| 1. |
- Barcala, Maximiliano Estravis, et al.
(author)
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Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species
- 2024
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In: The Plant Journal. - 0960-7412 .- 1365-313X. ; 117:3, s. 944-955
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Journal article (peer-reviewed)abstract
- Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
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| 2. |
- Calleja-Rodriguez, Ainhoa, et al.
(author)
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Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine
- 2020
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21
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Journal article (peer-reviewed)abstract
- Background Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. Results Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. Conclusions Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.
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| 3. |
- Funda, Tomas, et al.
(author)
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Determination of paternal and maternal parentage in lodgepole pine seed : full versus partial pedigree reconstruction
- 2014
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In: Canadian Journal of Forest Research. - : Canadian science publishing. - 0045-5067 .- 1208-6037. ; 44:9, s. 1122-1127
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Journal article (peer-reviewed)abstract
- Estimating seed orchards' maternal and paternal gametic contributions is of importance in assessing the genetic quality of seed crops. The advantage of full over partial pedigree reconstruction in investigating the mating dynamics in a lodgepole pine (Pinus contorta Dougl. ex. Loud. ssp. latifolia Engelm.) seed orchard population (N = 74) was demonstrated using nuclear and chloroplast microsatellite markers. We analyzed offspring of equivalent sample sizes representing full (bulk seed with unknown maternal and paternal parentage (n = 635)) and partial (11 maternal family arrays (n = 619)) pedigree reconstruction methods. Small differences in selfing rate, gene flow, and male reproductive success were observed between the two methods; however, the full pedigree reconstruction enabled simultaneous estimation of female-related fertility parameters (female reproductive success and effective number of maternal parents) that partial pedigree reconstruction could not provide. The use of bulk random sample of seed from orchards' crops is recommended when male and female fertility parameters, as well as selfing and contamination rates, are needed for seed orchards' seed crops genetic rating.
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| 4. |
- Funda, Tomas, et al.
(author)
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Genetic improvement of the chemical composition of Scots pine (Pinus sylvestrisL.) juvenile wood for bioenergy production
- 2020
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In: GCB Bioenergy. - : Wiley. - 1757-1693 .- 1757-1707. ; 12, s. 848-863
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Journal article (peer-reviewed)abstract
- Chemical composition is one of the key characteristics that determines wood quality and in turn its suitability for different end products and applications. The inclusion of chemical compositional traits in forest tree improvement requires high-throughput techniques capable of rapid, non-destructive and cost-efficient assessment of large-scale breeding experiments. We tested whether Fourier-transform infrared (FTIR) spectroscopy, coupled with partial least squares regression, could serve as an alternative to traditional wet chemistry protocols for the determination of the chemical composition of juvenile wood in Scots pine for tree improvement purposes. FTIR spectra were acquired for 1,245 trees selected in two Scots pine (Pinus sylvestrisL.) full-sib progeny tests located in northern Sweden. Predictive models were developed using 70 reference samples with known chemical composition (the proportion of lignin, carbohydrates [cellulose, hemicelluloses and their structural monosaccharides glucose, mannose, xylose, galactose, and arabinose] and extractives). Individual-tree narrow-sense heritabilities and additive genetic correlations were estimated for all chemical traits as well as for growth (height and stem diameter) and wood quality traits (density and stiffness). Genetic control of the chemical traits was mostly moderate. Of the major chemical components, highest heritabilities were observed for hemicelluloses (0.43-0.47), intermediate for lignin and extractives (0.30-0.39), and lowest for cellulose (0.20-0.25). Additive genetic correlations among chemical traits were, except for extractives, positive while those between chemical and wood quality traits were negative. In both groups (chemical and wood quality traits), correlations with extractives exhibited opposite signs. Correlations of chemical traits with growth traits were near zero. The best strategy for genetic improvement of Scots pine juvenile wood for bioenergy production is to decrease and stabilize the content of extractives among trees and then focus on increasing the cellulose:lignin ratio.
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| 5. |
- Funda, Tomas, et al.
(author)
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Low rates of pollen contamination in a Scots pine seed orchard in Sweden : the exception or the norm?
