Progress 09/15/07 to 09/14/12
Outputs
OUTPUTS: Obj. 1: 7123 loblolly and slash pines have been genotyped for 5380 SNPs (NCSU, TAMU, UFL). These genotypes have been used both for detection of associations with traits measured in previous studies and for newly measured traits, as well as for early evaluation of genomic selection methods. For Douglas-fir (OSU) the number of potential new SNPs found in all libraries was 278,979. A SNP array containing 8,769 ATBs was constructed and 5965 were found polymorphic and used to genotype 288 trees. Data are available at the CTGN link at http://dendrome.ucdavis.edu/resources/ downloads.php. Obj. 2: The tree breeding cycle was analyzed to determine the points at which MIB could be applied and then to define the manner in which MIB may be applied (i.e., forward or backward selection, informed breeding, informed project management applications, etc.). A manuscript is in preparation. A second approach was development of simulation software with Excel add-in Simetar to illustrate possible implementations of MIB and show how Monte Carlo simulation can be used to rank alternative breeding plans by expected economic returns. Obj. 3: A Plone content management system (Dendrome Plone) has been implemented for CTGN project content. Included at this location are updates of data, presentations, and education and extension activities. Genotype data delivered from Illumina are accumulated in the TreeGenes relational database and integrated with the available phenotypic data: the DNA Inventory/Sample Tracking Interface' component is currently receiving the final phenotypic information for Douglas-fir and slash pine and the full phenotypes collected for loblolly pine have been uploaded to the databases and stored within TreeGenes. Obj. 4: There are three components to the stock center: (1) the Loblolly Pine Genetic Stock Center, a clonal archive at the Southern Institute of Forest Genetics, Southern Research Station near Saucier, Mississippi, (2) the Douglas-Fir Genetic Stock Center, a clonal archive at the Pacific Northwest Research Station near Corvallis, Oregon, and (3) the UC Davis Molecular Genetic Stocks Center, comprised of DNA stored in -80 degree C freezers. The latter is now served by a website: http://dendrome.ucdavis.edu/ftgsc/. Objs. 5 and 6: CTGN investigators published on-line a suite of new teaching modules, offered as part of the Plant Breeding and Genomics Community of Practice with eXtension and designed to serve as complementary teaching aids for University instructors or as stand-alone lessons for students, practitioners, or laypeople. The full list of modules can be found at http://www.extension. org/pages/60370/. The many training opportunities offered during the project are noted in the Participants block below. During the life of the project, PD and co-PDs delivered approximately 100 outreach presentations, including invited talks, class lectures, posters, talks to professional societies and at conferences. These are listed at the CTGN website at the Education and Extension page. Five editions of the CTGN newsletter were produced and all are available at the Reports page of the CTGN website. PARTICIPANTS: Opportunities for Training and Development Curriculum development Spring quarter, 2011, UC Davis: "Introduction to Forest Biology" - (ECL 298), developed by PD David Neale and targeted graduate students. Syllabus available at CTGN website/Education and Extension/Curriculum development page. Spring quarter, 2010, UC Davis: "Complex trait dissection and methods in marker-assisted breeding" (GGG 298), developed by PD David Neale and targeted graduate students. Winter quarter, 2009, OSU: "Association Genetics and Breeding" (3 quarter credits), organized and taught by co-PDs David Harry and Glenn Howe and featured guest lectures from PDs within the Conifer, Wheat, Barley, and Solanaceae CAP projects. Attended by 10 graduate students representing Forestry (4), Crop and Soil Science (3), Horticulture (1), and Animal Science (2). Course structure included 13 lectures (80 minutes), 3 class periods featuring data and software exercises, and 3 class periods for discussion topics. Fall quarter, 2009, NCSU: "Quantitative Forest Genetics Methods" (FOR 728), developed and taught by co-PD Fikret Isik, incorporated genomics-based selection using mixed models. Workshops and symposia June 26, 2011, Brazil: A one-day genomic selection workshop, offered to 90 participants by co-PDs Fikret Isik and Ross Whetten prior to the IUFRO 2011 Tree Biotechnology Conference - "From genomes to integration and delivery". June 22-24, 2011, UC Davis: CTGN investigators planned, hosted, and participated in a 3-day international symposium, largely dedicated to genomic-based breeding in forest trees. 