Source: UNIVERSITY OF FLORIDA submitted to
ACCELERATED DEVELOPMENT OF OPTIMAL PINE FEEDSTOCKS FOR BIOENERGY AND RENEWABLE CHEMICALS USING GENOME-WIDE SELECTION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1004878
Grant No.
2013-67009-21200
Project No.
FLA-FOR-005362
Proposal No.
2013-04313
Multistate No.
(N/A)
Program Code
A6151
Project Start Date
Sep 1, 2013
Project End Date
Aug 31, 2018
Grant Year
2013
Project Director
Kirst, M.
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
AG-SCHL-FOREST RES / CONSERV
Non Technical Summary
Southern pines are a proven sustainable source of renewable biomass for bioenergy and renewable chemicals. The S.E. forest industry produces ~18% of the global supply of industrial roundwood, 25% of the global pulp supply and 40% of the global pine chemical supply. This industry also generates 77% of all industrial biomass energy in the U.S. by burning wood waste and lignin at high thermal efficiencies with combined gas cycle turbines. The 93 million hectares of standing pines in the S.E. include 15.6 million hectares of genetically improved plantations; all grow with low water, fertilizer and herbicide inputs on land that is largely not suitable for cultivation of food crops. This large extant southern pine resource, with its well established supply chain and predictable year round supply, has also drawn substantial commercial interest for new standalone electrical power generating facilities, wood pellet mills and liquid biofuels facilities. Thus, southern pines have the demonstrated potential to be a major source of biomass for biopower, biofuels, and renewable chemicals. However, for pines to meet their full potential as a major bioenergy crop, cultivars that are more productive and more efficiently converted into liquid fuels need to be developed. This aim will not be achieved using traditional breeding, which is logistically complex, expensive, and time-consuming in pines, where a single breeding cycle takes almost two decades. The overall objective of this project is to address these limitations.Our overall goals are to hyper-accelerate the genetic improvement of pines using DNA sequence information, to generate new cultivars tailored to produce high energy yields. To achieve these goals, as our first objective we will apply advanced methods to predict which crosses have to be made to generate families with high cellulose (for biofuels), high lignin (for biopower) or high terpene (for renewable chemicals/biofuels) content. In addition, as the second objective we will characterize DNA and trait variation for a new elite pine populations that will be used in the future for bioenergy purposes. In summary, the first aim will allow rapid (<3 years) development of loblolly pine cultivars with improved biomass yield and characteristics. In the second aim we will establish the foundation for long-term, sustainable genetic gain by creating the genotypic resources necessary for genome-wide selection of the next generation of pine breeding for bioenergy.
Animal Health Component
0%
Research Effort Categories
Basic
(N/A)
Applied
50%
Developmental
50%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2010611108150%
2020611108050%
Knowledge Area
202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
0611 - Conifer forests of the South;

Field Of Science
1080 - Genetics; 1081 - Breeding;
Goals / Objectives
Our overall objective remains to hyper-accelerate pine breeding, to generate cultivars of loblolly and slash pine tailored to produce high energy yields, that are ready for deployment within the duration of this project. To achieve these goals we will pursue the following objectives:In the first objective, available highly accurate GWS prediction models will be used to rapidly identify and generate crosses of loblolly pine designed to support the short-term needs of the bioenergy industry. Highly productive families with high cellulose (for biofuels), high lignin (for biopower) or high terpene (for renewable chemicals/biofuels) content will be generated from an elite breeding population. Genome-wide selection prediction models were previously developed for this population, which has been grown at multiple sites, and was phenotyped for growth, disease resistance and juvenile wood composition traits (lignin, cellulose, and terpene content).In the second objective, advanced breeding populations of loblolly and slash pine, that encompass broad genetic diversity of each species, will be genotyped and phenotyped to create GWS prediction models for growth traits, wood chemistry and terpene flow. These genetically diverse populations will serve as the foundation for the next generation of advanced pine feedstocks for the bioenergy, biofuels and renewable chemicals industries.
Project Methods
The methods to be used in this project include:Novel prediction models that account for additive and dominance effects will be applied to all traits measured in an existing pine breeding population, including biomass growth, wood composition and disease resistance, and the accuracies of these models will be evaluated.Improved models will be used to identify crosses expected to generate the highest yielding families. The performance of these models in idenfying the best families will be evaluated by analyzing their progeny for bioenergy and biofuel production.In order to develop prediction models for the next-generation loblolly and slash pine bioenergy feedstocks, elite breeding populations will be genotyped and phenotyped for early growth traits. The development of prediction models for these next-generation populations is beyond the scope of the project, but the resources generated here will serve as the foundation for their future use.

