Mapping quantitative trait loci for growth and wood property traits in Cryptomeria japonica across multiple environments

Mori, Hideki; Ueno, S.; Ujino‐Ihara, Tokuko; Fujiwara, Takeshi; Yamashita, Kana; Kanetani, Seiichi; Endo, Rika; Matsumoto, Asako; Uchiyama, Kentaro; Matsui, Yukari; Yoshida, Takahiro; Sakai, Yoshimi; Moriguchi, Yoshinari; Kusano, Ryouichi; Tsumura, Yoshihiko

doi:10.1007/s11295-019-1346-5

Cited by 15 publications

(30 citation statements)

References 51 publications

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“…As mentioned earlier, the tree populations in this study were derived from a local variety from the Kyushu region, where the Kumamoto site is located. Indeed, decreased tree growth at the Chiba site compared with that at the Kumamoto site was also previously reported [32]; the study found that the mean stem diameter of trees at the Kumamoto site was larger than at the Chiba site https://doi.org/10.1371/journal.pone.0228278.g004 despite the Kumamoto trees being 1 year younger. This indicates that Kumamoto is more suitable for tree growth and is probably more robust to drought conditions than the Chiba site, which may explain the contrasting growth patterns observed in our study.…”

Section: Climate Change Sensitivitysupporting

confidence: 80%

“…The plant material, common garden experiment, and linkage map previously described by [32] were used in this study. The C. japonica population used in this study comprised 139 genotypes, which were obtained from crossing between two F 1 progenies: YI96 (female parent) and YI38 (male parent).…”

Section: Plant Material Common Garden Experiment Linkage Mapmentioning

confidence: 99%

“…Both sites are characterized by contrasting climatic conditions in the growing season, particularly precipitation patterns. For instance, Kumamoto receives on average 2.5-fold more rainfall than Chiba during the growing season (May to August; [32]). We examined the effect of continuous dry (non-raining) days (hereafter, dry period) obtained from the precipitation data for each month (S2 Fig).…”

Section: Climate Datamentioning

confidence: 99%

“…Several studies have evaluated genomic regions that affect the growth and wood properties of C. japonica [30][31][32]. Long-term growth patterns of C. japonica have been evaluated using tree rings [33,34] and other methods (e.g., dendrometer; [35,36]).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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Long-lived forest tree species experience a wide range of environmental conditions throughout their lifespan. Evaluation of the underlying growth and development mechanisms of these species is essential to predict tree growth under climate change. This study investigated climate sensitivity to temperature, precipitation, dry periods, and the associated genomic regions in Cryptomeria japonica, Japan's most commercially important tree. We used tree rings and common garden experiments with three clonal replicates planted in two contrasting environments in Kyushu (Kumamoto site) and Honshu (Chiba site), Japan. Tree growth showed a significant negative correlation with the dry period (>4 days) in March of the year of tree-ring formation at the Chiba site. In contrast, temperature and precipitation had little influence on tree growth. Quantitative trait locus (QTL) analysis was performed to investigate climate sensitivity to dry periods at the Chiba site, revealing 13 significant QTLs. One QTL showed a substantially large contribution to the overall climate sensitivity, accounting for 12.4% of the total phenotypic variation. The phenotypic variance explained (PVE) by other QTLs ranged from 0.9% to 2.9%, and the total PVE by all QTLs was 35.6%. These findings indicate that the tree population at the Chiba site could be vulnerable to drought in early spring and that the QTL showing the greatest impact on climate sensitivity may be closely related to genes associated with tolerance or adaptation to drought stress. The QTLs identified in this study could be useful for molecular breeding, forest management, and predicting the growth of C. japonica under a changing climate.

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Section: Climate Change Sensitivitysupporting

confidence: 80%

Section: Plant Material Common Garden Experiment Linkage Mapmentioning

confidence: 99%

Section: Climate Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…Therefore, spatial analysis was necessary before GWAS and GS to account for these effects. For this, a spatial autocorrelation structure (AR1 × AR1) model, implemented in breedR packages of R [50,51], was applied.…”

Section: Spatial Analysis and Genotype Imputationmentioning

confidence: 99%

Potential of Genome-Wide Association Studies and Genomic Selection to Improve Productivity and Quality of Commercial Timber Species in Tropical Rainforest, a Case Study of Shorea platyclados

Sawitri

Tani

Na’iem

et al. 2020

Forests

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Shorea platyclados (Dark Red Meranti) is a commercially important timber tree species in Southeast Asia. However, its stocks have dramatically declined due, inter alia, to excessive logging, insufficient natural regeneration and a slow recovery rate. Thus, there is a need to promote enrichment planting and develop effective technique to support its rehabilitation and improve timber production through implementation of Genome-Wide Association Studies (GWAS) and Genomic Selection (GS). To assist such efforts, plant materials were collected from a half-sib progeny population in Sari Bumi Kusuma forest concession, Kalimantan, Indonesia. Using 5900 markers in sequences obtained from 356 individuals, we detected high linkage disequilibrium (LD) extending up to >145 kb, suggesting that associations between phenotypic traits and markers in LD can be more easily and feasibly detected with GWAS than with analysis of quantitative trait loci (QTLs). However, the detection power of GWAS seems low, since few single nucleotide polymorphisms linked to any focal traits were detected with a stringent false discovery rate, indicating that the species’ phenotypic traits are mostly under polygenic quantitative control. Furthermore, Machine Learning provided higher prediction accuracies than Bayesian methods. We also found that stem diameter, branch diameter ratio and wood density were more predictable than height, clear bole, branch angle and wood stiffness traits. Our study suggests that GS has potential for improving the productivity and quality of S. platyclados, and our genomic heritability estimates may improve the selection of traits to target in future breeding of this species.

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Molecular Basis of Forest Genetic Resource Improvement: Progress and Prospects

Gautam,

Thakur,

Kumar

2024

Biotechnological Approaches for Sustaining Forest Trees and Their Products

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Mapping quantitative trait loci for growth and wood property traits in Cryptomeria japonica across multiple environments

Cited by 15 publications

References 51 publications

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

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

Potential of Genome-Wide Association Studies and Genomic Selection to Improve Productivity and Quality of Commercial Timber Species in Tropical Rainforest, a Case Study of Shorea platyclados

Molecular Basis of Forest Genetic Resource Improvement: Progress and Prospects

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