Wegrzyn J.L.,University of California at Davis |
Eckert A.J.,University of California at Davis |
Choi M.,University of California at Davis |
Lee J.M.,University of California at Davis |
And 6 more authors.
New Phytologist | Year: 2010
•An association genetics approach was used to examine individual genes and alleles at the loci responsible for complex traits controlling lignocellulosic biosynthesis in black cottonwood (Populus trichocarpa). Recent interest in poplars as a source of renewable energy, combined with the vast genomic resources available, has enabled further examination of their genetic diversity. •Forty candidate genes were resequenced in a panel of 15 unrelated individuals to identify single nucleotide polymorphisms (SNPs). Eight hundred and seventy-six SNPs were successfully genotyped in a clonally replicated population (448 clones). The association population (average of 2.4 ramets per clone) was phenotyped using pyrolysis molecular beam mass spectrometry. Both single-marker and haplotype-based association tests were implemented to identify associations for composite traits representing lignin content, syringyl: guaiacyl ratio and C6 sugars. •Twenty-seven highly significant, unique, single-marker associations (false discovery rate Q < 0.10) were identified across 40 candidate genes in three composite traits. Twenty-three significant haplotypes within 11 genes were discovered in two composite traits. •Given the rapid decay of within-gene linkage disequilibrium and the high coverage of amplicons across each gene, it is likely that the numerous polymorphisms identified are in close proximity to the causative SNPs and the haplotype associations reflect information present in the associations between markers. No claim to original US government works. Journal compilation © New Phytologist Trust (2010).
Guerra F.P.,University of California at Davis |
Guerra F.P.,University of Talca |
Wegrzyn J.L.,University of California at Davis |
Sykes R.,National Renewable Energy Laboratory |
And 3 more authors.
New Phytologist | Year: 2013
Black poplar (Populus nigra) is a potential feedstock for cellulosic ethanol production, although breeding for this specific end use is required. Our goal was to identify associations between single nucleotide polymorphism (SNP) markers within candidate genes encoding cellulose and lignin biosynthetic enzymes, with chemical wood property phenotypic traits, toward the aim of developing genomics-based breeding technologies for bioethanol production. Pyrolysis molecular beam mass spectrometry was used to determine contents of five- and six-carbon sugars, lignin, and syringyl : guaiacyl ratio. The association population included 599 clones from 17 half-sib families, which were successfully genotyped using 433 SNPs from 39 candidate genes. Statistical analyses were performed to estimate genetic parameters, linkage disequilibrium (LD), and single marker and haplotype-based associations. A moderate to high heritability was observed for all traits. The LD, across all candidate genes, showed a rapid decay with physical distance. Analysis of single marker-phenotype associations identified six significant marker-trait pairs, whereas nearly 280 haplotypes were associated with phenotypic traits, in both an individual and multiple trait-specific manner. The rapid decay of LD within candidate genes in this population and the genetic associations identified suggest a close relationship between the associated SNPs and the causative polymorphisms underlying the genetic variation of lignocellulosic traits in black poplar. © 2012 New Phytologist Trust.
Albers H.J.,University of Wyoming |
Busby G.M.,Greenwood Resources, Inc. |
Hamaide B.,University Faculties of Saint-Louis |
Ando A.W.,Urbana University |
Polasky S.,University of Minnesota
PLoS ONE | Year: 2016
Establishing nature reserves protects species from land cover conversion and the resulting loss of habitat. Even within a reserve, however, many factors such as fires and defoliating insects still threaten habitat and the survival of species. To address the risk to species survival after reserve establishment, reserve networks can be created that allow some redundancy of species coverage to maximize the expected number of species that survive in the presence of threats. In some regions, however, the threats to species within a reserve may be spatially correlated. As examples, fires, diseases, and pest infestations can spread from a starting point and threaten neighboring parcels' habitats, in addition to damage caused at the initial location. This paper develops a reserve site selection optimization framework that compares the optimal reserve networks in cases where risks do and do not reflect spatial correlation. By exploring the impact of spatially-correlated risk on reserve networks on a stylized landscape and on an Oregon landscape, this analysis demonstrates an appropriate and feasible method for incorporating such post-reserve establishment risks in the reserve site selection literature as an additional tool to be further developed for future conservation planning. © 2016 Albers et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PubMed | University of Minnesota, Urbana University, University Faculties of Saint-Louis, Greenwood Resources, Inc. and University of Wyoming
Type: Journal Article | Journal: PloS one | Year: 2016
Establishing nature reserves protects species from land cover conversion and the resulting loss of habitat. Even within a reserve, however, many factors such as fires and defoliating insects still threaten habitat and the survival of species. To address the risk to species survival after reserve establishment, reserve networks can be created that allow some redundancy of species coverage to maximize the expected number of species that survive in the presence of threats. In some regions, however, the threats to species within a reserve may be spatially correlated. As examples, fires, diseases, and pest infestations can spread from a starting point and threaten neighboring parcels habitats, in addition to damage caused at the initial location. This paper develops a reserve site selection optimization framework that compares the optimal reserve networks in cases where risks do and do not reflect spatial correlation. By exploring the impact of spatially-correlated risk on reserve networks on a stylized landscape and on an Oregon landscape, this analysis demonstrates an appropriate and feasible method for incorporating such post-reserve establishment risks in the reserve site selection literature as an additional tool to be further developed for future conservation planning.
