Jan Stejskal - Academia.edu (original) (raw)

Papers by Jan Stejskal

Annals of Forest Science

Key message The lack of efficient phenotyping capacities has been recognized as a bottleneck in f... more Key message The lack of efficient phenotyping capacities has been recognized as a bottleneck in forestry phenotyping and breeding. Modern phenotyping technologies use systems equipped with various imaging sensors to automatically collect high volume phenotypic data that can be used to assess trees' various attributes. Context Efficient phenotyping has the potential to spark a new Green Revolution, and it would provide an opportunity to acquire growth parameters and dissect the genetic bases of quantitative traits. Phenotyping platforms aim to link information from several sources to derive knowledge about trees' attributes. Aims Various tree phenotyping techniques were reviewed and analyzed along with their different applications. Methods This article presents the definition and characteristics of forest tree phenotyping and reviews newly developed imaging-based practices in forest tree phenotyping. Results This review addressed a wide range of forest trees phenotyping appli...

Through stochastic simulations, accuracies of breeding values and response to selection were asse... more Through stochastic simulations, accuracies of breeding values and response to selection were assessed under traditional pedigree- (BLUP) and genomic-based evaluation methods (GBLUP) in forest tree breeding. The latter provides a methodological foundation for genomic selection. We evaluated the impact of clonal replication in progeny testing on the response to selection realized in seed orchards under variable marker density and target effective population sizes. We found that clonal replication in progeny trials boosted selection accuracy, thus provided additional genetic gains under BLUP. While a similar trend was observed for GBLUP, however, the added gains did not surpass those under BLUP. Therefore, breeding programs deploying extensive progeny testing with clonal propagation might not benefit from the deployment of genomic information. These findings could be helpful in the context of operational breeding programs.

Scientific Reports, 2021

We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway ... more We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low- (acuminata), medium- (europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRUCTURE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.

Scientific Reports, 2020

Norway spruce has a broad natural distribution range, which results in a substantial variety of i... more Norway spruce has a broad natural distribution range, which results in a substantial variety of its physiological and genetic variation. There are three distinct altitudinal ecotypes described in this tree species. The physiological optimum of each ecotype may be shifted due to ongoing climate change, especially in traits associated with water demand that might be crucial for adaptation. Dehydrins are proteins that help to mitigate the adverse effects of dehydration. Dehydrin gene expression patterns appeared to be a suitable marker for plant stress assessment. Genetically determined differences in response between individuals and populations were formerly studied, however, mainly in controlled conditions. We evaluated ecotypic variation in dehydrin gene expression in a clonal bank comprised of all three ecotypes. A genetic relationship among targeted trees was uncovered utilizing GBS (Genotyping by Sequencing) platform. We sampled 4–6 trees of each ecotype throughout 15 months peri...

Forests, 2019

Currently, there has been an increasing demand on seed orchard designs with respect to mitigating... more Currently, there has been an increasing demand on seed orchard designs with respect to mitigating inbreeding in advanced generations or facing severe mortality at sites. Optimum Neighborhood Algorithm design (ONA) excels in solving these issues, as shown in two case studies. The first demonstrates the application of the ONA for populating empty positions in an existing orchard. Following this concept, the ONA can be used for upgrading existing orchards, where only high-value parents are retained and new parents are introduced, thus avoiding the genetic penalty associated with the establishment of new-generation seed orchards. The second illustrates benefits of combining the ONA with the Minimum Inbreeding (MI) seed orchard design. Utilizing the MI, distances among clonal rows of selected clones were maximized on the orchard grid while the remaining single-tree positions were populated by ONA.

Frontiers in Genetics, 2020

Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile ... more Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile nature of trees makes adaptation to climate change challenging; thereby, ecological services and economic potential are under risk. Current long-term and costly gene resources management practices have been primarily directed at a few economically important species and are confined to defined ecological boundaries. Here, we present a novel in situ gene-resource management approach that conserves forest biodiversity and improves productivity and adaptation through utilizing basic forest regeneration installations located across a wide range of environments without reliance on structured tree breeding/conservation methods. We utilized 4,267 25-to 35-year-old European larch trees growing in 21 reforestation installations across four distinct climatic regions in Austria. With the aid of marker-based pedigree reconstruction, we applied multi-trait, multi-site quantitative genetic analyses that enabled the identification of broadly adapted and productive individuals. Height and wood density, proxies to fitness and productivity, yielded in situ heritability estimates of 0.23 ± 0.07 and 0.30 ± 0.07, values similar to those from traditional "structured" pedigrees methods. In addition, individual trees selected with this approach are expected to yield genetic response of 1.1 and 0.7 standard deviations for fitness and productivity attributes, respectively, and be broadly adapted to a range of climatic conditions. Genetic evaluation across broad climatic gradients permitted the delineation of suitable reforestation areas under current and future climates. This simple and resource-efficient management of gene resources is applicable to most tree species.