64 attendees. May 16-20, 2011, NCSU: The 5-day workshop "Genetic Data Analysis in Forest Tree Breeding", offered to 19 participants, including scientists from Korea and Chile, teaching statistical methods for analysis of progeny test data and applications of molecular marker genotypes to tree breeding. Organized by co-PD Fikret Isik and taught by Isik, co-PD Ross Whetten, and others. July 13-14, 2010: The two-day workshop "Genomics for applied tree breeding and ecosystem management: Application in gene conservation and climate change" was held at the USFS Dorena Genetic Resource Center, Cottage Grove OR and tailored to the needs of government service individuals and well attended (22 persons) with representation from state and regional BLM and USFS offices (12), University Extension Research groups (2), private company breeders (2), and University scientists (3) and graduate students (2) from Oregon, Washington, California, Colorado, and Hawaii. June 15-19, 2009, UC Davis: Genomics shortcourse, with 24 participants, representing seven countries. The shortcourse consisted of ten modules (54 to 110 slides in length), six of which featured exercises allowed manipulation of data sets in relevant genomics software applications. Trainees NCSU, graduate student Jaime Zapata, research assistant Joshua Steiger, and Harold Mackin (2006 FFA Agriscience Teacher of the Year). Univ. of Florida, grad student Patricio Munoz. TAMU, grad students Tomasz Koralewski and Vikram Chhatre. Internships Katie Coates, lab tech, WSU Puyallup Research and Extension Station. Vikram Chhatre, grad student, TAMU. TARGET AUDIENCES: The target audience for the education and extension efforts of this project are cooperative tree improvement associations, breeders, the general public, academics, and students of forestry and genetics, primarily at the undergraduate and graduate levels. The primary vehicles for outreach to these groups are presentations by CTGN project personnel at conferences and in classrooms, workshops, conferences, electronically distributed newsletters, and a publicly available website (http://dendrome.ucdavis.edu/ctgn/). PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The SNP data generated by the project and the tools and protocols for using them in breeding programs have been demonstrated and delivered to breeding coops beginning a transition phase where these programs can now use genome-wide SNP data for genomic selection in addition to traditional phenotypic selection. CTGN extension and education activities were the subject of ongoing research by the external evaluation consultant, Michael Coe of Cedar Lake Research Group in Portland OR. He conducted industry-wide surveys of tree improvement programs, interviewed tree improvement coop directors and staff members, and gathered feedback from participants in CTGN-sponsored events and workshops. In the final year, tree improvement coop member representatives and staff members completed a questionnaire about marker-informed methods in tree improvement and coop directors were interviewed on the status of marker-informed methods in the field. This information was analyzed and a final report was produced. Highlights of this report include the following points: Coop directors were uniformly positive about the CTGN contribution to research and development in marker-informed conifer breeding, as well as the enhanced communication and collaboration among researchers and breeders that was spurred by the project. Most of the programs are making long-term (e.g., 5-year) plans and investments aimed at restructuring their breeding populations or other operations in order to facilitate the use of more advanced marker-informed methods. These include designing crosses with complementary traits, accelerated introgression of alleles from different species, and improved efficiency in selection using specific markers or genomic (genome-wide) selection models. Some of these applications will require maintaining newly planted populations over time spans of many years before they are fully operational. There is need for more markers, implying that the basic research related to discovery and validation of markers will require more funding and more effort in order to complete the foundation needed for operational applications. Ancillary tools such as bioinformatics databases and software for statistical analysis, along with trained professionals to work with these large datasets, are also needed. Breeding programs face decisions about the extent to which they attempt to acquire and build these resources within their own operations vs. outsourcing to commercial vendors vs. "outsourcing" to collaborative partnerships. Structural changes in the wood products industry make it increasingly difficult for private industry to fund breeding and tree improvement programs generally, including both traditional and genomic approaches, since these represent long-term investments in an industry that is increasingly focused on near-term returns. New forms of public-private partnerships may be needed in order to realize the potential of 21st century conifer tree breeding and forest management.
