pinus thunbergii seedlings is anticipated in non-epidemic areas of pine wilt disease (PWD) in Japan. The scions of resistant clones, which are required to establi...

We assessed the narrow-sense heredity and genetic gains of multiple traits obtained using the indirect selection method for progeny of Cryptomeria japonica D. Don by artificial crossing. Using stress wave velocity and Pilodyn penetration depth as indicative parameters, wood properties could be improved in future generations of C. japonica plus trees and forest breeding programs will become more efficient. To advance generations of C. japonica D. Don breeding populations, the narrow-sense heredity and genetic gain of traits of progenies are required to assess the practical genetic performance of parental trees and improve traits. We assessed the genetic gains in both growth characteristics and wood properties by indirect selection using full-sib progenies of C. japonica plus trees produced through artificial crosses. In 18-year-old progenies of 549 trees, we assessed growth characteristics, dynamic modulus of elasticity, basic density, stress wave velocity, and Pilodyn penetration depth. Genetic parameters were calculated using a mixed model and the breedR package. The genetic correlation between growth characteristics and wood properties was low. The efficiencies of indirect selection for dynamic modulus of elasticity by stress wave velocity and for basic densities by Pilodyn penetration depth were higher than those for growth characteristics by stress wave velocity and Pilodyn penetration depth, respectively. Strong correlations were found between the parental clonal values and breeding values of parental trees predicted from progeny using stress wave velocity and Pilodyn penetration depth. Using stress wave velocity and Pilodyn penetration depth as indicative parameters, future generations of C. japonica plus trees could produce superior wood properties. Growth characteristics and wood properties are independent; thus, both traits could be genetically improved compatibly.

In the twentieth century, a substantial decline in Pinus thunbergii populations in Japan occurred due to the outbreak of pine wood nematode (PWN), Burshaphelencus xylophilus. A PWN-P. thunbergii resistant trees-breeding project was developed in the 1980s to provide reforestation materials to minimalize the pest damage within the population. Since climate change can also contribute to PWN outbreaks, an intensive reforestation plan instated without much consideration can impact on the genetic diversity of P. thunbergii populations. The usage and deployment of PWN-P. thunbergii resistant trees to a given site without genetic management can lead to a genetic disturbance. The Iki-no-Matsubara population was used as a model to design an approach for the deployment management. This research aimed to preserve local genetic diversity, genetic structure, and relatedness by developing a method for deploying Kyushu PWN-P. thunbergii resistant trees as reforestation-material plants into Iki-no-Matsubara. The local genotypes of the Iki-no-Matsubara population and the Kyushu PWN-P. thunbergii resistant trees were analyzed using six microsatellite markers. Genotype origins, relatedness, diversity, and structure of both were investigated and compared with the genetic results previously obtained for old populations of P. thunbergii throughout Japan. A sufficient number of Kyushu PWN-P. thunbergii resistant trees, as mother trees, within seed orchards and sufficient status number of the seedlings to deploy are needed when deploying the Kyushu PWN-P. thunbergii resistant trees as reforestation material planting into Iki-no-Matsubara population. This approach not only be used to preserve Iki-no-Matsubara population (genetic diversity, genetic structure, relatedness, and resilience of the forests) but can also be applied to minimize PWN damage. These results provide a baseline for further seed sourcing as well as develop genetic management strategies within P. thunbergii populations, including Kyushu PWN-P. thunbergii resistant trees.

Along with progress in sequencing technology and accumulating knowledge of genome and gene sequences, molecular breeding techniques have been developed for predicting the genetic potential of individual genotypes and for selecting superior individuals. For Japanese cedar (Cryptomeria japonica (L.f.) D.Don), which is the most common coniferous species in Japanese forestry, we constructed a custom primer panel for target amplicon sequencing in order to simultaneously determine 3034 informative single nucleotide polymorphisms (SNPs). We performed primary evaluation of the custom primer panel with actual sequencing and in silico PCR. Genotyped SNPs had a distribution over almost the entire region of the C. japonica linkage map and verified the high reproducibility of genotype calls compared to SNPs obtained by genotyping arrays. Genotyping was performed for 576 individuals of the F1 population, and genomic prediction models were constructed for growth and wood property-related traits using the genotypes. Amplicon sequencing with the custom primer panel enables efficient obtaining genotype data in order to perform genomic prediction, manage clones, and advance forest tree breeding.

