scholarly journals Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity

2020 ◽  
Author(s):  
Sonali Sachin Ranade ◽  
María Rosario García-Gil
Keyword(s):  
Cell Wall ◽  
Local Adaptation ◽  
Norway Spruce ◽  
Climatic Conditions ◽  
Exome Capture ◽  
Wall Thickening ◽  
Latitudinal Cline ◽  
Hypocotyl Length ◽  
Data Set ◽  
Genotype Frequencies

AbstractStudy of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. However, it is challenging to determine the genetic basis of adaptive variation especially in forest trees which have large and complex genomes. Norway spruce is a shade tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. In the current work, hypocotyl-length followed a latitudinal cline in response to SHADE (low red:far-red ratio). RNA-sequencing revealed differential gene expression in response to SHADE, between a southern and a northern natural population in Sweden. Exome capture included analysis of uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway and cold acclimation, and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation and immunity. Findings from this work primarily suggests that the northern populations of Norway spruce are better adapted towards disease resistance under shade by up-regulation of lignin pathway that is linked to immunity and it forms concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

scholarly journals Molecular signatures of local adaptation to light in Norway spruce

Planta ◽  
2021 ◽  
Vol 253 (2) ◽  
Author(s):  
Sonali Sachin Ranade ◽  
María Rosario García-Gil
Keyword(s):  
Cell Wall ◽  
Rna Sequencing ◽  
Local Adaptation ◽  
Norway Spruce ◽  
Climatic Conditions ◽  
Differentially Expressed ◽  
Exome Capture ◽  
Wall Thickening ◽  
Data Set ◽  
Genotype Frequencies

Abstract Main conclusion Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. Abstract The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

Seasonally varying relationship between stem respiration, increment and carbon allocation of Norway spruce trees

2020 ◽  
Vol 40 (7) ◽  
pp. 943-955
Author(s):  
Eva Darenova ◽  
Petr Horáček ◽  
Jan Krejza ◽  
Radek Pokorný ◽  
Marian Pavelka
Keyword(s):  
Cell Wall ◽  
Norway Spruce ◽  
Carbon Allocation ◽  
Stem Growth ◽  
Wall Thickening ◽  
Radial Increment ◽  
Stem Respiration ◽  
Energy Demands ◽  
The Relationship ◽  
Stem Radial Increment

Abstract Stem respiration is an important component of an ecosystem’s carbon budget. Beside environmental factors, it depends highly on tree energy demands for stem growth. Determination of the relationship between stem growth and stem respiration would help to reveal the response of stem respiration to changing climate, which is expected to substantially affect tree growth. Common measurement of stem radial increment does not record all aspects of stem growth processes, especially those connected with cell wall thickening; therefore, the relationship between stem respiration and stem radial increment may vary depending on the wood cell growth differentiation phase. This study presents results from measurements of stem respiration and increment carried out for seven growing seasons in a young Norway spruce forest. Moreover, rates of carbon allocation to stems were modeled for these years. Stem respiration was divided into maintenance (Rm) and growth respiration (Rg) based upon the mature tissue method. There was a close relationship between Rg and daily stem radial increment (dSRI), and this relationship differed before and after dSRI seasonal maximum, which was around 19 June. Before this date, Rg increased exponentially with dSRI, while after this date logarithmically. This is a result of later maxima of Rg and its slower decrease when compared with dSRI, which is connected with energy demands for cell wall thickening. Rg reached a maxima at the end of June or in July. The maximum of carbon allocation to stem peaked in late summer, when Rg mostly tended to decrease. The overall contribution of Rg to stem CO2 efflux amounted to 46.9% for the growing period from May to September and 38.2% for the year as a whole. This study shows that further deeper analysis of in situ stem growth and stem respiration dynamics is greatly needed, especially with a focus on wood formation on a cell level.

STRUCTURAL CHANGES IN PRIMARY LENTICELS OF NORWAY SPRUCE OVER THE SEASONS

IAWA Journal ◽  
2003 ◽  
Vol 24 (2) ◽  
pp. 105-116 ◽  
Author(s):  
Sabine Rosner ◽  
Birgit Kartusch
Keyword(s):  
Norway Spruce ◽  
Structural Changes ◽  
Phase 1 ◽  
Late Summer ◽  
Early Summer ◽  
Climatic Conditions ◽  
Wall Thickening ◽  
Intercellular Spaces ◽  
Phase 3