Publications
- Lorenz WW, Ayyampalayam S, Bordeaux JM, Howe GT, Jermstad KD, Neale DB, Rogers DL, and Dean JFD. 2012. Conifer DBMagic: A database housing multiple de novo transcriptome assemblies for 12 diverse conifer species. Tree Genetics and Genomes. Online. DOI 10.1007/s11295-012-0547-y
- Munoz Del Valle PR, Huber DA, and Martin TA. 2012. Relative contributions of crown and phenological traits to growth of a pseudo-backcross pine family ((slash x loblolly) x slash) and its pure species progenitors. Tree Genetics and Genomes. Online. DOI 10.1007/s11295-012-0514-7.
- Zapata-Valenzuela J, Isik F, Maltecca C, Wegryzn J, Neale D, McKeand S, and Whetten R. 2012. SNP markers trace familial linkages in a cloned population of Pinus taeda--prospects for genomic selection. Tree Genetics and Genomes. Online: DOI 10.1007/s11295-012-0516-5.
- Neale D. 2011. Genomics-based breeding in forest trees: Are we there yet BMC Proceedings 5(Suppl 7):14.
- Munoz Del Valle PR, Huber DA, and Butnor, JR. 2011. Phenotypic analysis of first-year traits in a pseudo-backcross {(slash x loblolly) x slash} and the open-pollinated families of the pure-species progenitors. Tree Genetics and Genomes 7:183-192.
- Wheeler N, Harry D. 2012. Introduction [Online Module 1]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60371/conifer-translational-genomics- network-online-module-1:-introduction]
- Wheeler N, Harry D. 2012. Genes, genomes, and Mendel [Online Module 2]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60372/conifer-translational-genomics- network-online-module-2:-genes-genomes-and-mendel]
- Wheeler N, Harry D. 2012. Population genetics [Online Module 3]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60376/conifer-translational-genomics- network-online-module-3:-population-genetics]
- Wheeler N, Harry D. 2012. Quantitative genetics [Online Module 4]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60384/conifer-translational-genomics- network-online-module-4:-quantitative-genetics]
- Wheeler N, Harry D. 2012. Introduction to tree breeding and provenance trials [Online Module 5]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60383/conifer-translational-genomics- network-online-module-5:-introduction-to-tree-breeding-and-provenance ]
- Wheeler N, Wegrzyn J, Harry D. 2012. Genetic markers [Online Module 6]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60385/conifer-translational-genomics- network-online-module-6:-genetic-markers]
- Wheeler N, Harry D. 2012. Measuring, organizing, and interpreting marker variation [Online Module 7]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60386/conifer-translational-genomics- network-online-module-7:-measuring-organizing-and-interpreting-marker ]
- Wheeler N, Harry D. 2012. Genetic mapping [Online Module 8]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60392/conifer-translational-genomics- network-online-module-8:-genetic-mapping]
- Wheeler N, Harry D. 2012. Mapping quantitative trait loci (QTL) [Online Module 9]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60395/conifer-translational-genomics- network-online-module-9:-mapping-quantitative-trait-loci-qtl]
- Wheeler N, Harry D. 2012. Linkage disequilibrium [Online Module 10]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60394/conifer-translational-genomics- network-online-module-10:-linkage-disequilibrium]
- Wheeler N, Harry D. 2012. Association genetics [Online Module 11]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/60393/conifer-translational-genomics- network-online-module-11:-association-genetics]
- Wheeler N. 2012. Marker informed breeding - program management [Online Module 12]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. Available at [http://www.extension.org/pages/61071/conifer-translational-genomics- network-online-module-12:-marker-informed-breeding-program-management ]