The paper evaluated dendrometric parameters of hybrid progenies of various Abies species obtained... more The paper evaluated dendrometric parameters of hybrid progenies of various Abies species obtained during measurements in the spring 2010 on the research plot in Kostelec nad ernými lesy. Data were processed and compared to the measurement taken in 2004. Results show that all hybrid progenies within the plot exceeded A. alba in investigated parameters. Only two of the progenies achieved worse results in mean height-A. koreana × (A. cilicica × A. cephalonica) and progeny of spontaneous hybrid no. 2. Considering height and diameter A. nordmanniana was evaluated as the most productive. On the contrary A. gracilis is considered unsuitable for further culture and research due to the mortality of 100%.

Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile ... more Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile nature of trees makes adaptation to climate change challenging; thereby, ecological services and economic potential are under risk. Current long-term and costly gene resources management practices have been primarily directed at a few economically important species and are confined to defined ecological boundaries. Here, we present a novel in situ gene-resource management approach that conserves forest biodiversity and improves productivity and adaptation through utilizing basic forest regeneration installations located across a wide range of environments without reliance on structured tree breeding/conservation methods. We utilized 4,267 25-to 35-year-old European larch trees growing in 21 reforestation installations across four distinct climatic regions in Austria. With the aid of marker-based pedigree reconstruction, we applied multi-trait, multi-site quantitative genetic analyses that enabled the identification of broadly adapted and productive individuals. Height and wood density, proxies to fitness and productivity, yielded in situ heritability estimates of 0.23 ± 0.07 and 0.30 ± 0.07, values similar to those from traditional "structured" pedigrees methods. In addition, individual trees selected with this approach are expected to yield genetic response of 1.1 and 0.7 standard deviations for fitness and productivity attributes, respectively, and be broadly adapted to a range of climatic conditions. Genetic evaluation across broad climatic gradients permitted the delineation of suitable reforestation areas under current and future climates. This simple and resource-efficient management of gene resources is applicable to most tree species.

The minimum-inbreeding (MI) seed orchard layout, formulated originally as a global quadratic assi... more The minimum-inbreeding (MI) seed orchard layout, formulated originally as a global quadratic assignment problem, was expanded into realistic problem sizes that are often encountered in operational forestry, where two modifications were tested: (1) the merging algorithm of independent MI's solutions (i.e., smaller blocks) and (2) the extended global (genetic-tabu) algorithm. Extending the global heuristic algorithm of the quadratic assignment problem seems to be the most efficient strategy. The reported minimum-inbreeding distance of the extended MI scheme was the lowest in comparison to the completely randomized and the randomized, replicated, staggered clonal-row (R 2 SCR) seed orchard design schemes. These conclusions also hold for more complex scenarios when added relatedness among orchard's parents or unequal deployment was considered. This improved MI scheme is suitable to large and complex advancedgeneration seed orchards, where many practical constraints have to be jointly considered.

Through stochastic simulations, estimates of breeding values accuracies and response to selection... more Through stochastic simulations, estimates of breeding values accuracies and response to selection were assessed under traditional pedigree-based and genomic-based evaluation methods. More specifically, several key parameters such as the trait's heritability (0.2 and 0.6), the number of QTLs underlying the trait (100 to 200), and the marker density (1 to 10 SNPs/cM) were evaluated. Additionally, impact of two contrasting mating designs (partial diallel vs. single-pair mating) was investigated. Response to selection was then assessed in a seed production population (seed orchard consisting of unrelated selections) for different effective population sizes (N e = 5 to 25). The simulated candidate population comprised a fixed size of 2050 individuals with fast linkage disequilibrium decay, generally found in forest tree populations. Following the genetic/genomic evaluation, topranked individuals were selected to meeting the predetermined effective population size in target production population. The combination of low h 2 , high N e , and dense marker coverage resulted at maximum relative genomic prediction efficiency and the most efficient exploitation of the Mendelian sampling term (within-family additive genetic variance). Since genomic prediction of breeding values constitutes the methodological foundation of genomic selection, our results can be used to address important questions when similar scenarios are considered.

