Genotoxic compounds, as common contaminants of the air environment, are of interest in air pollution monitoring. There are several methods to determine the level of these contaminants in different localities, many of which may be difficult to access with the use of conventional active and passive samplers. In the present study, the needles Pinus mugo Turra and Picea abies were used to monitor sampling localities in Austria, Slovakia, and the Czech Republic. Needles were extracted and chemical analysis and the genotoxicity bioassay SOS chromotest were used to obtain complex information about the chemical mixture of pollutants present and their genotoxic effects. The SOS chromotest method was optimized by using a CPRG chromogenic substrate to reduce the false positive genotoxic effect of needle extracts. Pinus mugo Turra and Picea abies were identified as suitable passive sampling matrices for long-term air monitoring using the same plants sampled at the same time. The presented study brings an innovative method for the fast screening and identification of localities loaded by genotoxic active air contaminants.
- MeSH
- borovice chemie genetika MeSH
- látky znečišťující vzduch analýza MeSH
- lidé MeSH
- monitorování životního prostředí metody MeSH
- poškození DNA genetika MeSH
- smrk chemie genetika MeSH
- testy genotoxicity metody MeSH
- znečištění ovzduší analýza MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Rakousko MeSH
- Slovenská republika MeSH
Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13 000 yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.
Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce (Picea glauca) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm.
Unlike angiosperms, gymnosperms use two different enzymes for the reduction of protochlorophyllide to chlorophyllide: the light-dependent protochlorophyllide oxidoreductase (LPOR) and the dark-operative protochlorophyllide oxidoreductase (DPOR). In this study, we examined the specific role of both enzymes for chlorophyll synthesis in response to different light/dark and temperature conditions at different developmental stages (cotyledons and needles) of Norway spruce (Picea abies Karst.). The accumulation of chlorophyll and chlorophyll-binding proteins strongly decreased during dark growth in secondary needles at room temperature as well as in cotyledons at low temperature (7 °C) indicating suppression of DPOR activity. The levels of the three DPOR subunits ChlL, ChlN, and ChlB and the transcripts of their encoding genes were diminished in dark-grown secondary needles. The low temperature had minor effects on the transcription and translation of these genes in cotyledons, which is suggestive for post-translational control in chlorophyll biosynthesis. Taking into account the higher solubility of oxygen at low temperature and oxygen sensitivity of DPOR, we mimicked low-temperature condition by the exposure of seedlings to higher oxygen content (33%). The treatment resulted in an etiolated phenotype of dark-grown seedlings, confirming an oxygen-dependent control of DPOR activity in spruce cotyledons. Moreover, light-dependent suppression of mRNA and protein level of DPOR subunits indicates that more efficiently operating LPOR takes over the DPOR function under light conditions, especially in secondary needles.
- MeSH
- chlorofyl genetika metabolismus MeSH
- oxidoreduktasy působící na CH-CH vazby biosyntéza metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- smrk enzymologie genetika metabolismus MeSH
- světlo MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Norsko MeSH
The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates' offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of "half-sibling" in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.
- MeSH
- algoritmy MeSH
- fenotyp MeSH
- genetická variace MeSH
- genom rostlinný * MeSH
- genomika * metody MeSH
- genotyp MeSH
- genotypizační techniky MeSH
- kvantitativní znak dědičný MeSH
- modely genetické MeSH
- opylení genetika MeSH
- smrk klasifikace genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce (Picea engelmannii × glauca) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3-40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31-0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation (r=0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04-0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.
- MeSH
- genotyp MeSH
- genotypizační techniky metody MeSH
- jednonukleotidový polymorfismus MeSH
- modely genetické * MeSH
- populační genetika MeSH
- selekce (genetika) * MeSH
- smrk genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Britská Kolumbie MeSH
BACKGROUND: Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost. RESULTS: Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3. CONCLUSIONS: The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.
- MeSH
- algoritmy MeSH
- dřevo * MeSH
- genomika metody MeSH
- genotypizační techniky * MeSH
- modely genetické MeSH
- sekvenční analýza * MeSH
- šlechtění rostlin metody MeSH
- smrk genetika růst a vývoj MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Our study focused on the possible association between the cryotolerance of Norway spruce (Picea abies (L.) Karst.) embryogenic cultures and the anatomical structures of their embryogenic suspensor mass (ESM), their growth rate and their content of endogenous polyamines (PAs). The anatomical characteristics and PA content during cryopreservation and regrowth were studied in the ESMs of AFO 541 and C110 cultures, which have comparable ESM anatomy but diverse growth rates, PA content and regeneration abilities after cryopreservation. Different levels of tolerance to exogenous treatment were already apparent after transfer of the ESMs to liquid media. The endogenous free PAs were maintained at high levels, with spermidine being the predominant PA in the ESM of AFO 541, while in the ESM of C110 the content of putrescine and spermidine was almost identical and rather low, the content of spermidine being approximately one-third that in the ESM of AFO 541. Osmotic pretreatment, using a double application of sorbitol followed by an application of dimethyl sulfoxide (DMSO) resulted in the continual disintegration of polyembryogenic centers and suspensors in both cell lines. A continual decrease in the level of PAs was observed during the cell osmotic pretreatment. The cells that retained their viability and regrowth ability after cryopreservation were the meristematic cells inside the embryonal heads and the cells in the intermediate area between suspensor and meristems. Restoration of AFO 541 growth after cryopreservation was almost immediate; however, the C110 ESM culture regrew with difficulty, often exhibiting callogenesis. High levels of PA-soluble conjugates and an increase in the amount of PAs bound to high-molecular-mass substances was observed in cells of AFO 541 on Day 6 after thawing and also to some extent on Day 11. On Day 21 after thawing, the amount of free putrescine and spermidine in the AFO 541 cells reached the level observed in the suspension culture before the cryotreatment. The extremely low level of PAs determined in the ESM of C110 3 weeks after thawing agreed with the cell viability and rate of regrowth observed in this culture. The possible role of PAs in the process of cryopreservation of Norway spruce cultures is discussed.
- MeSH
- buněčné linie MeSH
- dimethylsulfoxid farmakologie MeSH
- kryoprezervace metody MeSH
- polyaminy metabolismus MeSH
- semena rostlinná anatomie a histologie cytologie účinky léků fyziologie MeSH
- smrk anatomie a histologie embryologie genetika růst a vývoj MeSH
- sorbitol farmakologie MeSH
- studené klima MeSH
- zmrazování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- elektrochemie metody MeSH
- esterasy analýza MeSH
- finanční podpora výzkumu jako téma MeSH
- financování organizované MeSH
- glutathion analýza MeSH
- kadmium škodlivé účinky MeSH
- klíčení MeSH
- látky znečišťující půdu MeSH
- počítačové zpracování obrazu MeSH
- semenáček cytologie enzymologie genetika MeSH
- smrk genetika růst a vývoj MeSH