- Wheeler N. 2012. Association discovery and evaluation [Online Module 13]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/61072/conifer-translational-genomics- network-module-13:-marker-information-breeding-association-discovery- a]
- Isik F. 2012. Using markers to predict breeding values [Online Module 14]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/63412/conifer-translational-genomics- network-online-module-14:-using-markers-to-predict-breeding-values]
- Whetten R. 2012. Genomic selection [Online Module 15]. Genomics in Tree Breeding and Forest Ecosystem Management, Conifer Translational Genomics Network. eXtension Foundation. [http://www.extension.org/pages/63413/conifer-translational-genomic-n etwork-online-module-15:-genomic-selection]
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Progress 09/15/10 to 09/14/11
Outputs
OUTPUTS: This project was superseded by CA-D-PLS-2038-CG. Output for Project year 2 (Sept. 1, 2010 through August 31, 2011): Obj. 1: 7123 loblolly and slash pines have been genotyped for 5380 SNPs (NCSU, TAMU, UFL). These genotypes have been used both for detection of associations with traits measured in previous studies and for newly measured traits, as well as for early evaluation of genomic selection methods. For Douglas-fir (OSU) the number of potential new SNPs found in all libraries was 450,483. A SNP array containing 9000 ATBs is now under construction and will be used to genotype 1152 trees. Data and phenotypes available at TreeGenes (http://dendrome.ucdavis.edu/treegenes/). Obj. 2: The tree breeding cycle was analyzed to determine the points at which MIB could be applied and then to define the manner in which MIB may be applied (i.e., forward or backward selection, informed breeding, informed project management applications, etc.). A manuscript is in preparation. A second approach was development of simulation software with Excel add-in Simetar to illustrate possible implementations of MIB and show how Monte Carlo simulation can be used to rank alternative breeding plans by expected economic returns. Obj. 3: A Plone content management system (Dendrome Plone) has been implemented for CTGN project content. Included at this location are updates of data, presentations, and education and extension activities. Genotype data delivered from Illumina are accumulated in the TreeGenes relational database and integrated with the available phenotypic data: the DNA Inventory/Sample Tracking Interface' component is currently receiving the final phenotypic information for Douglas-fir and slash pine and the full phenotypes collected for loblolly pine have been uploaded to the databases and stored within TreeGenes. Obj. 4: There are three components to the stock center: (1) the Loblolly Pine Genetic Stock Center, a clonal archive at the Southern Institute of Forest Genetics, Southern Research Station near Saucier, Mississippi, (2) the Douglas-Fir Genetic Stock Center, a clonal archive at the Pacific Northwest Research Station near Corvallis, Oregon, and (3) the UC Davis Molecular Genetic Stocks Center, comprised of DNA stored in -80 degree C freezers. The latter is now served by a website: http://dendrome.ucdavis.edu/ftgsc/. Objs. 5 and 6: CTGN investigators published on-line a suite of new teaching modules, offered as part of the Plant Breeding and Genomics Community of Practice with eXtension and designed to serve as complementary teaching aids for University instructors or as stand-alone lessons for students, practitioners, or laypeople. The full list of modules can be found at http://www.extension. org/pages/60370/. In this project year, PD and co-PDs delivered approximately 26 outreach presentations, including invited talks, class