Geraldes A.,University of British Columbia |
Hefer C.A.,University of British Columbia |
Capron A.,University of British Columbia |
Kolosova N.,University of British Columbia |
And 7 more authors.
Molecular Ecology | Year: 2015
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ∼100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past. © 2015 John Wiley & Sons Ltd.
Stanton B.J.,Greenwood Resources, Inc.
Silvae Genetica | Year: 2011
Eleven Populus × generosa populations were developed in the Pacific Northwest by annual controlled hybridization of P. deltoides and P. trichocarpa between 1991 and 2001. Mass selection for Melampsora leaf rust resistance was observed in the field as a threshold character in identifying seedling phenotypes for clonally replicated evaluation. The effectiveness of the approach was assessed for each annual population by comparing the distribution of phenotypes in unselected seedling populations with the distribution of selected genotypes in the clonal field tests established in successive years and evaluated at the approximate same level of disease severity using two selection thresholds corresponding to chlorotic and healthy tissue. Bi-directional selection was used as an initial check on the efficacy of the procedure and resulted in a wide separation in liability between the positive (0.06 threshold units (T. U.)) and negative (-2.45 T. U.) selection groups when tested as clones. The other 10 seedling populations that were subjected solely to directional selection exhibited a mean increase in incidence above the first selection threshold at the clonal stage (47 versus 81%) that was accompanied by an improvement in population liability (-0.06 versus 0.50 T. U.) and a reduction in population standard deviation (0.83 versus 0.54 T. U.). The change in liability was strongly related by polynomial regression to selection intensity and a grouping of populations based on infection-season precipitation r 2 = 0.98). The mean liability of four of the 10 seedling populations observed during years of high infection-season rainfall was six-fold lower than the mean liability of those populations observed during the other six years of lower infection-season rainfall (-0.12 T.U. versus -0.02 T. U., respectively), indicating that populations undergoing evaluation during years of heavy precipitation experienced more intense rust exposure. Moreover, quadratic functions showed that populations undergoing rust evaluation during years of high rainfall were more responsive to increases in selection intensity above the vertex of the function (i.e. 13.20 versus 3.43 T. U.). Realized heritability averaged 0.63 for all ten populations subjected solely to directional selection.
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 460.00K | Year: 2011
Red alder is the predominant commercial hardwood species of the Pacific Northwest. It is an early successional species that rapidly regenerates following fire or clearcutting and normally precedes the establishment of the historically preferred Douglas-fir. As such, past conifer forestry management practices were designed to speed the transition to Douglas-fir through alder eradication efforts. Consequently, today there is a critical shortage of quality alder logs at the same time the species has become highly prized in domestic and international hardwood furniture, cabinetry, and specialty product markets. Accordingly, red alder plantations are now the leading strategy to forestall the supply shortage of quality saw logs because of favorable rates of financial return in addition to their unique contribution to overall ecosystem function. The success of an alder plantation industry is contingent upon elite, well-adapted planting stock, capable of improved yields and wood quality. GreenWood Resources proposes an alder genetic improvement program that replicates its highly successful and integrated hybrid poplar genetic improvement and plantation management programs. Phase II results will lead to improved alder varieties capable of high yields, reduced risk of spring frost injury, increased site adaptability and improved wood quality. Our work will lead directly to development of GreenWood Resources' red alder nursery business. This is a necessary and important prelude to GreenWood's development of a short-rotation, high-yield alder tree farm investment fund. This fund will secure the Pacific Northwest's red alder sawmilling, lumber, furniture, door, cabinetry, and specialty products industries.
