Efficient selection of a biallelic and nonchimeric gene-edited tree using Oxford Nanopore Technologies sequencing.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 nuclease system is a versatile and essential biotechnological tool in the life sciences that allows efficient genome editing. When generating gene-edited trees, T0-generation plants are often used for subsequent analysis because of the time that is required to obtain the desired mutants via crossing. However, T0-generation plants exhibit various unexpected mutations, which emphasizes the need to identify mutants with expected mutation patterns. The two critical checkpoints in this process are to confirm the expected mutation patterns in both alleles and to exclude somatic chimeric plants. In this study, we generated gene-edited Cryptomeria japonica plants and established a method to determine chimerism and mutation patterns using fragment analysis and Oxford Nanopore Technologies (ONT)-based amplicon sequencing. In the first screening, fragment analysis, i.e., indel detection via amplicon analysis, was used to predict indel mutation patterns in both alleles and to discriminate somatic chimeric plants in 188 candidate mutants. In the second screening, we precisely determined the mutation patterns and chimerism in the mutants using ONT-based amplicon sequencing, where confirmation of both alleles can be achieved using allele-specific markers flanking the single guide RNA target site. In the present study, a bioinformatic analysis procedure was developed and provided for the rapid and accurate determination of DNA mutation patterns using ONT-based amplicon sequencing. As ONT amplicon sequencing has a low running cost compared with other long-read analysis methods, such as PacBio, it is a powerful tool in plant genetics and biotechnology to select gene-edited plants with expected indel patterns in the T0-generation.

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.

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.

Mesophyll conductance in leaves of Japanese white birch (Betula platyphylla var. japonica) seedlings grown under elevated CO2 concentration and low N availability.

To test the hypothesis that mesophyll conductance (gm ) would be reduced by leaf starch accumulation in plants grown under elevated CO2 concentration [CO2 ], we investigated gm in seedlings of Japanese white birch grown under ambient and elevated [CO2 ] with an adequate and limited nitrogen supply using simultaneous gas exchange and chlorophyll fluorescence measurements. Both elevated [CO2 ] and limited nitrogen supply decreased area-based leaf N accompanied with a decrease in the maximum rate of Rubisco carboxylation (Vc,max ) on a CO2 concentration at chloroplast stroma (Cc ) basis. Conversely, only seedlings grown at elevated [CO2 ] under limited nitrogen supply had significantly higher leaf starch content with significantly lower gm among the treatment combinations. Based on a leaf anatomical analysis using microscopic photographs, however, there were no significant difference in the area of chloroplast surfaces facing intercellular space per unit leaf area among treatment combinations. Thicker cell walls were suggested in plants grown under limited N by increases in leaf mass per area subtracting non-structural carbohydrates. These results suggest that starch accumulation and/or thicker cell walls in the leaves grown at elevated [CO2 ] under limited N supply might hinder CO2 diffusion in chloroplasts and cell walls, which would be an additional cause of photosynthetic downregulation as well as a reduction in Rubisco activity related to the reduced leaf N under elevated [CO2 ].

Seasonal variation of heartwood formation in Larix kaempferi.

Heartwood in tree stems provides natural durability and ornamental values to wood products as well as antimicrobial properties to protect living stems from decay. Control of the amount and quality of heartwood is required because of its importance in wood utilization. Despite the importance, the mechanism of heartwood formation has been poorly understood. To obtain further knowledge for understanding this mechanism, we studied the seasonal variation of various components of heartwood formation in Larix kaempferi (Lamb.) Carrière. Dehydration of tracheids at the boundary between sapwood and intermediate wood occurred continuously during the study period. The death of ray parenchyma cells at intermediate wood occurred from spring to summer. The deposition of heartwood substance took place in autumn to winter. Thus, different components of heartwood formation were active in different seasons. Since heartwood formation is a system consisting of several components within a series of continuing processes, understanding the seasonal change of heartwood formation requires monitoring these components simultaneously.

Characterization of resistance to pine wood nematode infection in Pinus thunbergii using suppression subtractive hybridization.

BACKGROUND: Pine wilt disease is caused by the pine wood nematode, Bursaphelenchus xylophilus, which threatens pine forests and forest ecosystems worldwide and causes serious economic losses. In the 40 years since the pathogen was identified, the physiological changes occurring as the disease progresses have been characterized using anatomical and biochemical methods, and resistant trees have been selected via breeding programs. However, no studies have assessed the molecular genetics, e.g. transcriptional changes, associated with infection-induced physiological changes in resistant or susceptible trees. RESULTS: We constructed seven subtractive suppression hybridization (SSH) cDNA libraries using time-course sampling of trees inoculated with pine wood nematode at 1, 3, or 7 days post-inoculation (dpi) in susceptible trees and at 1, 3, 7, or 14 dpi in resistant trees. A total of 3,299 sequences was obtained from these cDNA libraries, including from 138 to 315 non-redundant sequences in susceptible SSH libraries and from 351 to 435 in resistant SSH libraries. Using Gene Ontology hierarchy, those non-redundant sequences were classified into 15 subcategories of the biological process Gene Ontology category and 17 subcategories of the molecular function category. The transcriptional components revealed by the Gene Ontology classification clearly differed between resistant and susceptible libraries. Some transcripts were discriminative: expression of antimicrobial peptide and putative pathogenesis-related genes (e.g., PR-1b, 2, 3, 4, 5, 6) was much higher in susceptible trees than in resistant trees at every time point, whereas expression of PR-9, PR-10, and cell wall-related genes (e.g., for hydroxyproline-rich glycoprotein precursor and extensin) was higher in resistant trees than in susceptible trees at 7 and 14 dpi. CONCLUSIONS: Following inoculation with pine wood nematode, there were marked differences between resistant and susceptible trees in transcript diversity and the timing and level of transcripts expressed in common; in particular, expression of stress response and defense genes differed. This study provided new insight into the differences in the physiological changes between resistant and susceptible trees that have been observed in anatomical and biochemical studies.

Effects of elevated CO2 concentration on growth, annual ring structure and photosynthesis in Larix kaempferi seedlings.

We evaluated the effects of elevated carbon dioxide concentration ([CO2]) and two nutrient regimes on stem growth rate, annual ring structure and temporal variations in photosynthetic characteristics of seedlings of Japanese larch (Larix kaempferi (Lamb.) Carr.). Seedlings were grown in phytotron chambers in an ambient (360 ppm) or an elevated (720 ppm) [CO2] in two nutrient regimes for one growing season. Elevated [CO2] reduced stem height and increased stem basal diameter compared with ambient [CO2]. The effect of elevated [CO2] on growth tended to be greater at high-nutrient supply than at low-nutrient supply. Elevated [CO2] had no significant effect on ring width or the number of tracheids per radial file. There was no obvious difference in cell wall thickness or the relative area of the cell wall between seedlings grown in ambient or elevated [CO2]. Although growth in elevated [CO2] resulted in a slight increase in cell diameter, the increase had a relatively minor effect on the relative area of the cell wall. Net assimilation rate increased in response to elevated [CO2]; however, the increase in whole-crown photosynthetic rate (Total Agrowth) in seedlings in the elevated [CO2] treatment was minimal because of the smaller specific needle area and acclimation of the photosynthetic characteristics of the needles to the growth [CO2]. In conclusion, we observed no obvious enhancement in the capacity for carbon fixation in Japanese larch seedlings grown in the presence of elevated [CO2] that might be attributable to changes in stem growth. However, elevated [CO2] caused changes in the temporal pattern of stem growth and in some anatomical features of the tracheids.