lectures, posters, talks to professional societies and at conferences. These are listed at the CTGN website at the Education and Extension page. A fourth edition of the CTGN newsletter was released in March, 2011 and is available at the Reports page of the CTGN website. PARTICIPANTS: Spring quarter, 2011: At UC Davis, , the course "Introduction to Forest Biology" - (ECL 298), was developed by PD David Neale, and targeted graduate students. The course syllabus is available at the CTGN website at the Education and Extension/Curriculum development page. May 16-20, 2011: The 5-day workshop "Genetic Data Analysis in Forest Tree Breeding" was offered to 19 participants, including scientists from Korea and Chile, teaching statistical methods for analysis of progeny test data and applications of molecular marker genotypes to tree breeding. It was organized by CTGN co-PD Fikret Isik and taught by Isik, co-PD Ross Whetten, and two colleagues at NCSU. June 22-24, 2011: CTGN investigators planned, hosted, and participated in a 3-day international symposium, largely dedicated to genomic-based breeding in forest trees, held at UC Davis. There were 64 attendees. June 26, 2011: A one-day genomic selection workshop was offered to 90 participants by PDs Isik and Whetten in Brazil prior to the IUFRO 2011 Tree Biotechnology Conference - "From genomes to integration and delivery". TARGET AUDIENCES: The target audience for the education and extension efforts of this project are cooperative tree improvement associations, breeders, the general public, academics, and students of forestry and genetics, primarily at the undergraduate and graduate levels. The primary vehicles for outreach to these groups are presentations by CTGN project personnel at conferences and in classrooms, workshops, conferences, electronically distributed newsletters, and a publicly available website. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The SNP data generated by the project and the tools and protocols for using them in breeding programs have been demonstrated and delivered to breeding coops leading to the beginning of a transition phase where these programs can now use genome-wide SNP data for genomic selection in addition to traditional phenotypic selection. CTGN extension and education activities were the subject of ongoing research by our external evaluation consultant, Michael Coe of Cedar Lake Research Group in Portland, Oregon. There have been industry-wide surveys of tree improvement programs, interviews with tree improvement coop directors and staff members, and feedback gathered from participants in CTGN-sponsored events and workshops. In summer 2011, tree improvement coop member representatives and staff members were offered a chance to contribute their current thoughts and recommendations about future directions by completing a questionnaire about marker-informed methods in tree improvement; coop directors were invited to participate in interviews on the status of marker-informed methods in the field. This information is under analysis.
Publications
- Neale D (2011) Genomics-based breeding in forest trees: Are we there yet BMC Proceedings 5(Suppl 7):14.
- Jayawickrama KJS, Ye TZ, and Howe GT (2011) Heritabilities, intertrait genetic correlations, GxE interaction and predicted genetic gains for acoustic velocity in mid-rotation coastal Douglas-fir. Silvae Genet. 60:1-18.
- Munoz Del Valle PR, Huber DA, and Butnor, JR (2011) Phenotypic analysis of first-year traits in a pseudo-backcross {(slash x loblolly) x slash} and the open-pollinated families of the pure-species progenitors. Tree Genetics and Genomes 7:183-192.
- Echt CS, Saha A, Krutovsky KV, Wimalanathan K, Erpelding JE, Liang C, and Nelson CD (2011) An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genetics 12:17.
