Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) The objectives of this project are to develop a comprehensive molecular marker system for switchgrass, develop a saturated linkage map of switchgrass, and perform QTL analysis to tie selected markers to specific traits that are being evaluated in our mapping populations. Approach (from AD-416) Analysis of marker segregation data in a F1 and advanced generation mapping populations consisting of over 250 individuals will provide accurate estimates of genome length, marker coverage, linkage phase and the degree of recombination in each parent along with patterns of segregation distortion. The mapping population will be evaluated in two different environments in replicated trials for morphological and reproductive characteristics associated with biomass production. Additional QTL population(s) will be developed and genotyped with selected markers if little variation is present in the mapping population. Mapping of traits controlling quantitative trait loci (QTL) in tetraploid accessions of switchgrass as well as is other multivalent tetraploids that include many plant species, such as potato, sugarcane and rose, are of paramount importance to agricultural production and biological research. In collaboration with scientists at the University of Pennsylvania we developed a statistical method for mapping multivalent tetraploid QTLs by considering their unique cytogenetic properties. This method is built in the mixture model-based framework and implemented with the Expectation Maximization (EM) algorithm. The method allows the simultaneous estimation of quantitative trait loci positions, the magnitute of their effects, the degree of recombination between sub- genomes and the frequency of a process known as double-reduction as well as the assessment of the estimation precision of these parameters. Simulated data was used to examine the statistical properties of the method and validate its utilization. The new method and its software will provide a useful tool for QTL mapping in tetraploids that undergo double reduction.
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) The objectives of this project are to develop a comprehensive molecular marker system for switchgrass, develop a saturated linkage map of switchgrass, and perform QTL analysis to tie selected markers to specific traits that are being evaluated in our mapping populations. Approach (from AD-416) Analysis of marker segregation data in a F1 and advanced generation mapping populations consisting of over 250 individuals will provide accurate estimates of genome length, marker coverage, linkage phase and the degree of recombination in each parent along with patterns of segregation distortion. The mapping population will be evaluated in two different environments in replicated trials for morphological and reproductive characteristics associated with biomass production. Additional QTL population(s) will be developed and genotyped with selected markers if little variation is present in the mapping population. Documents Reimbursable with DOE. Log 32789 (9/07). Formerly 5325-21000- 013-06R (1/10). Switchgrass linkage maps were constructed in collaboration with the Samuel Roberts Noble Foundation. The male and female map lengths and number of markers were 1376 cM and 563 in the female map and 1645 cM and 542 in the male map, with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homoeologous pairs that represent the each subgenome derived from recent polyploidization. Comparative analysis of each homology group to the sorghum genome identified clear syntenic relationships and collinear tracts. The ratio of coupling to repulsion phase linkages indicated strong disomic inheritance. At Noble Foundation, a separate linkage map is being developed in a population derived from a cross between an individual from cultivar Alamo as the female parent and cultivar Summer (VS16) as the male parent (NF- UGA population). Mapping and phenotyping of this population is now in progress for the purposes of performing marker-trait association. A third population was developed at Samuel Roberts Noble Foundation for trait mapping based on the ALB and NF-UGA populations. Field planting and evaluation of this population is now underway. A total of 251 progeny, two sets of the parents and an Alamo control individual were planted. Plants have also been established in two locations and are also being phenotyped for marker trait association. Great progress has been made in the development of statistical models for mapping trait loci in controlled crosses of switchgrass in collaboration with the University of Pennsylvania. The models allow simultaneous estimation of trait positions, trait effects, the chromosomal pairing factor and the degree of double reduction as well as the assessment of the estimation precision of these parameters.
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Progress 08/01/07 to 08/31/10
Outputs
Progress Report Objectives (from AD-416): The objectives of this project are to develop a comprehensive molecular marker system for switchgrass, develop a saturated linkage map of switchgrass, and perform QTL analysis to tie selected markers to specific traits that are being evaluated in our mapping populations. Approach (from AD-416): Analysis of marker segregation data in a F1 and advanced generation mapping populations consisting of over 250 individuals will provide accurate estimates of genome length, marker coverage, linkage phase and the degree of recombination in each parent along with patterns of segregation distortion. The mapping population will be evaluated in two different environments in replicated trials for morphological and reproductive characteristics associated with biomass production. Additional QTL population(s) will be developed and genotyped with selected markers if little variation is present in the mapping population. Mapping of traits controlling quantitative trait loci (QTL) in tetraploid accessions of switchgrass as well as in other multivalent tetraploids that include many plant species, such as potato, sugarcne and rose, are of paramount importance to agricultural production and biological research. In collaboration with scientists at the University of Pennsylvania, we developed a statistical method for mapping multivalent tetraploid QTLs by considering their unique cytogenetic properties. This method is built in the mixture model-based framework and implemented with the Expectation Maximization (EM) algorithm. The method allows the simultaneous estimation of quantitative trait loci positions, the magnitude of their effects, the degree of recombination between sub- genomes and the frequency of a process known as double-reduction as well as the assessment of the estimation precision of these arameters. Simulated data was used to exammine the statistical properties of the method and validate its utilization. The new method and its software will provide a useful tool for QTL mapping in tetraploids that undergo double reduction. This project is relevant to the development of switchgrass genetic resources in support of bioenergy feedstock improvement that is an objective of the parent project.