- 2015
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In: Scandinavian Journal of Forest Research. - : Informa UK Limited. - 0282-7581 .- 1651-1891. ; 30:7, s. 573-586
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Journal article (peer-reviewed)abstract
- We investigated mating structure and gene flow in a clonal seed orchard of Scots pine (Pinus sylvestris L.) over three consecutive pollination seasons (2010-2012) with nine nuclear microsatellite markers. The paternity of 1991 offspring from four maternal parents was assigned to 28 candidate fathers using an exclusion procedure and a likelihood-based method implemented in the program CERVUS. Relative reproductive success was highly variable among pollen parents but consistent across years and ranged from 0.1% to 18.3%. Consequently, the seed crops' effective number of fathers was reduced to 52.9%, 48.8%, and 45.7% of the census in the three seasons, respectively. Self-fertilization fluctuated around the orchard's expected value of 5.1%, reaching 4.05%, 7.71%, and 6.61%, respectively. Pollen contamination was estimated to be 5.64%, 7.29%, and 4.89%, respectively, after correction for cryptic gene flow. CERVUS provided similar results as the exclusion method, but estimates greatly varied depending on the input parameters, mainly the proportion of fathers sampled. These results indicate the studied seed orchard is a well-functioning production population with only minor negative effects of self-fertilization and pollen contamination on the quality of seed crops. Genotyping issues associated with microsatellites as a potential source of false paternity assignment and exclusion are discussed.
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| 6. |
- Funda, Tomas, et al.
(author)
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Mating dynamics of Scots pine in isolation tents
- 2016
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In: Tree Genetics & Genomes. - : Springer Berlin/Heidelberg. - 1614-2942 .- 1614-2950. ; 12:6
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Journal article (peer-reviewed)abstract
- Seed orchards are forest tree production populations for supplying the forest industry with consistent and abundant seed crops of superior genetic quality. However, genetic quality can be severely affected by non-random mating among parents and the occurrence of background pollination. This study analyzed mating structure and background pollination in six large isolation tents established in a clonal Scots pine seed orchard in northern Sweden. The isolation tents were intended to form a physical barrier against background pollen and induce earlier flowering relative to the surrounding trees. We scored flowering phenology inside and outside the tents and tracked airborne pollen density inside and outside the seed orchard in three consecutive pollination seasons. We genotyped 5683 offspring collected from the tents and open controls using nine microsatellite loci, and assigned paternity using simple exclusion method. We found that tent trees shed pollen and exhibited maximum female receptivity approximately 1 week earlier than trees in open control. The majority of matings in tents (78.3 %) occurred at distances within two trees apart (about 5 m). Self-fertilization was relatively high (average 21.8 %) in tents without supplemental pollination (SP), but it was substantially reduced in tents with SP (average 7.7 %). Pollen contamination was low in open controls (4.8-7.1 %), and all tents remained entirely free of foreign pollen. Our study demonstrates that tent isolation is effective in blocking pollen immigration and in manipulating flowering phenology. When complimented with supplemental pollination, it could become a useful seed orchard management practice to optimize the gain and diversity of seed orchard crops.
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| 7. |
- Funda, Tomas, et al.
(author)
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Predicting the chemical composition of juvenile and mature woods in Scots pine (Pinus sylvestris L.) using FTIR spectroscopy
- 2020
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In: Wood Science and Technology. - : Springer. - 0043-7719 .- 1432-5225. ; 54, s. 289-311
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Journal article (peer-reviewed)abstract
- The chemical composition of wood is one of the key features that determine wood quality. The focus of this study was on identifying differences between juvenile and mature woods in Scots pine (Pinus sylvestris L.) and developing models for predicting the chemical composition of these two wood types. Chemical traits, determined by traditional wet chemistry techniques, included the proportion of lignin, polysaccharides and extractives. Partial least squares regression of Fourier transform infrared (FTIR) spectra was used for model building. The model performance was primarily evaluated by root mean squared error of predictions (RMSEP). High predictive power was attained for the content of lignin (RMSEP of 0.476 and 0.495 for juvenile and mature woods, respectively) and extractives (0.302 and 0.471), good predictive power for cellulose (0.715 and 0.696) and hemicelluloses in juvenile wood (0.719) and low predictive power for hemicelluloses in mature wood (0.823). A distinct band was observed at 1693 cm(-1), and its intensity was strongly associated with the content of extractives (r = 0.968 and 0.861 in juvenile and mature woods, respectively). FTIR has proved suitable for the rapid, non-destructive, cost-efficient assessment of the chemical composition of juvenile and mature woods in Scots pine. The band at 1693 cm(-1) is to be further investigated to unravel its link with individual extractive components.