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Progress 09/15/09 to 09/14/10
Outputs
OUTPUTS: This project has been superseded by CA-D-PLS-2038-CG and the continued progress under that designation has been reported in an AD-421 for that project. At the close of year 2 under the CA-D*-PLS-7716-CG project designation, the following accomplishments were achieved: Obj. 1: Pipelines were established for sample collection, high-throughput DNA isolation, and submission for genotyping for the loblolly pine, slash pine, and douglas-fir populations. By the end of the second year, most of the loblolly pine samples had been processed, the slash pine and douglas-fir work was underway. Obj. 2: Progress was made on two fronts: conceptualization and graphical description of the logistical nature of MAS implementation in the tree breeding cycle, and the creation of an analytical tool for conducting stochastic simulation of tree breeding alternatives using MAS, the objective of which is to provide economic insights on probability of success (financial return) for an array of tree breeding scenarios. Obj. 3: The project Plone Website had been initiated, a DNA inventory system for integration into the Treegenes database was in place, and a custom LIMS was in place to guide the integration of samples into the DNA isolation stream. Obj. 4: Inventories and plantings had been completed for the holdings of what will become the Loblolly Pine Genetic Stock Center and the Douglas-Fir Genetic Stock Center. Assembly of materials for UC Davis Molecular Genetic Stocks Center continued. Obj. 5: A short-course, held June 15-19, 2009 on the UC Davis campus, was attended by 24 participants, representing seven countries: nine graduate students/post-doctoral fellows and 15 professionals, nine of whom had Ph.Ds. There were seven tree breeders in the group. Primary instruction was provided by D. Harry and N. Wheeler, with support from co-PDs F. Isik, R. Whetten, T. Byram, and J. Wegrzyn. A special topics course "Association Genetics and Breeding" was organized and presented at Oregon State University (3 quarter credits, winter quarter, 2009) by Co-PD D Harry. Prior to that, at North Carolina State University - Fall quarter, 2009, CTGN co-PD F. Isik taught "Quantitative Forest Genetics Methods" (FOR 728). The course incorporated genomics-based selection using mixed models. Graduate students working with the NCSU Cooperative Tree Improvement Program attended the course. Obj. 6: Co-PDs delivered 50 outreach presentations, including invited talks, class lectures, posters, talks to professional societies, and conference talks. The funds remaining from the two years as an NRI project have paid for the final genotyping of loblolly pine samples and for the services of the project evaluator. PARTICIPANTS: A short-course, held June 15-19, 2009 on the UC Davis campus, was attended by 24 participants, representing seven countries: nine graduate students/post-doctoral fellows and 15 professionals, nine of whom had Ph.Ds. There were seven tree breeders in the group. Primary instruction was provided by D. Harry and N. Wheeler, with support from co-PDs F. Isik, R. Whetten, T. Byram, and J. Wegrzyn. A special topics course "Association Genetics and Breeding" was organized and presented at Oregon State University (3 quarter credits, winter quarter, 2009) by Co-PD D Harry. Prior to that, at North Carolina State University - Fall quarter, 2009, CTGN co-PD F. Isik taught "Quantitative Forest Genetics Methods" (FOR 728). The course incorporated genomics-based selection using mixed models. Graduate students working with the NCSU Cooperative Tree Improvement Program attended the course. Co-PDs delivered 50 outreach presentations, including invited talks, class lectures, posters, talks to professional societies, and conference talks. TARGET AUDIENCES: The target audience for the education and extension efforts of this project are cooperative tree improvement associations, breeders, the general public, academics, and students of forestry and genetics, primarily at the undergraduate and graduate levels. The primary vehicles for outreach to these groups are presentations by CTGN project personnel at conferences and in classrooms, workshops, conferences, electronically distributed newsletters, and a publicly available website PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The project status was delivered to breeding cooperatives formally on an annual basis and informally more frequently as project PDs interact with their colleagues in the breeding coops. The overall goal for project impact is that the use of genome-wide SNP data for genomic selection will be demonstrated and facilitated and thus incorporated in the practices of conifer tree improvement cooperatives in addition to their use of traditional phenotypic selection.
