Climate sensitivity of Cryptomeria japonica in two contrasting environments: Perspectives from QTL mapping

Climate-Associated Genetic Variation and Projected Genetic Offsets for Cryptomeria japonica D. Don Under Future Climate Scenarios

Revealing the spatial distribution of adaptive genetic variation is both a challenging and crucial task in evolutionary ecology, essential for understanding local adaptation within species, and in management, for predicting species responses to future climate change. This understanding is particularly important for long-lived tree species, which may not be able to migrate quickly enough to adapt to rapid climate changes and may need to rely on their standing genetic variation. In this study, we focused on Cryptomeria japonica, a major component of Japan's temperate forests and an important forestry species adapted to the humid environment of monsoon Asia. We extracted climate-associated genetic variation from the entire genome and evaluated its distribution and vulnerability under future climate scenarios using spatial modeling techniques. We analyzed 31,676 high-quality SNPs from 249 individuals across 22 natural populations of C. japonica, covering its entire distribution range. We identified 239 candidate climate-associated SNPs and found winter temperature, summer precipitation, and winter precipitation as the most significant factors explaining the genetic variation in these SNPs. The climate-associated genetic variation deviated from non-associated (neutral) genetic variation in the opposite (the Sea of Japan and Pacific Ocean) sides of Japanese archipelago, suggesting natural selection of different climate conditions in these regions. Difference in estimated allele frequency at the climate-associated loci (genetic offset) between the present and future (2090 in the SSP5-8.5 scenario) climate conditions was predicted to be larger in three areas (not only southwestern Japan but also coastal area on the Sea of Japan side and inland area on the Pacific Ocean side in northeastern Japan). This prediction implies the discrepancy between standing genetic variation at the present and that adaptive to the future climate in these areas, which underscores the necessity for proactive management to adjust the adaptive genetic variation.

Drought-responsive transcriptional regulations and expressional marker genes of Japanese cedar, Cryptomeria japonica (L.f.) D. Don

The selection of plant genotypes characterized by wellness and stable growth under drought-stress conditions amid ongoing climate change is an important challenge in forest tree breeding. The introduction of molecular markers will enable efficient selection of breeding materials that are resistant to drought stress in forest trees as well as in crop species. Japanese cedar, Cryptomeria japonica (Thunb. ex L.f.) D. Don, the most dominant forest species in Japan, grows well on mesic sites and is characterized by intraspecific variation in its drought-stress response. Here, we analyzed the physiological characteristics and gene expression profiles of multiple C. japonica genotypes under both control and drought-stress conditions to identify drought-responsive genes and develop gene expression markers that could assess the physiological status of cuttings based on their gene expression responses to dehydration. The two representative genes that showed a large expressional change in the later period after water withholding were both homologs of COR47, a gene in the dehydrin protein family, and of ERF016, a member of the dehydration-responsive element-binding transcription factor family in Arabidopsis. We developed both intermediate- and small-scale sets of gene-expression analysis platforms that allowed us to correlate gene expression with the physiological responses of cuttings to drought. The results highlight the potential to assess the environmental adaptability with gene expression analysis in C. japonica.

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.

Genotype-by-environment interaction and genetic dissection of heartwood color in Cryptomeria japonica based on multiple common gardens and quantitative trait loci mapping

The heartwood color of a major plantation tree Cryptomeria japonica shows high variability among clones and cultivars, and brighter heartwood has higher value in the usage of non-laminated wood such as in traditional construction, which makes heartwood color an important trait in breeding of this species. However, the genetic basis of the interactions between genetics and the environment on heartwood color has been understudied while these are necessary for effective breeding programs in multiple environmental condition. The objectives of the present study were to evaluate the effects of genetics and environments on heartwood color and how they interact in contrasting environments, and to identify genomic regions controlling heartwood color in C. japonica across multiple environments. Heartwood color in terms of L*a*b* color space and spectral reflectance was measured in common gardens established in three contrasting sites. Quantitative trait loci (QTL) that affect heartwood color were identified using previously constructed highly saturated linkage maps. Results found that heartwood color was largely genetically controlled, and genotype-by-environment interaction explained one-third of the total genetic variance of heartwood color. The effect of the environment was small compared to the effect of genetics, whereas environmental effects largely varied among heartwood color traits. QTL analysis identified a large number of QTLs with small to moderate effects (phenotypic variation explained of 6.6% on average). Some of these QTLs were stably expressed in multiple environments or had pleiotropic effects on heartwood color and moisture content. These results indicated that genetic variation in phenotypic plasticity plays an important role in regulating heartwood color and that the identified QTLs would maximize the breeding efficiency of heartwood color in C. japonica in heterogeneous environments.

High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus

Introduction

Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms.

Method

A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis.

Results

Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation.

Discussion

While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.

Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data

Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, FST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, FST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.