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 348.17K | Year: 2009
Highly productive, third-rotation commercial plantations have been successfully managed in the United States by the pulp and paper, timber, and the environmental-remediation industries for more than 40 years with great success in terms of wood yields and job creation. The success of the poplar plantation industry has consistently been shown to be dependent the propagation of elite varieties that have undergone hybridization and intense selection for improved agronomic characteristics. Hybrid poplar will similarly play a large role in the future supply of cellulosic energy feedstock as a key component of the Nation's 30x30 goals for the renewable transportation fuels industry. However a new class of poplar varieties of improved chemistry composition will be needed that are capable of bio-fuels manufacture with improved conversion economics. The breeding of such varieties will require the development and integration of novel molecular tools into existing traditional hybridization and varietal selection program. To accomplish this, GreenWood Resources currently conducting an association genetics study to identify genes controlling cellulose production in black cottonwood (Populus trichocarpa) based on single nucleotide polymorphisms (SNP's). We are now completing a comparative study with European black poplar (P. nigra) so as to augment GreenWood's conventional hybridization program for these two important poplar species using molecular markers and bioinformatics to improve biomass composition and the economics of liquid fuels conversion. (The goal is a re-designed reciprocal recurrent selection program for inter-sectional hybridization of P. trichocarpa and P. nigra. ) A large 612-genotype collection of P. nigra has been cloned and established at two contrasting locations in the Pacific Northwest. We have sequenced the same lignin and cellulose biosynthetic pathway genes identified in the P. trichocarpa study to discover new SNPs. We propose to: 1) Phenotype the 612 clones for an array of chemical and structural traits at each of the two locations, 2) Genotype the collection for important SNPs, and 3) Study the genotype-phenotype associations and the effect to which they interact with planting site. The comparative study in P. nigra will also provide insight into the pattern of genetic diversity between the two species from distinct sections of the genus. The comparison will also advance our understanding of the manner in which reciprocal parental populations should be managed as a marker-assisted breeding program for improved first-generation hybridization for enhanced bio-fuels application.
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 83.44K | Year: 2010
Red alder is the predominant commercial hardwood species of the Pacific Northwest. It is an early successional species that rapidly regenerates following fire or clearcutting and normally precedes the establishment of the historically preferred Douglas-fir. As such, past conifer forestry management practices were designed to speed the transition to Douglas-fir through alder eradication efforts. Consequently, a shortage of quality alder logs has materialized throughout the Pacific Northwest Range at the same time it has become highly prized by the domestic and international hardwood furniture, cabinetry, and specialty product markets where it now commands a premium price. Red alder is also viewed quite favorably for its contribution to ecosystem function in forests along the west slope of the Cascade Mountain. Accordingly, it is now a preferred species among hardwood industries and small woodlot owners' associations for the regeneration of selected forest sites. Red alder possesses abundant genetic variation that constitutes a resource with which the species can be domesticated for high-yield plantation management to forestall the supply shortage of quality sawlogs. The project will develop improved alder planting stock by achieving four objectives: (1) Combined provenance-progeny testing leading to a site specific intra-specific selective breeding program, (2) Inter-specific hybridization with white alder to capture hybrid vigor, (3) Varietal selection and testing using softwood cutting propagation to exploit the full range of genetic variation in segregating populations, and (4) Mass multiplication using in vitro propagation techniques to allow for efficient commercial deployment of elite varieties. Anticipated results include: (1) Improved alder varieties capable of high yields, reduced risk of spring frost injury, increased site adaptability and improved wood quality and (2) A complete vegetative propagation system that allows for cost-efficient varietal testing and mass multiplication of elite selections. Our work will promote GreenWood Resources' efforts to develop an alder tree farm investment fund that will secure the Pacific Northwest's hardwood sawmilling industry.
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 100.00K | Year: 2012
GreenWood Resources proposes to develop hybrid poplar growing stock of improved water-use efficiency using a strategy of species selection, inter-specific hybridization, and varietal selection. The proposed work will lead to an increase in the cost-efficiency of current sawlog production and future biomass production at GreenWood's Boardman Tree Farm. Improvement in the physiology of varietal water use efficiency will also lead to reductions in greenhouse gas emission. Moreover, growing stock of improved water use efficiency will enable short-rotation forestry as a renewable source of cellulosic energy feedstock on sites of marginal agricultural quality using low-input silviculture in targeted regions of the western United States. The water-use efficient hybrid poplar energy varieties developed in this project will initially be used in developing biomass feedstock plantation support for a local cellulosic bio-refinery.