Publications
- No publications reported this period
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Progress 09/15/08 to 09/14/09
Outputs
OUTPUTS: Activities Genotyping: 4179 loblolly samples, with DNA from 3744 of these extracted and submitted for genotyping; Collaborator NCSU (loblolly pine): 2500 eastern loblolly pine foliage samples submitted to UC Davis for DNA extraction and SNP genotyping; the Atlantic Coastal Elite clonally replicated test population was established to test implementation of marker-trait associations identified by the Project; wood quality phenotypic analysis is underway. Collaborator TAMU (loblolly pine): Samples collected for genotyping from 5 populations and phenotypic data released to public database; breeding population structure for all selections were established with classical co-ancestry matrices. Collaborator U Florida (slash pine): Backcross 1 Full sib trial has been planted, foliage has been collected for DNA analysis, and phenotyping was completed; crosses to establish a mapping population were completed; 500 of planned 1000 cores collected for wood quality phenotyping; foliage was collected from 500 of the 1000 individuals in the Forward Selection Breeding Population for DNA analysis. Collaborator OSU (douglas-fir): Phenotyping done for wood stiffness, vegetative bud flush, and reproductive bud phenology on 830 clonally replicated parents in nine grafted seed orchards; 141 full-sib families were phenotyped for fall cold hardiness. Events Five-day short-course (Genomics in Tree Breeding and Forest Ecosystems) held June 15-19, 2009, on the UC Davis campus, and attended by 24 participants, representing seven countries. Participants included nine graduate students/post-doctoral fellows and 15 professionals, nine of whom had Ph.Ds. There were seven tree breeders in the group. Special topics course (Association Genetics and Breeding) was created and delivered at Oregon State University (3 quarter credits, winter quarter, 2009) and attended by 10 graduate students representing Forestry (4), Crop and Soil Science (3), Horticulture (1), and Animal Science (2). Course structure included 13 lectures (80 minutes), 3 class periods featuring data and software exercises, and 3 class periods for discussion topics. PDs delivered over 40 outreach presentations, including invited talks, class lectures, posters, talks to professional societies, and conference talks. Products Plone Project Website; DNA Inventory System for Integration into the TreeGenes database; Development of Custom LIMS system for Integration into DNA Inventory; A menu-driven Java program for simulating tree phenotypes and SNP haplotypes was developed and will be used to (1) test alternative mating designs, field designs, and sampling strategies for QTL discovery and (2) evaluate alternative analytical approaches, including genomic selection. This program will also serve as an educational tool for teaching about association genetics. A CTGN CAP brochure was developed and widely circulated at tree crop improvement meetings, other scientific meetings, and as mailings to interested parties. Two workshops in December 2008 on use of BLUP tools that incorporated potential use of SNP markers in breeding value estimation were well attended, including by members of our coop staffs and regular membership. PARTICIPANTS: Project Directors David Neale, UC Davis: Project Director, responsible for overall project coordination, budget management, reporting, and project documentation. Jill Wegrzyn, UC Davis: Co-PD, responsible for bioinformatics pipeline development, webhosting, and forest tree information resources. Dudley Huber, U Florida: Co-PD, co-team leader of the association validation effort, responsible for all breeding, testing, phenotyping, and association testing in slashpine. Steve McKeand, NCSU: Co-PD, co-team leader for MAS/MAB applications development, sharing responsibility for breeding, testing, and phenotyping in loblolly pine in the eastern range of the species. Tom Byram, TAMU: Co-PD, co team leader for MAS/MAB applications development, responsible for all breeding, testing, and phenotyping of loblolly pine in the western range of the species. Glenn Howe, OSU: Co-PD, co-team leader for association validation, collaborator on association methods development, responsible for phenotyping and association testing in Douglas-fir. Nicholas Wheeler and David Harry, OSU: Co-PDs, co-team leaders for Outreach, Education, and Training, responsible for mentoring Kenan Fellows, insuring training modules get tested and distributed, and lay articles written, coordinators of undergraduate and graduate student training at all institutions relative to workshops and symposia. Jeff Dean, U Georgia: Co-PD, co-team leader of Outreach, Education, and Training, responsible for developing and maintaining a quarterly newsletter intended for the conifer genomics community. Dana Nelson (US Forest Service, Southern Institutes of Forest Genetics and Forest Ecosystems Biology) and Brad St. Clair (US Forest Service, Pacific Northwest Research Station): Co-PDs, contributing to the development of the Genetic Stock Center. Collaborators Fikret Isik, NCSU: Collaborator, sharing responsibility for breeding, testing, and phenotyping in loblolly pine in the eastern range of the species. Ross Whetten, NCSU: Collaborator, responsible