The wood properties were examined for Larix sibirica naturally grown in Tosontsengel, Mongolia. The dynamic Young's modulus of the logs ranged from 6.31 to 9.65 GPa. The mean values of wood...

The norlignan (NorL) content in extractives of sugi (Cryptomeria japonica) shows a decreasing tendency from the outer to the inner part of the heartwood (hW). The hypothesis, that this effect may be due to polymerization, which aggravates NorL extraction, has been explored in the present study. To this purpose, samples were collected and extracted from the outer, middle and inner parts of the hW. Fractionation procedures of NorL-oligomers by LH-20 column chromatography were established, and the fractions were characterized by advanced analytical methods such as HPLC-SEC and HPLC combined with electrospray ionization ion trap mass spectrometry (HPLC-ESI-ion-trap-MS). Agatharesinol and sequirin C were the most abundant compounds. Several individual NorL-dimers and -trimers were detected for the first time, and four kinds of NorL-dimers and seven kinds of NorL-trimers were semi-quantitatively analyzed by HPLC-ESI-MS combined with selected ion monitoring (SIM). The oligomer contents show an increasing tendency from the outer part toward the middle and inner part of the hW, which accounts mainly for the monomeric NorL decrement in the same direction.

Seasonal phenomena in plants are primarily affected by day length and temperature. The shoot transcriptomes of trees grown in the field and a controlled-environment chamber were compared to characterize genes that control annual rhythms and the effects of day length- and temperature-regulated genes in the gymnosperm Japanese cedar (Cryptomeria japonica D. Don), which exhibits seasonally indeterminate growth. Annual transcriptome dynamics were clearly demonstrated by principal component analysis using microarray data obtained under field-grown conditions. Analysis of microarray data from trees grown in a controlled chamber identified 2,314 targets exhibiting significantly different expression patterns under short-day (SD) and long-day conditions, and 2,045 targets exhibited significantly different expression patterns at 15°C (LT; low temperature) versus 25°C. Interestingly, although growth was suppressed under both SD and LT conditions, approximately 80% of the SD- and LT-regulated targets differed, suggesting that each factor plays a unique role in the annual cycle. The top 1,000 up-regulated targets in the growth/dormant period in the field coincided with more than 50% of the SD- and LT-regulated targets, and gene co-expression network analysis of the annual transcriptome indicated a close relationship between the SD- and LT-regulated targets. These results indicate that the respective effects of day length and temperature interact to control annual transcriptome dynamics. Well-known upstream genes of signaling pathways responsive to environmental conditions, such as the core clock (LHY/CjLHYb and CCA1/CjLHYa) and PEBP family (MFT) genes, exhibited unique expression patterns in Japanese cedar compared with previous reports in other species, suggesting that these genes control differences in seasonal regulation mechanisms between species. The results of this study provide new insights into seasonal regulation of transcription in Japanese cedar.

In order to provide basic information on genetic improvement potential in Cryptomeria japonica (sugi), we estimated genetic parameters, direct and indirect genetic gains and optimum selection ages for growth traits based on the data obtained from 429 progeny test sites located throughout Japan. Medians of narrow-sense heritabilites for height and diameter at breast height (DBH) were ranged in 0.289–0.445 and 0.235–0.276, respectively. The heritability of height significantly increased after the age of 15 years. On the other hand, there were no significant differences among ages in the heritability of DBH. Medians of the age-age genetic correlations were similar when the age differences of the pairs were the same, and tended to decrease as the age differences became larger for both height and DBH. The maximum efficiencies for gain per year when the target age is assumed to be 30 years were obtained at an age of 5 years in height and of 10 years in DBH, respectively. As the values at an age of 5 years in height varied greatly depending on test site, there would likely be selection errors. Thus, the early selection at 1/3 the target age is efficient in sugi.

