| 1. |
- Funda, Tomas, et al.
(författare)
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Mating dynamics of Scots pine in isolation tents
- 2016
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Ingår i: Tree Genetics & Genomes. - : Springer Berlin/Heidelberg. - 1614-2942 .- 1614-2950. ; 12:6
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Tidskriftsartikel (refereegranskat)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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| 2. |
- Torimaru, Takeshi, et al.
(författare)
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Evaluation of pollen contamination in an advanced Scots pine seed orchard in Sweden
- 2009
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Ingår i: Silvae Genetica. - : J.D. Sauerländer's Verlag. - 0037-5349 .- 2509-8934. ; 58:5-6, s. 262-269
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Tidskriftsartikel (refereegranskat)abstract
- The pollination pattern in a Scots pine (Pinus sylvestris L.) seed orchard consisting of 28 clones was studied using nine microsatellite (SSR) loci. The nine SSR loci produced unique multilocus genotypes for each of the orchard's 28 clones and allowed paternal assignment of the studied 305 seed using paternity exclusion probability of 99.9%. Fifty two percent of the studied seeds were sired by outside the orchard pollen sources (i.e., pollen contamination) and as expected, low selfing (2.3%) was detected. These results are valuable for the evaluation of the seed orchard function and the impact of contamination on the expected genetic gain.
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| 3. |
- Borthakur, Dulal, et al.
(författare)
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Current status and trends in forest genomics
- 2022
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Ingår i: Forestry Research. - : Maximum Academic Press. - 2767-3812. ; 2
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Forskningsöversikt (refereegranskat)abstract
- Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.
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| 4. |
- Chen, Xinyu, et al.
(författare)
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Variations in electrical impedance and phase angle among seedlings of Pinus densata and parental species in Pinus tabuliformis habitat environment
- 2015
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Ingår i: Journal of Forestry Research. - : Northeast Forestry University. - 1007-662X .- 1993-0607. ; 26:3, s. 777-783
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Tidskriftsartikel (refereegranskat)abstract
- Electrical impedance (EI) and phase angle (PHI) parameters in AC impedance spectroscopy are important electrical parameters in the study of medical pathology. However, little is known about their application in variation and genetic relationship studies of forest trees. In order to test whether impedance parameters could be used in genetic relationship analysis among conifer species, EI and PHI were measured in a seedling experiment test composed of Pinus tabuliformis, Pinus yunnanensis, and Pinus densata in a habitat of Pinus tabuliformis. The results showed that variations in both EI and PHI among species were significant in different electric frequencies, and the EI and PHI values measured in the two populations of P. densata were between the two parental species, P. yunnanensis and P. tabuliformis. These results show that these two impedance parameters could reflect the genetic relationship among pine species. This was the first time using the two AC impedance spectroscopy parameters to test the genetic relationship analysis between tree species, and would be a hopeful novel reference methodology for future studies in evolution and genetic variation of tree species.
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| 5. |
- Funda, Tomas, et al.
(författare)
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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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Ingår i: Scandinavian Journal of Forest Research. - : Informa UK Limited. - 0282-7581 .- 1651-1891. ; 30:7, s. 573-586
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Tidskriftsartikel (refereegranskat)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. |
- Hall, David, 1974-, et al.
(författare)
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Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing
- 2020
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Ingår i: Heredity. - : Nature Publishing Group. - 0018-067X .- 1365-2540. ; 124:5, s. 633-646
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Tidskriftsartikel (refereegranskat)abstract
- Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.
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| 7. |
- Hall, David, 1974-, et al.
(författare)
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The effect of gene flow on frost tolerance in Scots pine – Latitudinal translocation of genetic material
- 2023
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Ingår i: Forest Ecology and Management. - : Elsevier. - 0378-1127 .- 1872-7042. ; 544
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Tidskriftsartikel (refereegranskat)abstract
- Extensive gene flow can be detrimental to local adaptation and similarly, forestry seed sources such as seed orchards can be heavily influenced by external pollination, especially if the orchard material has been translocated a great distance. Here we conducted a coordinated genotyping-phenotyping study to examine how external pollination events and fecundity variation in a Pinus sylvestris seed orchard influence the genetic composition and the seed-lots’ autumn frost hardiness when genetic material had been translocated 630 km south. The results were then compared to those of a in situ established seed orchard. We genotyped and phenotype >1000 seedlings from these orchards, and constructed their pedigrees and scored their autumn frost tolerance in a controlled climate chamber environment. The hardiness scores were compared with a reference of nine natural stands along a latitudinal cline. We find substantial variation in fecundity and external pollination over crop years, thus unpredictable genetic composition because the contribution of some orchard clones is high in one crop but low in another. We observed that seedlings produced by mating among orchard genotypes were less hardy than expected (corresponding to an origin of −0.6°N) but the opposite in externally pollinated seedlings (+0.3 to +0.7°N). The freeze damage levels reflect the origin of parental genotypes, but to a smaller degree than expected (13% lower than expected damage levels for externally pollinate seedlings and 21% greater damage levels for internally pollinates seedlings). These results suggest that orchard parents’ origins, mating composition and orchard local environment could all affect the seed crops’ quality and their climate adaptation. Seed orchard crops are the key to realize the gain in forestry from breeding efforts. However, genetic monitoring of seed crops is necessary to improve the performance of seed orchards further and adjust deployment areas of seed crops in a timely manner for a more dynamic forestry, considering climate change and biodiversity demands.
