Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic control of tracheid properties in Norway spruce wood

ABSTRACT: Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

SUBMITTER: Baison J

PROVIDER: S-EPMC7581746 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce.

Project description:Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

| S-EPMC9396349 | biostudies-literature

Functional Relationships of Wood Anatomical Traits in Norway Spruce.

Project description:The quantitative assessment of wood anatomical traits offers important insights into those factors that shape tree growth. While it is known that conduit diameter, cell wall thickness, and wood density vary substantially between and within species, the interconnection between wood anatomical traits, tree-ring width, tree height and age, as well as environment effects on wood anatomy remain unclear. Here, we measure and derived 65 wood anatomical traits in cross-sections of the five outermost tree rings (2008-2012) of 30 Norway spruce [Picea abies (L.) H. Karst.] trees growing along an altitudinal gradient (1,400-1,750 m a.s.l.) in the northern Apennines (Italy). We assess the relationship among each anatomical trait and between anatomical trait groups according to their function for (i) tree-ring growth, (ii) cell growth, (iii) hydraulic traits, and (iv) mechanical traits. The results show that tree height significantly affects wood hydraulic traits, as well as number and tangential diameter of tracheids, and ultimately the total ring width. Moreover, the amount of earlywood and latewood percentage influence wood hydraulic safety and efficiency, as well as mechanical traits. Mechanically relevant wood anatomical traits are mainly influenced by tree age, not necessarily correlated with tree height. An additional level of complexity is also indicated by some anatomical traits, such as latewood lumen diameter and the cell wall reinforcement index, showing large inter-annual variation as a proxy of phenotypic plasticity. This study unravels the complex interconnection of tree-ring tracheid structure and identifies anatomical traits showing a large inter-individual variation and a strong interannual coherency. Knowing and quantifying anatomical variation in cells of plant stem is crucial in ecological and biological studies for an appropriate interpretation of abiotic drivers of wood formation often related to tree height and/or tree age.

| S-EPMC7266088 | biostudies-literature

Norway spruce genetic map

Project description:An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies)

| PRJEB25757 | ENA

Loss of diversity in wood-inhabiting fungal communities affects decomposition activity in Norway spruce wood.

Project description:Hundreds of wood-inhabiting fungal species are now threatened, principally due to a lack of dead wood in intensively managed forests, but the consequences of reduced fungal diversity on ecosystem functioning are not known. Several experiments have shown that primary productivity is negatively affected by a loss of species, but the effects of microbial diversity on decomposition are less studied. We studied the relationship between fungal diversity and the in vitro decomposition rate of slightly, moderately and heavily decayed Picea abies wood with indigenous fungal communities that were diluted to examine the influence of diversity. Respiration rate, wood-degrading hydrolytic enzymes and fungal community structure were assessed during a 16-week incubation. The number of observed OTUs in DGGE was used as a measure of fungal diversity. Respiration rate increased between early- and late-decay stages. Reduced fungal diversity was associated with lower respiration rates during intermediate stages of decay, but no effects were detected at later stages. The activity of hydrolytic enzymes varied among decay stages and fungal dilutions. Our results suggest that functioning of highly diverse communities of the late-decay stage were more resistant to the loss of diversity than less diverse communities of early decomposers. This indicates the accumulation of functional redundancy during the succession of the fungal community in decomposing substrates.

| S-EPMC4032996 | biostudies-literature

X-RAY DENSITOMETRY OF NORWAY SPRUCE SUBFOSSIL WOOD FROM THE AUSTRIAN ALPS.