Background and Objectives: To determine whether the progeny of pinewood nematode-resistant Pinus thunbergii Parl. clones selected in the southwestern region of Japan could be successful in reforestation in the northern region, we investigated the magnitude of the genotype&ndash, environment interaction effect on the resistance against Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle in P. thunbergii. Materials and Methods: We inoculated P. thunbergii seedlings of six full-sib families, with various resistance levels, with B. xylophilus in nurseries at three experimental sites in the northern and southern regions of Japan. All parental clones of the tested families originated from southwestern Japan, and selection of parental clones for resistance was performed in the same region. Sound rates after nematode inoculation were calculated, and survival analysis, correlation analysis and variance component analysis were performed. Results and Conclusions: Families with high sound rate in the southern region also showed a high sound rate in the northern region. In almost all cases, Spearman&rsquo, s correlation coefficients for sound rates were more than 0.698 among sites. The variance component of the interaction between site and family was small compared to that of site and family separately. Thus, we conclude that the resistant clones selected in the southern region would retain their genetic resistance in the northern regions.

Pine wilt disease (PWD) caused by the pinewood nematode (PWN) (Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle) is a worldwide issue. Infection is considered to be promoted mainly by the increased air temperature, but it is important to investigate whether the effect of high temperature similarly influences the different ranks of resistant clone. In the present study, we conducted PWN inoculation tests using six common open-pollinated families of resistant Pinus thunbergii Parl. The tests were conducted at nurseries of five test sites across Japanese archipelago between 2015 and 2017. Our analysis focused specifically on temperature. Firstly, we examined the effects of test sites, inoculation year, and their interaction on unaffected seedling rate and found that the unaffected seedling rate of all tested pine families decreased as the cumulative temperature increased. We found that the unaffected seedling rate decreased as the cumulative temperature increased for all tested pine families. In general, higher cumulative temperatures were required for having an effect on the unaffected seedling rates of higher PWN-resistant families. Typically, early cumulative temperatures, i.e., 19 days after inoculation, had the greatest effect on the unaffected seedling rates of PWN-resistant pines. However, the relationship between cumulative temperature and predicted unaffected seedling rate follow similar rate for all families. Thus, the order of resistance level is maintained in terms of the cumulative temperature required for having an effect.

A genome-wide association study (GWAS) was conducted on more than 30,000 single nucleotide polymorphisms (SNPs) in unrelated first-generation plus tree genotypes from three populations of Japanese cedar Cryptomeria japonica D. Don with genomic prediction for traits of growth, wood properties and male fecundity. Among the assessed populations, genetic characteristics including the extent of linkage disequilibrium (LD) and genetic structure differed and these differences are considered to be due to differences in genetic background. Through population-independent GWAS, several significant SNPs found close to the regions associated with each of these traits and shared in common across the populations were identified. The accuracies of genomic predictions were dependent on the traits and populations and reflected the genetic architecture of traits and genetic characteristics. Prediction accuracies using SNPs selected based on GWAS results were similar to those using all SNPs for several combinations of traits and populations. We discussed the application of genome-wide studies for C. japonica improvement.

