Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar)

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

Pine wood nematode resistance in Finnish plus-tree progenies of Scots pine

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Inheritance of growth ring components and the possibility of early selection for higher wood density in Japanese cedar (Cryptomeria japonica D. Don)

Abstract Key message We elucidated the age trends of narrow-sense heritability and phenotypic/genetic correlations and the age–age genetic correlation of growth ring components of Cryptomeria japonica D. Don by investigating progenies of controlled crossings by soft X-ray densitometry analysis. Wood density in the C. japonica breeding program can be efficiently improved by selecting trees with a higher earlywood density and latewood percentage as early as forest stand ages of 5–9 years. Context Wood density within the trunk is affected by the intra-ring wood density profile and its age trend from pith to bark. Wood density can be efficiently improved by clarifying whether wood density and highly correlated intra-ring components are under additive genetic control. Aims The aim of this study was to elucidate the age trends of narrow-sense heritability and phenotypic/genetic correlations of growth ring components and investigate the possibility of early selection for improving wood density in Cryptomeria japonica. Methods We quantified seven growth ring components (width, density, earlywood/latewood width, average earlywood/latewood density, and latewood percentage) for 5112 annual rings of 342 18-year-old trees derived from 24 controlled pollinated full-sib families of C. japonica plus tree clones by soft X-ray densitometry analysis. Genetic parameters and correlations among the seven growth ring components were analyzed using a linear mixed model and the breedR package. Results Earlywood density and latewood percentage exhibited a higher phenotypic and genetic correlation with ring density than the other ring components at almost all ages. Earlywood density and latewood percentage exhibited a lower correlation with ring width than the other ring components after a stand age of 5 years. The age–age genetic correlation of earlywood density and latewood percentage was 0.70 for a stand age of 17 years and was strong at stand ages of 5 and 9 years. Conclusion Efforts focusing on improving earlywood density and latewood percentage may contribute to improving wood density efficiently in tree breeding programs for C. japonica. Traits related to the ring density of C. japonica trees can possibly be selected as early as stand ages of 5–9 years, and the required period for progeny selection may be substantially shortened when selecting trees with high wood density

Reforestation or Genetic Disturbance: A Case Study of Pinus thunbergii in the Iki-no-Matsubara Coastal Forest (Japan)

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

Reforestation or Genetic Disturbance: A Case Study of <i>Pinus thunbergii</i> in the Iki-no-Matsubara Coastal Forest (Japan)

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

Additional file 1 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Additional file 1. Stacked percent of the ORFs with top hits against NCBI nr database in each region on the Venn diagram. Blue shows the plant and fungal species (gbpln) in the GenBank nucleotide divisions. Orange shows ratio of “no hit”. Gray showed ratio of other divisions. LK and LG shows Japanese and Kuril larch, respectively

Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions.

Environmental responses are critical for plant growth and survival under different climate conditions. To elucidate the underlying biological mechanisms of environmental responses in Japanese cedar (Cryptomeria japonica D. Don), the annual transcriptome dynamics of common clonal trees (Godai1) planted at three different climate sites (Yamagata, Ibaraki, and Kumamoto Prefectures) were analyzed using microarrays. Both principal component analysis (PCA) and hierarchical clustering of the microarray data indicated the transition to dormant transcriptome status occurred earlier and the transition to active growth status later in the colder region. Interestingly, PCA also indicated that the transcriptomes of trees grown under three different conditions were similar during the growth period (June to September), whereas the transcriptomes differed between sites during the dormant period (January to March). In between-site comparisons, analyses of the annual expression profiles of genes for sites 'Yamagata vs. Kumamoto', 'Yamagata vs. Ibaraki', and 'Ibaraki vs. Kumamoto' identified 1,473, 1,137, and 925 targets exhibiting significantly different expression patterns, respectively. The total of 2,505 targets that exhibited significantly different expression patterns in all three comparisons may play important roles in enabling cuttings to adapt to local environmental conditions. Partial least-squares regression analysis and Pearson correlation coefficient analysis revealed that air temperature and day length were the dominant factors controlling the expression levels of these targets. GO and Pfam enrichment analyses indicated that these targets include genes that may contribute to environmental adaptation, such as genes related to stress and abiotic stimulus responses. This study provided fundamental information regarding transcripts that may play an important role in adaptation to environmental conditions at different planting sites