Project description:The processing of subfossil wood poses some difficulties in densitometric research. Problems arise because of the physio-chemical changes of wood occurring in the sedimentation environment. Subfossil wood modification can result from the uptake of mineral and organic substances into the wood tissue. It can also occur as the effect of microbiological degradation of wood. The goal of this study was to identify the appropriate method of subfossil wood preparation for the densitometric research. For this purpose the wood of Norway spruce from Lake Schwarzensee was subjected to extraction in deionized water, acetone and diluted acetic acid. The application of acetic acid did not significantly influence the density of the wood and acetone seemed to be too aggressive. The best result was obtained by rinsing the samples in cold de-ionized water. This extraction procedure allowed removal of unwanted water-soluble, organic and inorganic compounds from wood and simultaneously did not lead to the degradation of subfossil samples.

| S-EPMC4854978 | biostudies-literature

Norway spruce

Project description:Norway spruce bacteria Raw sequence reads

| PRJNA430787 | ENA

Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce.

Project description:Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.

| S-EPMC6852177 | biostudies-literature

Multi-trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce.

Project description:Plantation-grown trees have to cope with an increasing pressure of pest and disease in the context of climate change, and breeding approaches using genomics may offer efficient and flexible tools to face this pressure. In the present study, we targeted genetic improvement of resistance of an introduced conifer species in Canada, Norway spruce (Picea abies (L.) Karst.), to the native white pine weevil (Pissodes strobi Peck). We developed single- and multi-trait genomic selection (GS) models and selection indices considering the relationships between weevil resistance, intrinsic wood quality, and growth traits. Weevil resistance, acoustic velocity as a proxy for mechanical wood stiffness, and average wood density showed moderate-to-high heritability and low genotype-by-environment interactions. Weevil resistance was genetically positively correlated with tree height, height-to-diameter at breast height (DBH) ratio, and acoustic velocity. The accuracy of the different GS models tested (GBLUP, threshold GBLUP, Bayesian ridge regression, BayesCπ) was high and did not differ among each other. Multi-trait models performed similarly as single-trait models when all trees were phenotyped. However, when weevil attack data were not available for all trees, weevil resistance was more accurately predicted by integrating genetically correlated growth traits into multi-trait GS models. A GS index that corresponded to the breeders' priorities achieved near maximum gains for weevil resistance, acoustic velocity, and height growth, but a small decrease for DBH. The results of this study indicate that it is possible to breed for high-quality, weevil-resistant Norway spruce reforestation stock with high accuracy achieved from single-trait or multi-trait GS.

| S-EPMC6935592 | biostudies-literature

Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce.

Project description:Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within-season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects. Our findings indicate that integration of association mapping and co-expression networks enhances our understanding of complex wood traits.

| S-EPMC5063130 | biostudies-literature

Short-term impacts of energy wood harvesting on ectomycorrhizal fungal communities of Norway spruce saplings.

Project description:The increased demand for harvesting energy wood raises questions about its effects on the functioning of the forest ecosystems, soil processes and biodiversity. Impacts of tree stump removal on ectomycorrhizal fungal (EMF) communities of Norway spruce saplings were studied with 454-pyrosequencing in a 3-year field experiment replicated in 3 geographical areas. This is possibly the most thorough investigation of EMF communities associated with saplings grown on sites subjected to energy wood harvesting. To separate impacts of tree stump and logging residue removal on EMF and plant variables, we used three harvesting treatments with increasing complexity from patch mounding alone (P) to patch mounding combined with logging residue removal (RP), and patch mounding combined with both logging residue and stump removal (SRP). Saplings grown in uncut forests (F) served as references for harvesting treatments. A majority of sequences (>92%) and operational taxonomic units (OTUs, 55%) were assigned as EMF. EMF OTU richness, fungal community composition or sapling growth did not differ between harvesting treatments (P, RP and SRP), while EMF OTU richness, diversity and evenness were highest and sapling growth lowest in the undisturbed reference forests (F). The short study period may partially explain the similarities in fungal and sapling variables in different harvesting treatments. In conclusion, our results indicate that neither stump removal nor logging residue removal have significant additional negative impacts on EMF communities or growth of Norway spruce saplings in the short-term compared with the impacts of more conventional harvesting methods, including clear cutting and patch mounding.

| S-EPMC4331576 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data