Seasonal production of lenticel tissues was compared between Norway spruce trees (Picea abies (L.) Karst.) from a mountain site (1200 m), where they are autochthonous, and seven allochthonous lowland sites (250–600 m).The periodic changes of lenticel structure were grouped into four stages, based on the degree of their opening: phase 1 - winter dormancy; phase 2 - beginning of meristem activity in spring; phase 3 - production of non-suberised filling tissue in early summer, which causes the disruption of the closing layer formed in the previous growing season; and phase 4 - differentiation of a new closing layer in late summer. Structural changes in lenticels of P. abies may be interpreted as a long-term reaction to climatic conditions, balancing transpiration and respiration. During the most active period of wood production, lenticels were found in their most permeable phase, phase 3. The production of a new closing layer takes place when summer temperatures reach maximum values, and when demand for effective regulation of transpiration is high. During phase 4 transpiration is successfully controlled because differentiating cells of the new closing layer are already suberised, although not in their final rounded shape, and therefore have small intercellular spaces. High annual variability in stratification of lenticel tissues, such as the proportion between closing layer and filling tissue, wall thickening and size of intercellular spaces, also indicates possible long-term regulation mechanisms for transpiration.

scholarly journals Genetic control of tracheid properties in Norway spruce wood

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
J. Baison ◽  
Linghua Zhou ◽  
Nils Forsberg ◽  
Tommy Mörling ◽  
Thomas Grahn ◽  
...  
Keyword(s):  
Cell Wall ◽  
Picea Abies ◽  
Norway Spruce ◽  
Wall Thickness ◽  
Association Studies ◽  
Cell Wall Thickness ◽  
Exome Capture ◽  
Probability Method ◽  
Genome Wide Association Studies ◽  
Selection Probability

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.

scholarly journals Genetic control of tracheid properties in Norway spruce wood

2019 ◽  
Author(s):  
J Baison ◽  
Linghua Zhou ◽  
Nils Forsberg ◽  
Tommy Mörling ◽  
Thomas Grahn ◽  
...  
Keyword(s):  
Cell Wall ◽  
Picea Abies ◽  
Candidate Genes ◽  
Norway Spruce ◽  
Wall Thickness ◽  
Cell Wall Thickness ◽  
Exome Capture ◽  
List Type ◽  
Selection Probability ◽  
Significant Qtls

Abstract➢ Through the use of genome-wide association (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such an 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 high quality Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a LASSO based association mapping method using a functional multi-locus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). Expression of the identified candidate genes was examined using publicly available spruce databases.➢ The analysis have provided 31 loci and 26 mostly novel candidate genes, majority of which showing specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among most promising candidates, the analysis identified Picea abies BIG GRAIN 2 (PabBG2) with predicted function in auxin transport and sensitivity, and MA_373300g0010 - similar to wall-associated receptor kinases (WAKs), both associated to cell wall thickness.➢ The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce. The presence of many traits with several significant QTLs supports the notion that the majority of these traits are polygenic in nature.

A Computational Method for the Identification of Endolysins and Autolysins

2020 ◽  
Vol 27 (4) ◽  
pp. 329-336 ◽  
Author(s):  
Lei Xu ◽  
Guangmin Liang ◽  
Baowen Chen ◽  
Xu Tan ◽  
Huaikun Xiang ◽  
...  
Keyword(s):  
Support Vector Machine ◽  
Cell Wall ◽  
Experimental Results ◽  
Computational Method ◽  
Lytic Enzyme ◽  
Support Vector ◽  
Lytic Enzymes ◽  
Data Set ◽  
Optimal Feature ◽  
Better Than