Progress 09/01/16 to 08/31/17

Outputs
Target Audience:Extension and outreach: Participants of the Cooperative Forest Genetics Research Program (several members from forestry companies and the State of Florida and State of Georgia Divisions of Forestry) Participants of other tree breeding cooperatives (NCSU TIP cooperative and Texas A&M Western Gulf Cooperative) Scientists in plant breeding and genetics Formal classroom instruction: Graduate students in plant breeding and genetics courses (Plant Breeding Techniques and Advanced Genetics) Laboratory instruction: Graduate students directly involved in the projects research. Changes/Problems:A delay in the generation of phenotypic data from field trials of loblolly pine has resulted in the inability to develop prediction models for that species, despite the availability of genotypic data. The collection of this data is dependent on the agreement of the breeding cooperative stakeholders to measure it - becuase of the limited growth, the memebers have decided to delay this measurement for one year. We expect them to be available in the Spring of 2018, and the completion of the objective of generating prediction models for this population. What opportunities for training and professional development has the project provided?The project has provided opportunity for training for three graduate student. Training has also been provided to breeders and scientists from the forestry community, through workshops and presentations made in sceintific and stakeholder meetings. How have the results been disseminated to communities of interest?In addition to previously described produces, results have been disseminated through presentations to stakeholders in the Cooperative Forest Genetics Research Program annual meeting. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, genomic prediction models for the loblolly pine populationswill be completed. The remaining objectives of the project have been completed.

Impacts
What was accomplished under these goals? First objective Genome wide selection prediction models were used to identify and generate crosses of loblolly pine designed to support the short-term needs of the bioenergy industry, including families with high cellulose (for biofuels), high lignin (for biopower) and high terpene (for renewable chemicals/biofuels) content. Seedlings derived from these crosses are currently being field tested, and will be phenotyped when they reach >3 years of age (2018). Second objective Advanced breeding populations of loblolly and slash pine have been genotyped. Currently the slash pine population has been phenotyped for growth triats. The loblolly pine population was initially scheduled forphenotypingin 2017, but becuase of low growth, measurements were delayed to 2018. Development of prediction models has been completed for the slash pine population. Models will be established for the loblolly pine population when phenotypes become available.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: M�ller BSF, Neves LG, de Almeida Filho JE, Resende MFR Jr, Mu�oz PR, Dos Santos PET, Filho EP, Kirst M, Grattapaglia D. Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. BMC Genomics. 2017 Jul 11;18(1):524.


Progress 09/01/15 to 08/31/16

Outputs
Target Audience: Participants of the Cooperative Forest Genetics Research Program (several members from forestry companies and the State of Florida and State of Georgia Divisions of Forestry) Participants of other tree breeding cooperatives (NCSU TIP cooperative and Texas A&M Western Gulf Cooperative) Graduate students in plant breeding and genetics courses Graduate students directly involved in the projects research Scientists in plant breeding and genetics Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has provided opportunity for training for three graduate student. Training has also been provided to breeders and scientists from the forestry community, through workshops and presentations made in sceintific and stakeholder meetings. How have the results been disseminated to communities of interest?In addition to previously described produces, results have been disseminated through presentations to stakeholders in the Cooperative Forest Genetics Research Program annual meeting. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, genomic prediction models for all the populations that we proposed to analyze will be completed.

Impacts
What was accomplished under these goals? First objective - genome wide selectionprediction models were used to identify and generate crosses of loblolly pine designed to support the short-term needs of the bioenergy industry, including families with high cellulose (for biofuels), high lignin (for biopower) andhigh terpene (for renewable chemicals/biofuels) content. Seedlings derived from these crosses are currently being field tested, and will be phenotyped when they reach >3 years of age. Second objective - advanced breeding populations of loblolly and slash pine have been genotyped. Currently the slash pine population has been phenotyped for growth triats (loblolly pine population will be phenotyped in the Spring 2017). Development of prediction models is currently under way for the slash pine population. Models will be established for the loblolly pine population when phenotypes become available.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: de Almeida Filho, J.E., J.F. Guimar�es, F.F.E. Silva, M.D. de Resende, P. Mu�oz, M. Kirst and M.F. Resende Jr. (2016) The contribution of dominance to phenotype prediction in a pine breeding and simulated population. Heredity 117:33-41.