In order to predict the effects of future atmospheric conditions on forest productivity, it is necessary to clarify the physiological responses of major forest tree species to high concentrations of ozone (O3) and carbon dioxide (CO2). Furthermore, intraspecific variation of these responses should also be examined in order to predict productivity gains through tree improvements in the future. We investigated intraspecific variation in growth and photosynthesis of Cryptomeria japonica D. Don, a major silviculture species in Japan, in response to elevated concentrations of O3 (eO3) and CO2 (eCO2), separately and in combination. Cuttings of C. japonica were grown and exposed to two levels of O3 (ambient and twice-ambient levels) in combination with two levels of CO2 (ambient and 550 µmol mol-1 in the daytime) for two growing seasons in a free-air CO2 enrichment experiment. There was no obvious negative effect of eO3 on growth or photosynthetic traits of the C. japonica clones, but a positive effect was observed for annual height increments in the first growing season. Dry mass production and the photosynthetic rate increased under eCO2 conditions, while the maximum carboxylation rate decreased. Significant interaction effects of eO3 and eCO2 on growth and photosynthetic traits were not observed. Clonal effects on growth and photosynthetic traits were significant, but the interactions between clones and O3 and/or CO2 treatments were not. Spearman's rank correlation coefficients between growth traits under ambient conditions and for each treatment were significantly positive, implying that clonal ranking in growth abilities might not be affected by either eO3 or eCO2. The knowledge obtained from this study will be helpful for species selection in afforestation programs, to continue and to improve current programs involving this species, and to accurately predict the CO2 fixation capacity of Japanese forests.

大久保育種素材保存園に植栽されている14年生のスギ精英樹のつぎ木クローン，745クローン2149個体を対象に胸高直径，応力波伝播速度およびピロディン陥入量を測定した。より正確にこれら形質を評価するため，すべての調査した個体についてジェノタイピングを行った。胸高直径，応力波伝播速度およびピロディン陥入量は，有意なクローン間差が認められた。応力波伝播速度およびピロディン陥入量の平均値や変動係数は，これまで報告されている値と大きな差は認められなかった。胸高直径，応力波伝播速度およびピロディン陥入量の相関関係は，総じて低い値を示し，成長形質と材質形質がともに優れたスギの創出が可能であることが示唆された。大久保育種素材保存園と3つの検定林との間に共通して植栽されているクローンを対象に，相関関係を検討した結果，応力波伝播速度およびピロディン陥入量ともに遺伝子型と環境の交互作用が小さいことが示され，同時に，比較的早期に選抜することが可能であることが示唆された。

北海道に設定されている環境条件の異なる3カ所の採種園に植栽されているトドマツ精英樹クローンを対象に, 応力波伝播速度, ピロディン値を測定した。各採種園における解析結果から, 既報の動的ヤング率や容積密度における解析結果と同様の結果が得られた。応力波伝播速度およびピロディン値を指標として, 環境と遺伝子型の交互作用を検討するため分散分析を行った結果, 応力波伝播速度, ピロディン値ともクローン間および採種園間に有意な差があったが, 環境と遺伝子型の交互作用に有意な差が認められなかった。環境と遺伝子型の交互作用が認められなかったことや各採種園間の共通クローンの積率相関や順位相関の相関係数が比較的高かったことから, 応力波伝播速度とピロディン値は, 採種園間のクローンの順位の変動が小さいと考えられた。

トドマツ精英樹14クローン42個体を用いて，曲げヤング率（MOE），曲げ強さ（MOR）および気乾密度を調査した。それぞれの形質の調査は，樹心部（髄から17年輪まで）と辺縁部（18年輪以降）に分けて行った。また，そのうちの7クローン21個体を用いて，晩材仮道管S2層のミクロフィブリル傾角（MFA）の半径方向の変動を調査した。気乾密度とMOEおよびMORは，それぞれ有意な相関関係を示した。MFAの半径方向の変動パターンは，特に髄周辺の年輪部位においてクローン間で異なっていた。MFA，気乾密度，MOEの関係から，MOEの変動に対するMFAの影響は小さく，気乾密度の影響が大きいと考えられた。気乾密度，MOE，MORの樹心部と辺縁部の間には有意な相関関係にあり，比較的早期にこれらを評価できると考えられた。