Key message: The lack of efficient phenotyping capacities has been recognized as a bottleneck in ... more Key message: The lack of efficient phenotyping capacities has been recognized as a bottleneck in forestry phenotyping and breeding. Modern phenotyping technologies use systems equipped with various imaging sensors to automatically collect high volume phenotypic data that can be used to assess trees' various attributes. Context: Efficient phenotyping has the potential to spark a new Green Revolution, and it would provide an opportunity to acquire growth parameters and dissect the genetic bases of quantitative traits. Phenotyping platforms aim to link information from several sources to derive knowledge about trees' attributes. Aims: Various tree phenotyping techniques were reviewed and analyzed along with their different applications. Methods: This article presents the definition and characteristics of forest tree phenotyping and reviews newly developed imaging-based practices in forest tree phenotyping. Results: This review addressed a wide range of forest trees phenotyping applications, including a survey of actual inter-and intra-specific variability, evaluating genotypes and species response to biotic and abiotic stresses, and phenological measurements. Conclusion: With the support of advanced phenotyping platforms, the efficiency of traits phenotyping in forest tree breeding programs is accelerated.

Foliar reflectance is readily used in evaluating physiological status of agricultural crops and f... more Foliar reflectance is readily used in evaluating physiological status of agricultural crops and forest stands. However, in the case of forest trees, underlying genetics of foliar spectral reflectance and pigment content have rarely been investigated. We studied a structured population of Scots pine, replicated on two sites, with the selected trees´pedigree reconstructed via DNA markers. This allowed us to decompose phenotypic variance of pigment and reflectance traits into its causal genetic components, and to estimate narrow-sense heritability (h 2). We found statistically significant h 2 ranging from 0.07 to 0.22 for most of the established reflectance indices. Additionally, we investigated the profile of heritable variation along the reflectance curve in 1 nm wavelength (WL) bands. We show that the maximum h 2 value (0.39; SE 0.13) across the 400 to 2500 nm spectral range corresponds to the red edge inflection point, in this case to 722 nm WL band. Resultant h 2 distribution indicates that additive gene effects fluctuate along the reflectance curve. Furthermore, h 2 of the most widely used formats of reflectance indices, i.e. the simple ratio and the normalized difference, was estimated for all WL bands combined along the observed reflectance spectrum. The highest h 2 estimates for both formats were obtained by combining WL bands of the red edge spectrum. These new genetically driven pigment-and spectral reflectance-based markers (proxies of adaptive traits) may facilitate selection of stress resistant plant genotypes. Recent development of high-resolution spectral sensors carried by airborne and spaceborn devices make foliage spectral traits a viable technology for mass phenotyping in forest trees.

We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway ... more We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low-(acuminata), medium-(europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRU CTU RE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.

Currently, there has been an increasing demand on seed orchard designs with respect to mitigating... more Currently, there has been an increasing demand on seed orchard designs with respect to mitigating inbreeding in advanced generations or facing severe mortality at sites. Optimum Neighborhood Algorithm design (ONA) excels in solving these issues, as shown in two case studies. The first demonstrates the application of the ONA for populating empty positions in an existing orchard. Following this concept, the ONA can be used for upgrading existing orchards, where only high-value parents are retained and new parents are introduced, thus avoiding the genetic penalty associated with the establishment of new-generation seed orchards. The second illustrates benefits of combining the ONA with the Minimum Inbreeding (MI) seed orchard design. Utilizing the MI, distances among clonal rows of selected clones were maximized on the orchard grid while the remaining single-tree positions were populated by ONA.

In forest tree breeding, assisted migration has been proposed to accelerate the adaptive response... more In forest tree breeding, assisted migration has been proposed to accelerate the adaptive response to climate change. Response functions are currently fitted across multiple populations and environments, enabling selections of the most appropriate seed sources for a specific reforestation site. So far, the approach has been limited to capturing adaptive variation among populations, neglecting tree-to-tree variation residing within a population. Here, we combined the response function methodology with the in-situ breeding approach, utilizing progeny trials of European larch (Larix decidua) across 21 test sites in Austria ranging from Alpine to lowland regions. We quantified intra-population genetic variance and predicted individual genetic performance along a climatic gradient. This approach can be adopted in most breeding and conservation programs, boosting the speed of adaptation under climate change.