Background: Cell lytic enzyme is a kind of highly evolved protein, which can destroy the cell structure and kill the bacteria. Compared with antibiotics, cell lytic enzyme will not cause serious problem of drug resistance of pathogenic bacteria. Thus, the study of cell wall lytic enzymes aims at finding an efficient way for curing bacteria infectious. Compared with using antibiotics, the problem of drug resistance becomes more serious. Therefore, it is a good choice for curing bacterial infections by using cell lytic enzymes. Cell lytic enzyme includes endolysin and autolysin and the difference between them is the purpose of the break of cell wall. The identification of the type of cell lytic enzymes is meaningful for the study of cell wall enzymes. Objective: In this article, our motivation is to predict the type of cell lytic enzyme. Cell lytic enzyme is helpful for killing bacteria, so it is meaningful for study the type of cell lytic enzyme. However, it is time consuming to detect the type of cell lytic enzyme by experimental methods. Thus, an efficient computational method for the type of cell lytic enzyme prediction is proposed in our work. Method: We propose a computational method for the prediction of endolysin and autolysin. First, a data set containing 27 endolysins and 41 autolysins is built. Then the protein is represented by tripeptides composition. The features are selected with larger confidence degree. At last, the classifier is trained by the labeled vectors based on support vector machine. The learned classifier is used to predict the type of cell lytic enzyme. Results: Following the proposed method, the experimental results show that the overall accuracy can attain 97.06%, when 44 features are selected. Compared with Ding's method, our method improves the overall accuracy by nearly 4.5% ((97.06-92.9)/92.9%). The performance of our proposed method is stable, when the selected feature number is from 40 to 70. The overall accuracy of tripeptides optimal feature set is 94.12%, and the overall accuracy of Chou's amphiphilic PseAAC method is 76.2%. The experimental results also demonstrate that the overall accuracy is improved by nearly 18% when using the tripeptides optimal feature set. Conclusion: The paper proposed an efficient method for identifying endolysin and autolysin. In this paper, support vector machine is used to predict the type of cell lytic enzyme. The experimental results show that the overall accuracy of the proposed method is 94.12%, which is better than some existing methods. In conclusion, the selected 44 features can improve the overall accuracy for identification of the type of cell lytic enzyme. Support vector machine performs better than other classifiers when using the selected feature set on the benchmark data set.

scholarly journals A Data-Driven Surrogate Approach for the Temporal Stability Forecasting of Vegetation Covered Dikes

Water ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 107
Author(s):  
Elahe Jamalinia ◽  
Faraz S. Tehrani ◽  
Susan C. Steele-Dunne ◽  
Philip J. Vardon
Keyword(s):  
Numerical Simulation ◽  
Water Flux ◽  
Temporal Stability ◽  
Synthetic Data ◽  
Climatic Conditions ◽  
Training Data ◽  
Data Driven ◽  
Data Set ◽  
Surface Cracking ◽  
Real Time Analysis

Climatic conditions and vegetation cover influence water flux in a dike, and potentially the dike stability. A comprehensive numerical simulation is computationally too expensive to be used for the near real-time analysis of a dike network. Therefore, this study investigates a random forest (RF) regressor to build a data-driven surrogate for a numerical model to forecast the temporal macro-stability of dikes. To that end, daily inputs and outputs of a ten-year coupled numerical simulation of an idealised dike (2009–2019) are used to create a synthetic data set, comprising features that can be observed from a dike surface, with the calculated factor of safety (FoS) as the target variable. The data set before 2018 is split into training and testing sets to build and train the RF. The predicted FoS is strongly correlated with the numerical FoS for data that belong to the test set (before 2018). However, the trained model shows lower performance for data in the evaluation set (after 2018) if further surface cracking occurs. This proof-of-concept shows that a data-driven surrogate can be used to determine dike stability for conditions similar to the training data, which could be used to identify vulnerable locations in a dike network for further examination.

Field performance and early test results of offspring from two Norway spruce seed orchards containing clones transferred to warmer climates

2007 ◽  
Vol 37 (3) ◽  
pp. 515-522 ◽  
Author(s):  
Tore Skrøppa ◽  
Ketil Kohmann ◽  
Øystein Johnsen ◽  
Arne Steffenrem ◽  
Øyvind M. Edvardsen
Keyword(s):  
Norway Spruce ◽  
Field Performance ◽  
Seed Orchard ◽  
Field Trials ◽  
Climatic Conditions ◽  
Test Results ◽  
Seed Orchards ◽  
Low Altitude ◽  
Natural Stands ◽  
Seed Crops

We present results from early tests and field trials of offspring from two Norway spruce ( Picea abies (L.) Karst.) seed orchards containing clones that have been transferred from high altitudes to sea level and from northern to southern latitudes. Seedlings from seeds produced in the low-altitude seed orchard developed frost hardiness later at the end of the growth season, flushed later in field trials, and grew taller than seedlings from seeds produced in natural stands. They had the lowest mortality rate and the lowest frequency of injuries in the field trials. Similar results were observed in seedlings from seeds produced in the southern seed orchard. We found no adverse effects of the changed growth rhythm. Seedlings from two seed crops in the southern orchard, produced in years with a warm and a cold summer, had different annual growth rhythms. The results are explained mainly by the effects of the climatic conditions during the reproductive phase. Seed crops from different years in the same seed orchard may produce seedlings that perform as if they were from different provenances. It is argued that the effects of the climatic conditions during seed production must contribute to the variation among provenances of Norway spruce.

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