スギで開発された簡便かつ非破壊的な心材含水率の推定法である横打撃共振法を，トドマツ精英樹クローンに適用した。立木状態で横打撃共振周波数（f）と直径（d）を測定したところ，dと1/fは高い相関関係にあり，その回帰直線はクローン毎に異なっていた。また，腐朽個体の検出にも応用できる可能性が示唆された。1/dfと実際に伐採して調べた心材含水率との関係を調べたところ，両者の間には，個体値，クローン平均値とも有意な正の相関関係が認められた。相関係数は，クローン平均値の方が個体値に比べ高かった。1/dfと心材含水率の関係には，d，辺材含水率，心材率など複数の形質が影響していると考えられた。1/dfの個体値の順位より，心材含水率の異なる3つのグループ（高い，中間，低い）に分けることが可能であると考えられた。特に，心材含水率の低いグループは，他のグループに比べて高い精度で選抜できると考えられた。これらの結果から，横打撃共振法は，非破壊的に心材含水率の低いグループを選抜することができ，トドマツにおける心材含水率の遺伝的改良に有効な方法であると考えられた。

トドマツ精英樹や育種母材のクローンを用いて，円板全体の容積密度（平均容積密度）の樹高方向の変動を調査した。また，立木状態で測定したピロディンによる打ち込み深さ（ピロディン値）と平均容積密度との関係を調査した。平均容積密度の樹高方向の変動パターンはクローンごとに異なっており，いくつかのタイプに分類できた。平均容積密度の最適な測定部位を検討した結果，地際からの高さ 1～3 m部位において樹幹を代表する値として用いることが可能であり，この地上高部位において遺伝的な違いを比較できると考えられた。立木状態で樹皮の上から測定したピロディン値（樹皮付きピロディン値），樹皮を剥皮したピロディン値（ピロディン値）と平均容積密度の間には，個体値，クローン平均値とも有意な負の相関関係が認められた。測定の簡便さから，樹皮付きピロディン値が有効な指標であると考えられた。以上より，胸高部位でトドマツの立木の樹皮付きピロディン値を測定することで，非破壊的に個体やクローンの平均容積密度を評価する有効な材質指標になることが示唆された。

トドマツ精英樹や育種母材を用いて樹高方向の丸太の動的ヤング率の変動を調べ，樹幹全体の平均値を推定するのに最適な地上高部位を検討した。また，立木の応力波伝播速度と丸太の動的ヤング率の関係を調べ，トドマツにおける応力波伝播速度測定法の有用性を検討した。丸太の動的ヤング率の樹高方向の変動は，各クローンにおける個体間では，ほぼ同様の変動傾向を示した。また地際から地上高 3 mまでの部位において樹幹全体を代表する値として用いることが可能であり，胸高部位を含むこの地上高部位においてクローン間の遺伝的な違いを比較できると考えられた。立木の応力波伝播速度と丸太の動的ヤング率には，個体値，クローン平均値とも有意な正の相関関係が認められた。特にクローンにおいて相関関係が高かった。これより，胸高部位付近でトドマツの立木の応力波伝播速度を測定することにより，非破壊的に動的ヤング率の推定が可能であり，クローン評価に有効な材質指標になることが示唆された。

Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica.

Background Forest trees have ecological and economic importance, and Japanese cedar has highly valued wood attributes. Thus, studies of molecular aspects of wood formation offer practical information that may be used for screening and forward genetics approaches to improving wood quality. Results After identifying expressed sequence tags in Japanese cedar tissue undergoing xylogenesis, we designed a custom cDNA microarray to compare expression of highly regulated genes throughout a growing season. This led to identification of candidate genes involved both in wood formation and later cessation of growth and dormancy. Based on homology to orthologous protein groups, the genes were assigned to functional classes. A high proportion of sequences fell into functional classes related to posttranscriptional modification and signal transduction, while transcription factors and genes involved in the metabolism of sugars, cell-wall synthesis and lignification, and cold hardiness were among other classes of genes identified as having a potential role in xylem formation and seasonal wood formation. Conclusions We obtained 55,051 unique sequences by next-generation sequencing of a cDNA library prepared from cambial meristem and derivative cells. Previous studies on conifers have identified unique sequences expressed in developing xylem, but this is the first comprehensive study utilizing a collection of expressed sequence tags for expression studies related to xylem formation in Japanese cedar, which belongs to a different lineage than the Pinaceae. Our characterization of these sequences should allow comparative studies of genome evolution and functional genetics of wood species.