Norway spruce has a broad natural distribution range, which results in a substantial variety of i... more Norway spruce has a broad natural distribution range, which results in a substantial variety of its physiological and genetic variation. There are three distinct altitudinal ecotypes described in this tree species. The physiological optimum of each ecotype may be shifted due to ongoing climate change, especially in traits associated with water demand that might be crucial for adaptation. Dehydrins are proteins that help to mitigate the adverse effects of dehydration. Dehydrin gene expression patterns appeared to be a suitable marker for plant stress assessment. Genetically determined differences in response between individuals and populations were formerly studied, however, mainly in controlled conditions. We evaluated ecotypic variation in dehydrin gene expression in a clonal bank comprised of all three ecotypes. A genetic relationship among targeted trees was uncovered utilizing GBS (Genotyping by Sequencing) platform. We sampled 4-6 trees of each ecotype throughout 15 months period. Subsequently, we assessed the RNA expression of dehydrin genes by qRT-PCR. For this study, we deliberately selected dehydrins from different categories. Our findings detected significant differences among ecotypes in dehydrin expression. The association of recorded climatic variables and individual gene expression across the study period was evaluated and revealed, for certain genes, a correlation between dehydrin gene expression and precipitation, temperature, and day-length. Quantitative real-time PCR (qRT-PCR). Specific primers for reference actin gene and dehydrin genes PaDhn6, PaDhn4.5, and PaCAP1 were designed according to 24. Oligonucleotides were synthesized by Eurofins

Through stochastic simulations, accuracies of breeding values and response to selection were asse... more Through stochastic simulations, accuracies of breeding values and response to selection were assessed under traditional pedigree-(BLUP) and genomic-based evaluation methods (GBLUP) in forest tree breeding. The latter provides a methodological foundation for genomic selection. We evaluated the impact of clonal replication in progeny testing on the response to selection realized in seed orchards under variable marker density and target effective population sizes. We found that clonal replication in progeny trials boosted selection accuracy, thus providing additional genetic gains under BLUP. While a similar trend was observed for GBLUP, however, the added gains did not surpass those under BLUP. Therefore, breeding programs deploying extensive progeny testing with clonal propagation might not benefit from the deployment of genomic information. These findings could be helpful in the context of operational breeding programs.

European Journal of Forest Research, 2016

Hybridization experiments among fir (Abies) species contribute to clarification of both crossabil... more Hybridization experiments among fir (Abies) species contribute to clarification of both crossability and evolutionary relationships of organisms at least from the second half of the nineteenth century. The main aim of our study was to find possible effects of hybridization on survival rate and two growth parameters (height and diameter at the breast height) of fir trees at various levels of complexity in the Czech Republic. We compared (1) pure species consisting of seven fir taxa, (2) open pollinated hybrids comprising of twenty-one hybrid progenies of Greek Fir (A. cephalonica), Cilician Fir (A. cilicica) and Algerian Fir (A. numidica) and (3) artificial complex hybrids of Korean Fir (A. koreana) 9 (A. cilicica 9 A. cephalonica). For our analyses, we used combination of so-called traditional statistical methods and spatial modelling. Our results revealed that a higher level of hybridization and introgression may lead to a higher survival rate and furthermore, that neglecting of spatial autocorrelation in randomized complete block design might lead to wrong conclusions-because our analyses on height showed contrasting results between traditional and spatial modelling. The results of this study appear to be a good message for scientists dealing with forest tree breeding and facing a lack of confidence by practice. They might be also a good news for forestry practice, where foresters face high mortality during afforestation, e.g. in extreme environmental conditions. Our study highlighted that neglecting spatial autocorrelation could possibly lead to wrong conclusions in studies of similar spatial scale level.

Tree Physiology, 2016

Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity... more Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity in forest trees is generally limited, yet it is essential both for various practical forestry purposes and for better understanding of broader evolutionary mechanisms. In this study, we investigated genetic variation underlying selected chlorophyll a fluorescence (ChlF) parameters in structured populations of Scots pine (Pinus sylvestris L.) grown on two sites under non-stress conditions. These parameters were derived from the OJIP part of the ChlF kinetics curve and characterize individual parts of primary photosynthetic processes associated, for example, with the exciton trapping by light-harvesting antennae, energy utilization in photosystem II (PSII) reaction centers (RCs) and its transfer further down the photosynthetic electron-transport chain. An additive relationship matrix was estimated based on pedigree reconstruction, utilizing a set of highly polymorphic single sequence repeat markers. Variance decomposition was conducted using the animal genetic evaluation mixed-linear model. The majority of ChlF parameters in the analyzed pine populations showed significant additive genetic variation. Statistically significant heritability estimates were obtained for most ChlF indices, with the exception of DI 0 /RC, φ D0 and φ P0 (F v /F m) parameters. Estimated heritabilities varied around the value of 0.15 with the maximal value of 0.23 in the ET 0 /RC parameter, which indicates electron-transport flux from Q A to Q B per PSII RC. No significant correlation was found between these indices and selected growth traits. Moreover, no genotype × environment interaction (G × E) was detected, i.e., no differences in genotypes' performance between sites. The absence of significant G × E in our study is interesting, given the relatively low heritability found for the majority of parameters analyzed. Therefore, we infer that polygenic variability of these indices is selectively neutral.