for association testing and evaluation. Other personnel Patrick McGuire, UC Davis: Serve as project coordinator. John Liechty, UC Davis: Bioinformatics programmer. Michael Coe: Private consultant, serves as Education/Extension Evaluation Manager, responsible for assessing progress and performance on the education and extension components of the Project. Partner organizations North Carolina State University, Oregon State University, Texas A&M University, University of Florida, University of Georgia, and USDA Forest Service Pacific Northwest Research Station and Southern Institutes of Forest Genetics and Forest Ecosystems Biology provide facilities and services for Project directors in pursuit of Project objectives. Training and professional development The Project supports graduate student training and research with work on the Project by one graduate student each at NCSU and OSU. The 2009 shortcourse and the 2009 special topics course both enrolled graduate students and postdoctoral trainees. TARGET AUDIENCES: Select one of the following options: a) Not relevant to this project b) Nothing significant to report during this reporting period X c) Report narrative entered in the box below If c) is checked, narrative must be entered in this block (below). The laboratory protocols, markers and associated analytical procedures, and mapping and association data described above under Outputs/Activities and Products are distributed via presentations and public databases targeting other researchers, breeders, and crop improvement practitioners. The education and outreach programs described above under Outputs/Events provided training for undergraduate and graduate students, tree breeders, managers, lay-people, and other stakeholders. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The Project provides a new type of knowledge available for use by tree improvement programs: markers suitable for high-throughput analysis associated with traits relevant to conifer improvement. Through presentations, workshops, consulting, and up-coming publications, the Project demonstrates and trains practitioners in the use of the developed markers for tree improvement. Finally, the Project is generating tools (analytical programs, data display software, and databases) to facilitate use of the generated knowledge.
Publications
- No publications reported this period
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Progress 09/15/07 to 09/14/08
Outputs
OUTPUTS: The Conifer Translational Genomics Network Coordinated Agricultural Project (CTGN-CAP) is an integrated research, education and extension project aimed at maintaining and enhancing healthy forests and ecosystems by bringing genomic assisted breeding to application in the United States. CTGN-CAP is a collaborative effort of 20 scientists, tree breeders, post-doctoral fellows and graduate students representing eight university and government institutions. Participants include the Directors of the four largest cooperative tree improvement programs in the United States. Collectively, these cooperatives annually provide 1.3 billion improved seedlings for reforestation (~80% of commercial US tree planting needs). Together with cooperative members and stakeholders, Directors have selected economic and adaptive traits for improvement, including growth, disease and insect resistance, and wood quality, and have identified 10,000 trees that will be genotyped for > 20,00o SNP polymorphisms representing over six thousand genes. This effort should lead to verification of associations between genotypes and phenotypes in the elite populations of loblolly and slash pines and Douglas-fir. Though early in the project, high-throughput bioinformatics tools for resequencing analysis and SNP calling (PineSAP) and SNP diversity and divergence measures (DNASAM) have been developed and are available for public use. A high-throughput, low cost DNA extraction facility has been built to handle current and future needs of the forestry research community. CTGN will annually host (2009-1011) a week-long workshop on genomics assisted breeding in forestry for graduate and post-graduate audiences. Presented in 10 separate modules, the workshop will provide both lecture and computer-lab experience on topics ranging from population and quantitative genetics to association mapping and marker assisted selection. Refined teaching materials will be made available to universities for class-room instruction. As part of our extension program, CTGN members have already (first 9months) given > 25 presentations to nearly 1000 people representing forest plantation growers and owners, tree breeders, animal and crop breeders, cooperative members, international conference attendees and the lay public. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The CTGN project is expected to have a large impact on how forest trees are bred in the US by educating tree breeders on the application of genomic based approaches to tree breeding. However, it is a bit early in the CTGN project for this full impact to be realized. To date however, there is impact in that the tree breeding establish is aware of the goals of the CTGN project and breeders are enrolled in workshops organized by the CTGN project.
Publications
- No publications reported this period
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