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United States Department of Agriculture

Agricultural Research Service


Location: Dairy Forage Research

2012 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 is related to the following objective of the parent project: Objective 1. Develop new germplasm of perennial forage species that display increased yield and bioconversion potential. Completed all phenotypic analyses of the northern switchgrass association panel. Provided data to collaborators for use in developing associations between phenotype and genotype for a total of 32 quality traits potentially related to recalcitrance. Completed four years of biomass yield measurements at two locations for the WS4U-C2 half-sib families that will comprise the initial training population to develop genomic selection equations for potential assessment and validation. Phenotypic data, software, and personnel are queued up and ready to proceed once the exome-capture data is ready to roll out of the bioinformatics pipeline. Collected diverse switchgrass germplasm samples to represent the entire native range of the species, including the ranges of both upland and lowland ecotypes. Conducted detailed phylogenetic analysis of DNA-marker variation and plastic-sequence information of over 100 unique populations, identifying numerous sources of variation and previously unknown levels of genetic variability within the species. Provided the first resolvable spatial map of geographically distinct genetic groups of switchgrass, including the first documented natural hybrids between upland and lowland ecotypes. Chose upland and lowland genotypes, grew plants under uniform conditions, collected sample tissue for RNA isolation, and analyzed RNA-sequence data in preparation for development of a manuscript describing ecological and genetic variation in sequence expression of switchgrass, largely related to the upland versus lowland ecotype. Used knowledge gathered from DNA-marker studies to select a highly diverse set of switchgrass genotypes designed to document genetic variation in gene copy number and presence-absence variation. Documented variation for these characteristics between and within upland and lowland switchgrasses. Used existing sequence information from related species, combined with RNAseq information from switchgrass (see above) to identify gene space for designing comparative genome hybridization and exome capture studies that will be relevant to germplasm representing a wide array of geographic origins of switchgrass. Designed an exome-capture array that will be highly useful and valuable.

4. Accomplishments

Last Modified: 06/25/2017
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