Annals of Forest Science

Key message The lack of efficient phenotyping capacities has been recognized as a bottleneck in f... more Key message The lack of efficient phenotyping capacities has been recognized as a bottleneck in forestry phenotyping and breeding. Modern phenotyping technologies use systems equipped with various imaging sensors to automatically collect high volume phenotypic data that can be used to assess trees' various attributes. Context Efficient phenotyping has the potential to spark a new Green Revolution, and it would provide an opportunity to acquire growth parameters and dissect the genetic bases of quantitative traits. Phenotyping platforms aim to link information from several sources to derive knowledge about trees' attributes. Aims Various tree phenotyping techniques were reviewed and analyzed along with their different applications. Methods This article presents the definition and characteristics of forest tree phenotyping and reviews newly developed imaging-based practices in forest tree phenotyping. Results This review addressed a wide range of forest trees phenotyping appli...

Through stochastic simulations, accuracies of breeding values and response to selection were asse... more Through stochastic simulations, accuracies of breeding values and response to selection were assessed under traditional pedigree- (BLUP) and genomic-based evaluation methods (GBLUP) in forest tree breeding. The latter provides a methodological foundation for genomic selection. We evaluated the impact of clonal replication in progeny testing on the response to selection realized in seed orchards under variable marker density and target effective population sizes. We found that clonal replication in progeny trials boosted selection accuracy, thus provided additional genetic gains under BLUP. While a similar trend was observed for GBLUP, however, the added gains did not surpass those under BLUP. Therefore, breeding programs deploying extensive progeny testing with clonal propagation might not benefit from the deployment of genomic information. These findings could be helpful in the context of operational breeding programs.

Scientific Reports, 2021

We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway ... more We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low- (acuminata), medium- (europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRUCTURE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.

Scientific Reports, 2020

Norway spruce has a broad natural distribution range, which results in a substantial variety of i... more Norway spruce has a broad natural distribution range, which results in a substantial variety of its physiological and genetic variation. There are three distinct altitudinal ecotypes described in this tree species. The physiological optimum of each ecotype may be shifted due to ongoing climate change, especially in traits associated with water demand that might be crucial for adaptation. Dehydrins are proteins that help to mitigate the adverse effects of dehydration. Dehydrin gene expression patterns appeared to be a suitable marker for plant stress assessment. Genetically determined differences in response between individuals and populations were formerly studied, however, mainly in controlled conditions. We evaluated ecotypic variation in dehydrin gene expression in a clonal bank comprised of all three ecotypes. A genetic relationship among targeted trees was uncovered utilizing GBS (Genotyping by Sequencing) platform. We sampled 4–6 trees of each ecotype throughout 15 months peri...

Forests, 2019

Currently, there has been an increasing demand on seed orchard designs with respect to mitigating... more Currently, there has been an increasing demand on seed orchard designs with respect to mitigating inbreeding in advanced generations or facing severe mortality at sites. Optimum Neighborhood Algorithm design (ONA) excels in solving these issues, as shown in two case studies. The first demonstrates the application of the ONA for populating empty positions in an existing orchard. Following this concept, the ONA can be used for upgrading existing orchards, where only high-value parents are retained and new parents are introduced, thus avoiding the genetic penalty associated with the establishment of new-generation seed orchards. The second illustrates benefits of combining the ONA with the Minimum Inbreeding (MI) seed orchard design. Utilizing the MI, distances among clonal rows of selected clones were maximized on the orchard grid while the remaining single-tree positions were populated by ONA.

Frontiers in Genetics, 2020

Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile ... more Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile nature of trees makes adaptation to climate change challenging; thereby, ecological services and economic potential are under risk. Current long-term and costly gene resources management practices have been primarily directed at a few economically important species and are confined to defined ecological boundaries. Here, we present a novel in situ gene-resource management approach that conserves forest biodiversity and improves productivity and adaptation through utilizing basic forest regeneration installations located across a wide range of environments without reliance on structured tree breeding/conservation methods. We utilized 4,267 25-to 35-year-old European larch trees growing in 21 reforestation installations across four distinct climatic regions in Austria. With the aid of marker-based pedigree reconstruction, we applied multi-trait, multi-site quantitative genetic analyses that enabled the identification of broadly adapted and productive individuals. Height and wood density, proxies to fitness and productivity, yielded in situ heritability estimates of 0.23 ± 0.07 and 0.30 ± 0.07, values similar to those from traditional "structured" pedigrees methods. In addition, individual trees selected with this approach are expected to yield genetic response of 1.1 and 0.7 standard deviations for fitness and productivity attributes, respectively, and be broadly adapted to a range of climatic conditions. Genetic evaluation across broad climatic gradients permitted the delineation of suitable reforestation areas under current and future climates. This simple and resource-efficient management of gene resources is applicable to most tree species.