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) The objectives of this project are to develop a comprehensive molecular marker system for switchgrass, develop a saturated linkage map of switchgrass, and perform QTL analysis to tie selected markers to specific traits that are being evaluated in our mapping populations. Approach (from AD-416) Analysis of marker segregation data in a F1 and advanced generation mapping populations consisting of over 250 individuals will provide accurate estimates of genome length, marker coverage, linkage phase and the degree of recombination in each parent along with patterns of segregation distortion. The mapping population will be evaluated in two different environments in replicated trials for morphological and reproductive characteristics associated with biomass production. Additional QTL population(s) will be developed and genotyped with selected markers if little variation is present in the mapping population. Documents Reimbursable with DOE. Log 32789 (9/07). Significant Activities that Support Special Target Populations A molecular marker system for switchgrass has been developed in collaboration with the Samuel Roberts Noble Foundation. A linkage mapping population consisting of 242 individuals was developed from a cross between a cv. Kanlow individual as the female parent and a cv. Alamo individual as the male parent (the ALB population). The population is maintained at both Albany, CA and the Samuel Roberts Noble Foundation. A total of 729 markers have been used to construct linkage maps from the two parents. The linkage map will serve as the basis for comparative genomics to analyze similarities between the switchgrass genome and other grass species as well as the analysis of genome structure and reproductive behavior in switchgrass. At Noble Foundation, a separate linkage map is being developed in a population derived from a cross between an individual from cultivar Alamo as the female parent and cultivar Summer (VS16) as the male parent (NF- UGA population). Mapping of this population is now in progress. A third population was developed at Samuel Roberts Noble Foundation for trait mapping based on the ALB and NF-UGA populations. Field planting and evaluation of this population is now underway. A total of 251 progeny, two sets of the parents and an Alamo control individual were planted. Plants have also been propagated in the greenhouse to obtain enough planting materials for planting a second location trial. Great progress has been made in the development of statistical models for mapping trait loci in controlled crosses of switchgrass in collaboration with the University of Florida. The models allow simultaneous estimation of trait positions, trait effects, the chromosomal pairing factor and the degree of double reduction as well as the assessment of the estimation precision of these parameters.
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report Objectives (from AD-416) The objectives of this project are to develop a comprehensive molecular marker system for switchgrass, develop a saturated linkage map of switchgrass, and perform QTL analysis to tie selected markers to specific traits that are being evaluated in our mapping populations. Approach (from AD-416) Analysis of marker segregation data in a F1 and advanced generation mapping populations consisting of over 250 individuals will provide accurate estimates of genome length, marker coverage, linkage phase and the degree of recombination in each parent along with patterns of segregation distortion. The mapping population will be evaluated in two different environments in replicated trials for morphological and reproductive characteristics associated with biomass production. Additional QTL population(s) will be developed and genotyped with selected markers if little variation is present in the mapping population. Documents Reimbursable with DOE. Log 32789 (9/07). Significant Activities that Support Special Target Populations The goal of this project is to develop a linkage map for switchgrass incorporating EST-SSR. The project has filled one vacant research affiliate position and has made substantial progress at defining linkage groups using EST-SSR on a large mapping population. Additional screening is being conducted to identify new markers for closing the remaining gaps in the map. Field studies are being established to identify quantitative trait loci for switchgrass using the mapping population.
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Significant Activities that Support Special Target Populations This report serves to document research conducted under a reimbursable agreement between the ARS and the US Department of Energy. Additional details of research can be found in the report for the parent CRIS 5325- 21000-013-00D, Biotechnological Enhancement of Energy Crops. The goal of this project is to develop a linkage map for switchgrass incorporating EST-SSR. The project has just initiated and we are in the process of recruiting for one position that will be devoted solely to this work.
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