Progress 09/01/14 to 08/31/15

Outputs
Target Audience: Participants of the Cooperative Forest Genetics Research Program (several members from 8 forestry companies and the State of Florida and State of Georgia Divisions of Forestry) Participants of other tree breeding cooperatives (NCSU TIP cooperative and Texas A&M Western Gulf Cooperative) Graduate students in plant breeding and genetics courses (~ 40 students) Graduate students directly involved in the projects research (2 students) Scientists in plant breeding and genetics (over 500 participants that attended an online workshop supported by this project) Changes/Problems:No major challenges or probles have been encountered, that would require a change in the projects objectives. What opportunities for training and professional development has the project provided?The project has provided opportunity for training for two graduate student. How have the results been disseminated to communities of interest?In addition to previously described produces, results have been disseminated through presentations to stakeholders in the Cooperative Forest Genetics Research Program annual meeting. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, the DNA genotyping of all the populations that we proposed to analyze in this studywill be completed. In addition, seeds from crosses among individuals in the CCLONES population will be available for field testing. Within the next 18 months we expect that prediction models for the advanced generation populations will be completed also.

Impacts
What was accomplished under these goals? We have developed improved genome-wide prediction models that incorporate non-additive effects for a loblolly pine breeding population. Models were used to identify crosses predicted to generate families that are highly productive for cellulose (for biofuels), lignin (for biopower) or terpene (for renewable chemicals/biofuels) content. Establishment of the crosses is currently in progress. We are also genotyping two advanced breeding populations of loblolly and slash pine that encompass broad genetic diversity of each species. Genotyping of the loblolly pine population (3,000 individuals) with ~10,000 genetic markers is currently in progress and is expected to be completed by the springof 2016. Genotyping of the slash pine population will initiate in early 2016. Genotypic and phenotypic data from these populations will serve as the foundation for the next generation of advanced pine feedstocks for the bioenergy, biofuels and renewable chemicals industries.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Munoz, P.R., M.F.Jr. Resendeg, D.A. Huber, T. Quesada, M.D.V. Resende, D.B. Neale, J.L. Wegrzyn, M. Kirst and G.F. Peter. (2014) Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy. Crop Sciences 54:1115-1123.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mu�oz, P.R., M.F. Resende Jr.g, S.A. Gezan, M.D. Resende, G. de Los Campos, M. Kirst, D. Huber and G.F. Peter. (2015) Unraveling additive from nonadditive effects using genomic relationship matrices. Genetics 198:1759-1768.


Progress 09/01/13 to 08/31/14

Outputs
Target Audience: Target audience: Participants of the Cooperative Forest Genetics Research Program (several members from 8 forestry companies and the State of Florida and State of Georgia Divisions of Forestry) Participants of other tree breeding cooperatives (NCSU TIP cooperative and Texas A&M Western Gulf Cooperative) Graduate students in plant breeding and genetics courses (69 students) Graduate students directly involved in the projects research (1 students) Scientists in plant breeding and genetics (at various events) Efforts: Classroom instruction (courses: GMS6231 Genomics and Bioinformatics and PCB5065 Advanced Genetics) Outreach to members of the tree breeding cooperatives in the SE USA through seminars during the annual meetings, and annual site visits. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The project has provided opportunity for training for one graduate student. A second graduate student will be recruited during 2015. How have the results been disseminated to communities of interest? In addition to previously described produces, results have been disseminated through presentations to stakeholders in the Cooperative Forest Genetics Research Program annual meeting. What do you plan to do during the next reporting period to accomplish the goals? During the next reporting period DNA extraction for the slash pine population will be completed, and at least part of both slash and loblolly pine populations will be genotyped. In addition, crosses among individuals in the CCLONES population will be carried out, based on results of mate-pair allocation established during this year.

Impacts
What was accomplished under these goals? The following accomplishments have occurred in this project: Prediction models that account for additive and dominance effects have been applied to all traits measured in CCLONES, including biomass growth, wood composition and disease resistance. These improved mate-pair allocation models are now being used to identify crosses expected to generate the highest yielding families Genomic DNA from the next-generation loblolly pine has been extracted, to be subsequently genotyped.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Acosta, J.J., L.G. Neves, A.M. Fahrenkrog, J.M. Davis, J. Holliday and M. Kirst. 2014. Poster presentation: Demographics events and genome-wide genetic diversity of loblolly (Pinus taeda) and slash pine (Pinus elliottii). Plant and Animal Genome Conference XXII, January 11-15, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Chhatre, V.E., J. Westbrook, C.S. Echt, L.G. Neves, P.J. Martinez-Garcia, P.R. Munoz, M. Kirst, G.F. Peter, D. Neale, J.M. Davis and C.D. Nelson. 2014. Poster presentation: A high-density, consensus linkage map for loblolly pine. Plant and Animal Genome Conference XXII, January 11-15, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Resende Jr., M.F.R., S.A. Gezan, M.D.V. Resende, G. de los Campos, M. Kirst, D. Huber, G.F. Peter and P. Mu�oz. 2013. Poster presentation: Unraveling additive from non-additive effects using genomic relationship matrices. Impact of Large-scale Genomic Data on Statistical and Quantitative Genetics Conference, November 24-26, Seattle, USA.