The paper evaluated dendrometric parameters of hybrid progenies of various Abies species obtained... more The paper evaluated dendrometric parameters of hybrid progenies of various Abies species obtained during measurements in the spring 2010 on the research plot in Kostelec nad ernými lesy. Data were processed and compared to the measurement taken in 2004. Results show that all hybrid progenies within the plot exceeded A. alba in investigated parameters. Only two of the progenies achieved worse results in mean height-A. koreana × (A. cilicica × A. cephalonica) and progeny of spontaneous hybrid no. 2. Considering height and diameter A. nordmanniana was evaluated as the most productive. On the contrary A. gracilis is considered unsuitable for further culture and research due to the mortality of 100%.

Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile ... more Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile nature of trees makes adaptation to climate change challenging; thereby, ecological services and economic potential are under risk. Current long-term and costly gene resources management practices have been primarily directed at a few economically important species and are confined to defined ecological boundaries. Here, we present a novel in situ gene-resource management approach that conserves forest biodiversity and improves productivity and adaptation through utilizing basic forest regeneration installations located across a wide range of environments without reliance on structured tree breeding/conservation methods. We utilized 4,267 25-to 35-year-old European larch trees growing in 21 reforestation installations across four distinct climatic regions in Austria. With the aid of marker-based pedigree reconstruction, we applied multi-trait, multi-site quantitative genetic analyses that enabled the identification of broadly adapted and productive individuals. Height and wood density, proxies to fitness and productivity, yielded in situ heritability estimates of 0.23 ± 0.07 and 0.30 ± 0.07, values similar to those from traditional "structured" pedigrees methods. In addition, individual trees selected with this approach are expected to yield genetic response of 1.1 and 0.7 standard deviations for fitness and productivity attributes, respectively, and be broadly adapted to a range of climatic conditions. Genetic evaluation across broad climatic gradients permitted the delineation of suitable reforestation areas under current and future climates. This simple and resource-efficient management of gene resources is applicable to most tree species.

The minimum-inbreeding (MI) seed orchard layout, formulated originally as a global quadratic assi... more The minimum-inbreeding (MI) seed orchard layout, formulated originally as a global quadratic assignment problem, was expanded into realistic problem sizes that are often encountered in operational forestry, where two modifications were tested: (1) the merging algorithm of independent MI's solutions (i.e., smaller blocks) and (2) the extended global (genetic-tabu) algorithm. Extending the global heuristic algorithm of the quadratic assignment problem seems to be the most efficient strategy. The reported minimum-inbreeding distance of the extended MI scheme was the lowest in comparison to the completely randomized and the randomized, replicated, staggered clonal-row (R 2 SCR) seed orchard design schemes. These conclusions also hold for more complex scenarios when added relatedness among orchard's parents or unequal deployment was considered. This improved MI scheme is suitable to large and complex advancedgeneration seed orchards, where many practical constraints have to be jointly considered.

Through stochastic simulations, estimates of breeding values accuracies and response to selection... more Through stochastic simulations, estimates of breeding values accuracies and response to selection were assessed under traditional pedigree-based and genomic-based evaluation methods. More specifically, several key parameters such as the trait's heritability (0.2 and 0.6), the number of QTLs underlying the trait (100 to 200), and the marker density (1 to 10 SNPs/cM) were evaluated. Additionally, impact of two contrasting mating designs (partial diallel vs. single-pair mating) was investigated. Response to selection was then assessed in a seed production population (seed orchard consisting of unrelated selections) for different effective population sizes (N e = 5 to 25). The simulated candidate population comprised a fixed size of 2050 individuals with fast linkage disequilibrium decay, generally found in forest tree populations. Following the genetic/genomic evaluation, topranked individuals were selected to meeting the predetermined effective population size in target production population. The combination of low h 2 , high N e , and dense marker coverage resulted at maximum relative genomic prediction efficiency and the most efficient exploitation of the Mendelian sampling term (within-family additive genetic variance). Since genomic prediction of breeding values constitutes the methodological foundation of genomic selection, our results can be used to address important questions when similar scenarios are considered.

