Effectiveness of spatial analysis in Cryptomeria japonica D. Don (sugi) forward selection revealed by validation using progeny and clonal tests

International audienceAbstractKey messageAccurate evaluation of genetic performances of trees is crucial in order to improve the efficiency of forest tree breeding. We revealed that spatial analysis is effective for predicting individual tree breeding values at the forward selection stage ofCryptomeria japonicaD. Don (sugi) breeding program by using a novel validation approach.ContextIn the process of selecting genetically superior trees for breeding, appropriate handling of environmental effects is important in order to precisely evaluate candidate trees. Spatial analysis has been an effective statistical approach for genetic evaluation at sites with heterogeneous microenvironments. However, the efficiency of spatial analysis on forward selection has not been validated on a practical scale to date.AimsThis study aimed to reveal the effectiveness of spatial analysis, which incorporates spatially autocorrelated residuals into mixed models, for the prediction of breeding values at the forward selection stage by validation using progeny or clonal tests of forward-selected individuals.MethodsTree height was analyzed by ordinary randomized complete block design models and spatial models incorporating spatially autocorrelated residuals in a linear mixed model framework, and model selection was conducted at thirty Cryptomeria japonica D. Don breeding population sites having various topographical ruggedness. For validation, three clonal tests and one progeny test of individuals selected from three and four breeding populations, respectively, were used. The effectiveness of forward selection using the two models was evaluated based on the correlation between individual breeding values at the stage of forward selection and genotypic and breeding values that were estimated by clonal and progeny tests.ResultsSpatial models were more predictive than ordinary models in all cases. Spatial correlation parameters tend to increase with the topographical ruggedness index of each site. The correlation coefficients between breeding values at the time of forward selection and genotypic or breeding values evaluated in succeeding clonal and progeny tests were significantly higher in spatial models than in ordinary models in six out of nine cases.ConclusionValidation using progeny and clonal tests of forward-selected individual trees revealed that spatial analysis is more effective for the evaluation of genetic performance of individuals at the stage of forward selection in Cryptomeria japonica

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 (g(m)) would be reduced by leaf starch accumulation in plants grown under elevated CO2 concentration [CO2], we investigated g(m) 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 (V-c,(max)) on a CO2 concentration at chloroplast stroma (C-c) 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]

Effect of the western conifer seed bug <i>Leptoglossus occidentalis</i>, an invasive alien insect, on seed production reduction in Japanese black pine <i>Pinus thunbergii</i>

To determine the potential reduction of the seed productivity of Japanese black pine (Pinus thunbergii) by the western conifer seed bug (Leptoglossus occidentalis), two feeding experiments were conducted in the center of Kyushu Island, southwestern Japan, in fall of 2020. First, L. occidentalis individuals and a preharvested P. thunbergii cone were enclosed in a nonwoven fabric bag for 2 weeks, which yielded a mean filled seed rate of 18.8% compared with that of 35.6% in the control. Second, L. occidentalis individuals and harvested cones were enclosed in a plastic case for 1 week, affording a mean filled seed rate of 25.7% compared with that of 36.4% in the control. These results suggest that L. occidentalis feeding reduces the filled seed rate of P. thunbergii and damages the seed orchards of this species. Additionally, P. thunbergii seeds from cones damaged by L. occidentalis could be distinguished by their germination ability when sorted using an ethanol floatation technique. Overall, these findings suggest the importance of carefully monitoring L. occidentalis infestation in P. thunbergii seed orchards.</p

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