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United States Department of Agriculture

Agricultural Research Service

Research Project: TRANSLATIONAL RESEARCH AND BREEDING IN SWITCHGRASS USING MAIZE AS A MODEL DISCOVERY ENGINE
2013 Annual Report


1a.Objectives (from AD-416):
1. Germplasm characterization: a. Develop DNA markers that can be used as tools to select switchgrass plants with superior performance for Biofuel and bioenergy uses. b. Develop selection methods and models in which DNA markers can be used to select the best switchgrass plants in segregating populations and as parents for upland X lowland hybrids.

2. Translational research and breeding: a. Identify functional polymorphisms in switchgrass genes that are directly associated with important traits for Biofuel and bioenergy uses. b. Identify candidate genes from maize, sorghum, Setaria, and other species that are homologous to important polymorphic regions in switchgrass, describe the function of these genes, and develop generalized markers that can be used to implement marker selection in switchgrass.


1b.Approach (from AD-416):
1. Conduct amplification and polymorphism analyses using EST-SSR markers on switchgrass association panels, including marker screening, scoring, and analysis.

2. Conduct simulation studies on marker-assisted selection methodologies to optimize the deployment of both laboratory and field facilities to maximize genetic gain per unit of expenditure.

3. Develop SNP markers from sequence analysis of candidate regions.

4. Develop methods by which performance of both half-sib and full-sib family performance can be predicted from genotypic assessment of parents.


3.Progress Report:

This project supports Objective 1 of the parent project: Develop new germplasm of perennial forage species that display increased yield and bioconverion potential. Completed alpha-test and beta-test of the exome capture pipeline, generating approximately 1.2 million single-nucleotide polymorphism (M-SNP) markers in 50 million bases of gene space on the switchgrass genome. Completed one more year of data collection on genomic selection nurseries of switchgrass half-sib families. Created 26 new upland x lowland switchgrass hybrids for establishment in field evaluation trials. Submitted ~800 DNA samples to the Joint Genome Institute for analysis of DNA sequence information to provide SNP markers for phenotypic-genotypic association analyses. Collected samples for transcriptome analysis of genetic regulation of flowering time in switchgrass. Completed all sample collection and partial data analysis of nitrogen recycling experiments of upland and lowland switchgrass genotypes.


Last Modified: 11/27/2014
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