Location: Genomics and Gene Discovery
2012 Annual Report
(1) Use 454 sequencing technology to profile barcoded cDNA libraries derived from crowns, rhizomes and dormant buds during critical phases of transition.
(2) Employ stable 13C and 15N isotope enrichment for C and N utilization, sequestration, and cycling analysis.
(3) Perform metabolic profiling of sugars, starch, phenolics, protein, amino acids and lipids in genotypes and cultivars with known differences in winter survival and pre-frost maturity and senescence differences.
(4) We have developed unique Upland switchgrass populations by recurrent breeding for forage digestibility which is strongly associated with low lignin concentration in which winter survival and plant fitness has been significantly decreased. We will utilize the 454 sequence analysis platform on populations and genotypes with known differences in winter survival to uncover marker-trait associations that can be used to reduce the generations, and within generation time and expense of phenotyping in the breeding process by use of marker assisted selection.
Gene Profiling During Regreening and Dormancy of Bulked Segregants: The populations selected for this objective have been growing in replicated field nurseries in NE, and select genotypes with low winter survival have been clonally maintained in greenhouses. RNA will be isolated in early spring at the first sign of regreening, just post anthesis, and following first killing frost. RNA will be pooled and bulked by genotype. These RNAs will be analyzed as above by the creation of barcoded cDNA libraries and 454 sequencing.
Creation and Analysis of QTL and Association Mapping Panel in Breeding Stock Developed for the Northern Plains Climate that Show Significant Heterosis: There are 148 single-seed descent tetraploid plants in a marker population derived from a cross between an upland cv Summer and an adapted lowland cv Kanlow plant. This population will be expanded and replicated, along with 500 tetraploid upland and lowland lines derived from a foundation nursery. Material from this association panel will be evaluated for biomass yield, rapid spring regrowth, and heading date. Using available mapped EST-microsatellites will enable evaluation of population structure, and based on sequence profiling, we will resequence up to 10 kb from selected candidate loci in the 500 individual association panel.