Cryptomeria japonica
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB10268 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR238372_1.fastq.gz | Fastqsanger.gz | |||
| DRR238372_2.fastq.gz | Fastqsanger.gz | |||
| DRR238373_1.fastq.gz | Fastqsanger.gz | |||
| DRR238373_2.fastq.gz | Fastqsanger.gz | |||
| DRR238374_1.fastq.gz | Fastqsanger.gz |
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Project description:Local adaptation of plant species is a central issue for survival during global climate change, especially for long-lived forest trees, with their lengthy regeneration time and spatially limited gene flow. Identification of loci and/or genomic regions associated with local adaptation is necessary for knowledge of both evolution and molecular breeding for climate change. Cryptomeria japonica is an important species for forestry in Japan; it has a broad natural distribution and can survive in a range of different environments. The genetic structure of 14 natural populations of this species was investigated using 3930 SNP markers. Populations on the Pacific Ocean side of Japan are clearly different from those on the Japan Sea side, as discussed in previous studies. Structure analysis and population network trees show that peripheral populations, including the most northerly and southerly ones, have unique features. We found that the genetic differentiation coefficient is low, FST = 0.05, although it must account for the presence of important genes associated with adaptation to specific environments. In total, 208 outlier loci were detected, of which 43 were associated with environmental variables. Four clumped regions of outlier loci were detected in the genome by linkage analysis. Linkage disequilibrium (LD) was quite high in these clumps of outlier loci, which were found in linkage groups (LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when interchromosomal LD was also detected. The LG7 region is characteristic of the Yakushima population, which is a large, isolated, peripheral population occupying a specific environment resulting from isolation combined with volcanic activity in the region. The detected LD may provide strong evidence for selection between varieties.
| S-EPMC4267934 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-05-07 | GSE95619 | GEO
Project description:We investigated the nucleotide variation of a conifer, Cryptomeria japonica, and the divergence between this species and its closest relative, Taxodium distichum, at seven nuclear loci (Acl5, Chi1, Ferr, GapC, HemA, Lcyb, and Pat). Samples of C. japonica were collected from three areas, Kantou-Toukai, Hokuriku, and Iwate. No apparent geographic differentiation was found among these samples. However, the frequency spectrum of the nucleotide polymorphism revealed excesses of intermediate-frequency variants, which suggests that the population was not panmictic and a constant size in the past. The average nucleotide diversity, pi, for silent sites was 0.00383. However, values of pi for silent sites vary among loci. Comparisons of polymorphism to divergence among loci (the HKA test) showed that the polymorphism at the Acl5 locus was significantly lower. We also observed a nearly significant excess of replacement polymorphisms at the Lcyb locus. These results suggested possibilities of natural selection acting at some of the loci. Intragenic recombination was detected only once at the Chi1 locus and was not detected at the other loci. The low level of population recombination rate, 4Nr, seemed to be due to both low level of recombination, r, and small population size, N.
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Project description:Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.
2018-05-07 | GSE95616 | GEO
Project description:Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.
2018-05-07 | GSE95618 | GEO
Project description:Somatic embryogenesis (SE), which is in vitro regeneration of plant bodies from somatic cells, represents a useful means of clonal propagation and genetic engineering of forest trees. While protocols to obtain calluses and induce regeneration in somatic embryos have been reported for many tree species, the knowledge of molecular mechanisms of SE development is still insufficient to achieve an efficient supply of somatic embryos required for the industrial application. Cryptomeria japonica, a conifer species widely used for plantation forestry in Japan, is one of the tree species waiting for a secure SE protocol; the probability of normal embryo development appears to depend on genotype. To discriminate the embryogenic potential of embryonal masses (EMs) and efficiently obtain normal somatic embryos of C. japonica, we investigated the effects of genotype and transcriptome on the variation in embryogenic potential. Using an induction experiment with 12 EMs each from six genotypes, we showed that embryogenic potential differs between/within genotypes. Comparisons of gene expression profiles among EMs with different embryogenic potentials revealed that 742 differently expressed genes were mainly associated with pattern forming and metabolism. Thus, we suggest that not only genotype but also gene expression profiles can determine success in SE development. Consistent with previous findings for other conifer species, genes encoding leafy cotyledon, wuschel, germin-like proteins, and glutathione-S-transferases are likely to be involved in SE development in C. japonica and indeed highly expressed in EMs with high-embryogenic potential; therefore, these proteins represent candidate markers for distinguishing embryogenic potential.
| S-EPMC7771663 | biostudies-literature
Project description:Three new dimeric abietane-type diterpenoids, abieta-6,8,11,13-tetraen-12-yl 12-hydroxyabieta-8,11,13-trien-7α-yl peroxide (1), abieta-6,8,11,13-tetraen-12-yl 12-hydroxyabieta-8,11,13-trien-7β-yl peroxide (2), and 12-hydroxyabieta-8,11,13-trien-7β-yl 7-oxoabieta-5,8,11,13-tetraen-12-yl peroxide (3), together with four known abietane-type diterpenoids (4-7) were isolated from the methanol extract of the bark of Cryptomeria japonica. Their structures were elucidated on the basis of spectroscopic analysis and comparison of NMR data with those of known analogues. At a concentration of 50 μM, compounds 1, 2, and 3 showed 26.2%, 23.6%, and 35.7% inhibition towards xanthine oxidase enzyme, respectively. In addition, compound 3 also showed 24.9% inhibition toward angiotensin-converting enzyme (ACE).
| S-EPMC6600475 | biostudies-literature
Project description:We measured linkage disequilibrium in mostly noncoding regions of Cryptomeria japonica, a conifer belonging to Cupressaceae. Linkage disequilibrium was extensive and did not decay even at a distance of 100 kb. The average estimate of the population recombination rate per base pair was 1.55 × 10(-5) and was <1/70 of that in the coding regions. We discuss the impact of low recombination rates in a large part of the genome on association studies.
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Project description:Cryptomeria japonica BAC library sequencing
| PRJDB2935 | ENA
Project description:Development of SNP markers closely-linked to MALE STERILITY 1 (MS1) in Cryptomeria japonica
| PRJDB6559 | ENA