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| 8. |
- Fundová, Irena, et al.
(author)
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Non-Destructive Assessment of Wood Stiffness in Scots Pine (Pinus sylvestris L.) and its Use in Forest Tree Improvement
- 2019
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In: Forests. - : MDPI AG. - 1999-4907. ; 10
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Journal article (peer-reviewed)abstract
- Wood stiffness is an important wood mechanical property that predetermines the suitability of sawn timber for construction purposes. Negative genetic correlations between wood stiffness and growth traits have, however, been reported for many conifer species including Scots pine. It is, therefore, important that breeding programs consider wood stiffness and growth traits simultaneously. The study aims to (1) evaluate different approaches of calculating the dynamic modulus of elasticity (MOE, non-destructively assessed stiffness) using data from X-ray analysis (SilviScan) as a benchmark, (2) estimate genetic parameters, and (3) apply index selection. In total, we non-destructively measured 622 standing trees from 175 full-sib families for acoustic velocity (VEL) using Hitman and for wood density (DEN) using Resistograph and Pilodyn. We combined VEL with different wood densities, raw (DENRES) and adjusted (DENRES.TB) Resistograph density, Pilodyn density measured with (DENPIL) and without bark (DENPIL.B), constant of 1000 kg.m(-3) (DENCONST), and SilviScan density (DENSILV), to calculate MOEs and compare them with the benchmark SilviScan MOE (MOESILV). We also derived Smith-Hazel indices for simultaneous improvement of stem diameter (DBH) and wood stiffness. The highest additive genetic and phenotypic correlations of the benchmark MOESILV with the alternative MOE measures (tested) were attained by MOEDENSILV (0.95 and 0.75, respectively) and were closely followed by MOEDENRES.TB (0.91 and 0.70, respectively) and MOEDENCONST and VEL (0.91 and 0.65, respectively for both). Correlations with MOEDENPIL, MOEDENPIL.B, and MOEDENRES were lower. Narrow-sense heritabilities were moderate, ranging from 0.39 (MOESILV) to 0.46 (MOEDENSILV). All indices revealed an opportunity for joint improvement of DBH and MOE. Conclusions: MOEDENRES.TB appears to be the most efficient approach for indirect selection for wood stiffness in Scots pine, although VEL alone and MOEDENCONST have provided very good results too. An index combining DBH and MOEDENRES.TB seems to offer the best compromise for simultaneous improvement of growth, fiber, and wood quality traits.
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| 9. |
- Fundová, Irena, et al.
(author)
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Non-destructive wood density assessment of Scots pine (Pinus sylvestris L.) using Resistograph and Pilodyn
- 2018
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13
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Journal article (peer-reviewed)abstract
- We tested two methods for non-destructive assessment of wood density of Scots pine standing trees: one based on penetration depth of a steel pin (Pilodyn) and the other on micro-drilling resistance (Resistograph). As a benchmark we used wood density data from x-ray analysis (SilviScan). We assessed in total 622 trees of 175 full-sib families growing in a single progeny test. Pilodyn was applied with bark (PIL) and without bark (PILB). Raw Resistograph drilling profiles (RES) were adjusted (RESTB) in order to eliminate increasing trend caused by needle friction. Individual narrow-sense heritability of benchmark SilviScan density (DEN; 0.46) was most closely approached by that of adjusted RESTB (0.43). Heritabilities were lower for unadjusted RES (0.35) as well as for PIL and PILB (both 0.32). Additive genetic correlations of the benchmark DEN with RES, RESTB, PIL and PILB were 0.89, 0.96, 0.59 and 0.71, respectively. Our results suggest that Resistograph is a more reliable tool than Pilodyn for wood density assessment of Scots pine; however, we highly recommend adjusting Resistograph drilling profiles prior to further analyses.
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| 10. |
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