Key message: The lack of efficient phenotyping capacities has been recognized as a bottleneck in ... more Key message: The lack of efficient phenotyping capacities has been recognized as a bottleneck in forestry phenotyping and breeding. Modern phenotyping technologies use systems equipped with various imaging sensors to automatically collect high volume phenotypic data that can be used to assess trees' various attributes. Context: Efficient phenotyping has the potential to spark a new Green Revolution, and it would provide an opportunity to acquire growth parameters and dissect the genetic bases of quantitative traits. Phenotyping platforms aim to link information from several sources to derive knowledge about trees' attributes. Aims: Various tree phenotyping techniques were reviewed and analyzed along with their different applications. Methods: This article presents the definition and characteristics of forest tree phenotyping and reviews newly developed imaging-based practices in forest tree phenotyping. Results: This review addressed a wide range of forest trees phenotyping applications, including a survey of actual inter-and intra-specific variability, evaluating genotypes and species response to biotic and abiotic stresses, and phenological measurements. Conclusion: With the support of advanced phenotyping platforms, the efficiency of traits phenotyping in forest tree breeding programs is accelerated.

Foliar reflectance is readily used in evaluating physiological status of agricultural crops and f... more Foliar reflectance is readily used in evaluating physiological status of agricultural crops and forest stands. However, in the case of forest trees, underlying genetics of foliar spectral reflectance and pigment content have rarely been investigated. We studied a structured population of Scots pine, replicated on two sites, with the selected trees´pedigree reconstructed via DNA markers. This allowed us to decompose phenotypic variance of pigment and reflectance traits into its causal genetic components, and to estimate narrow-sense heritability (h 2). We found statistically significant h 2 ranging from 0.07 to 0.22 for most of the established reflectance indices. Additionally, we investigated the profile of heritable variation along the reflectance curve in 1 nm wavelength (WL) bands. We show that the maximum h 2 value (0.39; SE 0.13) across the 400 to 2500 nm spectral range corresponds to the red edge inflection point, in this case to 722 nm WL band. Resultant h 2 distribution indicates that additive gene effects fluctuate along the reflectance curve. Furthermore, h 2 of the most widely used formats of reflectance indices, i.e. the simple ratio and the normalized difference, was estimated for all WL bands combined along the observed reflectance spectrum. The highest h 2 estimates for both formats were obtained by combining WL bands of the red edge spectrum. These new genetically driven pigment-and spectral reflectance-based markers (proxies of adaptive traits) may facilitate selection of stress resistant plant genotypes. Recent development of high-resolution spectral sensors carried by airborne and spaceborn devices make foliage spectral traits a viable technology for mass phenotyping in forest trees.

We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway ... more We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low-(acuminata), medium-(europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRU CTU RE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.

Currently, there has been an increasing demand on seed orchard designs with respect to mitigating... more Currently, there has been an increasing demand on seed orchard designs with respect to mitigating inbreeding in advanced generations or facing severe mortality at sites. Optimum Neighborhood Algorithm design (ONA) excels in solving these issues, as shown in two case studies. The first demonstrates the application of the ONA for populating empty positions in an existing orchard. Following this concept, the ONA can be used for upgrading existing orchards, where only high-value parents are retained and new parents are introduced, thus avoiding the genetic penalty associated with the establishment of new-generation seed orchards. The second illustrates benefits of combining the ONA with the Minimum Inbreeding (MI) seed orchard design. Utilizing the MI, distances among clonal rows of selected clones were maximized on the orchard grid while the remaining single-tree positions were populated by ONA.

In forest tree breeding, assisted migration has been proposed to accelerate the adaptive response... more In forest tree breeding, assisted migration has been proposed to accelerate the adaptive response to climate change. Response functions are currently fitted across multiple populations and environments, enabling selections of the most appropriate seed sources for a specific reforestation site. So far, the approach has been limited to capturing adaptive variation among populations, neglecting tree-to-tree variation residing within a population. Here, we combined the response function methodology with the in-situ breeding approach, utilizing progeny trials of European larch (Larix decidua) across 21 test sites in Austria ranging from Alpine to lowland regions. We quantified intra-population genetic variance and predicted individual genetic performance along a climatic gradient. This approach can be adopted in most breeding and conservation programs, boosting the speed of adaptation under climate change.