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| 8. |
- Han, Xue-Min, et al.
(författare)
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Evolution and Function of the Populus SABATH Family Reveal That a Single Amino Acid Change Results in a Substrate Switch
- 2018
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Ingår i: Plant and Cell Physiology. - : Oxford University Press. - 0032-0781 .- 1471-9053. ; 59:2, s. 392-403
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Tidskriftsartikel (refereegranskat)abstract
- Evolutionary mechanisms of substrate specificities of enzyme families remain poorly understood. Plant SABATH methyltransferases catalyze methylation of the carboxyl group of various low molecular weight metabolites. Investigation of the functional diversification of the SABATH family in plants could shed light on the evolution of substrate specificities in this enzyme family. Previous studies identified 28 SABATH genes from the Populus trichocarpa genome. In this study, we re-annotated the Populus SABATH gene family, and performed molecular evolution, gene expression and biochemical analyses of this large gene family. Twenty-eight Populus SABATH genes were divided into three classes with distinct divergences in their gene structure, expression responses to abiotic stressors and enzymatic properties of encoded proteins. Populus class I SABATH proteins converted IAA to methyl-IAA, class II SABATH proteins converted benzoic acid (BA) and salicylic acid (SA) to methyl-BA and methyl-SA, while class III SABATH proteins converted farnesoic acid (FA) to methyl-FA. For Populus class II SABATH proteins, both forward and reverse mutagenesis studies showed that a single amino acid switch between PtSABATH4 and PtSABATH24 resulted in substrate switch. Our findings provide new insights into the evolution of substrate specificities of enzyme families.
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| 9. |
- Heuchel, Alisa, 1990-
(författare)
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Game of crops : genetic composition and adaptation of seed orchard crops
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Orchard populations are artificial and intensively managed populations of elite, best-performing trees that are established for mass production of genetically improved seeds. Seed orchards connect cycles of selection, breeding, and testing of plus-trees with the deployment of the improved seeds at the operational plantations. Long reproductive cycles and rotation age, irregular flowering of trees pose serious threats to the economic success of tree breeding and urge efficiency monitoring. This thesis describes genetic functioning of Swedish seed orchard of Scots pine and Norway spruce, diversity levels of orchard crops, their performance in the field in connection with their genetic background, and possible ways to stimulate flowering. It is especially relevant now when molecular technologies became more affordable and allow more intensive sampling and genome coverage.We detected differences between the two species in all genetic parameters and higher diversity levels in Scots pine crops. Crop diversity was at acceptable level though slightly reduced compared to reference population. We detected great variation in flowering in orchard parents, and the influence of linear deployment strategy on diversity, reproductive success, and effective number of orchard parents. Frost tolerance of a crop depended on the origin of orchard parents but up to a smaller extent than was previously expected.Seedlings orchard crops perform well in the field, and do not suffer from increased mortality while their counterparts from controlled crosses have variable performance and tend to form G-by-E interactions. Overall, selected seed sources perform better than forest seed lots, and this superiority is independent from the silvicultural methods at the between-sites level. Site preparation methods and planting positions play a larger role at each location and may enhance survival and growth. Seed weight correlates positively with height, while diameter is more affected by the planting position.Topgrafting showed varying degree of success but efficiently reduced time to flowering to 1 year after the grafting procedure. The extent of male and female flowering was dramatically different, and for satisfactory cone crops, there is a great need in the application of flowering stimulation methods.This is a first systematic attempt to analyse genetic background of mating and population structure of several crops from different orchards of the two species. It describes the success of Swedish tree breeding strategy in conserving genetic diversity, improving survival and economic traits, and provides the assessment of linear deployment strategy with the advanced molecular techniques. We emphasize the urgent need to efficiently stimulate flowering in both species for securing orchard production and balanced genetic composition.
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| 10. |
- Heuchel, Alisa, et al.
(författare)
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Genetic diversity and background pollen contamination in Norway spruce and Scots pine seed orchard crops
- 2022
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Ingår i: Forestry Research. - : Maximum Academic Press. - 2767-3812. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (HO) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher HO and BPC than spruce. BPC in pine crops varied from 87% at young orchard age to 12% at mature age, wherease this rate ranged between 27%−4% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30%−50% parents contibuting to 80% of the progeny. Selfing was low (2%−6%) in all seed crops. Compared to natural stands, orchard crops had slightly lower HO but no strong signal of inbreeding. Our results provide valuable references for orchard management.
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