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). Source
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. Source
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. Source
Agency: Department of Agriculture | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 79.90K | Year: 2008
Hybrid poplar plantations will play a large role in the supply of cellulosic feedstock, in meeting the Nation's 30x30 goals for the renewable transportation fuels industry. The success of the poplar plantation industry will be contingent on elite plant material that has undergone hybridization for improved agronomic characteristics. Hybridization between the cottonwoods and the poplars has been the preferred method of generating elite varieties. We propose to integrate molecular tools into a traditional hybridization program to breed a new class of varieties that are capable of bio-fuels production with improved conversion economics. To accomplish this, we are currently conducting an association genetics study to identify genes controlling cellulose production in black cottonwood, based on single nucleotide polymorphisms (SNP's). We now propose a comparative study with black poplar to complete our understanding of how best to re-design a hybridization program using molecular markers and bioinformatics. A large black poplar collection will be cloned and established at two contrasting locations in the Pacific Northwest. We will sequence the same lignin and cellulose biosynthetic pathway genes identified in the black cottonwood study to discover new SNPs that can be used in a Phase II association study. The comparative study will advance our understanding of the manner in which reciprocal parental populations should be managed in a marker-assisted breeding program for improved first-generation hybridization for enhanced bio-fuels application.
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.