Norway spruce has a broad natural distribution range, which results in a substantial variety of i... more Norway spruce has a broad natural distribution range, which results in a substantial variety of its physiological and genetic variation. There are three distinct altitudinal ecotypes described in this tree species. The physiological optimum of each ecotype may be shifted due to ongoing climate change, especially in traits associated with water demand that might be crucial for adaptation. Dehydrins are proteins that help to mitigate the adverse effects of dehydration. Dehydrin gene expression patterns appeared to be a suitable marker for plant stress assessment. Genetically determined differences in response between individuals and populations were formerly studied, however, mainly in controlled conditions. We evaluated ecotypic variation in dehydrin gene expression in a clonal bank comprised of all three ecotypes. A genetic relationship among targeted trees was uncovered utilizing GBS (Genotyping by Sequencing) platform. We sampled 4-6 trees of each ecotype throughout 15 months period. Subsequently, we assessed the RNA expression of dehydrin genes by qRT-PCR. For this study, we deliberately selected dehydrins from different categories. Our findings detected significant differences among ecotypes in dehydrin expression. The association of recorded climatic variables and individual gene expression across the study period was evaluated and revealed, for certain genes, a correlation between dehydrin gene expression and precipitation, temperature, and day-length. Quantitative real-time PCR (qRT-PCR). Specific primers for reference actin gene and dehydrin genes PaDhn6, PaDhn4.5, and PaCAP1 were designed according to 24. Oligonucleotides were synthesized by Eurofins

Through stochastic simulations, accuracies of breeding values and response to selection were asse... more Through stochastic simulations, accuracies of breeding values and response to selection were assessed under traditional pedigree-(BLUP) and genomic-based evaluation methods (GBLUP) in forest tree breeding. The latter provides a methodological foundation for genomic selection. We evaluated the impact of clonal replication in progeny testing on the response to selection realized in seed orchards under variable marker density and target effective population sizes. We found that clonal replication in progeny trials boosted selection accuracy, thus providing additional genetic gains under BLUP. While a similar trend was observed for GBLUP, however, the added gains did not surpass those under BLUP. Therefore, breeding programs deploying extensive progeny testing with clonal propagation might not benefit from the deployment of genomic information. These findings could be helpful in the context of operational breeding programs.

European Journal of Forest Research, 2016

Hybridization experiments among fir (Abies) species contribute to clarification of both crossabil... more Hybridization experiments among fir (Abies) species contribute to clarification of both crossability and evolutionary relationships of organisms at least from the second half of the nineteenth century. The main aim of our study was to find possible effects of hybridization on survival rate and two growth parameters (height and diameter at the breast height) of fir trees at various levels of complexity in the Czech Republic. We compared (1) pure species consisting of seven fir taxa, (2) open pollinated hybrids comprising of twenty-one hybrid progenies of Greek Fir (A. cephalonica), Cilician Fir (A. cilicica) and Algerian Fir (A. numidica) and (3) artificial complex hybrids of Korean Fir (A. koreana) 9 (A. cilicica 9 A. cephalonica). For our analyses, we used combination of so-called traditional statistical methods and spatial modelling. Our results revealed that a higher level of hybridization and introgression may lead to a higher survival rate and furthermore, that neglecting of spatial autocorrelation in randomized complete block design might lead to wrong conclusions-because our analyses on height showed contrasting results between traditional and spatial modelling. The results of this study appear to be a good message for scientists dealing with forest tree breeding and facing a lack of confidence by practice. They might be also a good news for forestry practice, where foresters face high mortality during afforestation, e.g. in extreme environmental conditions. Our study highlighted that neglecting spatial autocorrelation could possibly lead to wrong conclusions in studies of similar spatial scale level.

Tree Physiology, 2016

Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity... more Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity in forest trees is generally limited, yet it is essential both for various practical forestry purposes and for better understanding of broader evolutionary mechanisms. In this study, we investigated genetic variation underlying selected chlorophyll a fluorescence (ChlF) parameters in structured populations of Scots pine (Pinus sylvestris L.) grown on two sites under non-stress conditions. These parameters were derived from the OJIP part of the ChlF kinetics curve and characterize individual parts of primary photosynthetic processes associated, for example, with the exciton trapping by light-harvesting antennae, energy utilization in photosystem II (PSII) reaction centers (RCs) and its transfer further down the photosynthetic electron-transport chain. An additive relationship matrix was estimated based on pedigree reconstruction, utilizing a set of highly polymorphic single sequence repeat markers. Variance decomposition was conducted using the animal genetic evaluation mixed-linear model. The majority of ChlF parameters in the analyzed pine populations showed significant additive genetic variation. Statistically significant heritability estimates were obtained for most ChlF indices, with the exception of DI 0 /RC, φ D0 and φ P0 (F v /F m) parameters. Estimated heritabilities varied around the value of 0.15 with the maximal value of 0.23 in the ET 0 /RC parameter, which indicates electron-transport flux from Q A to Q B per PSII RC. No significant correlation was found between these indices and selected growth traits. Moreover, no genotype × environment interaction (G × E) was detected, i.e., no differences in genotypes' performance between sites. The absence of significant G × E in our study is interesting, given the relatively low heritability found for the majority of parameters analyzed. Therefore, we infer that polygenic variability of these indices is selectively neutral.