Diversity among lowland switchgrass (panicum virgatum l.) Based on microsatellite markers (SSR)
Dalid, C., S. Nayak, K. Chekovskiy, M. Saha, and H. Bhandari.  2016.  Proceedings, National Association of Plant Breeders, Annual Meeting (14-18, Nov, 2016) Raleigh, NC.

Abstract:
As an important crop for biofuel feedstock research understanding the extent of genetic variation among and within different population of switchgrass is necessary to enhance efficiency in cultivar development. Twenty-three populations of lowland switchgrass including 13 Plant Introduction accessions obtained from USDA Germplasm Resource Information Network (USDA-GRIN) and 10 improved cultivars and breeding lines are being phenotyped at the University of Tennessee, East Tennessee Research and Education Center (ETREC) Plant Science Unit. Each population is represented by 15 genotypes. Upland ‘Cave-in-rock’ and ‘Summer’ were also included for comparison. Young leaves were collected from field-grown plants and DNA samples were extracted from each individual using the CTAB method. Touch down PCR was done using 384- well thermal cyclers. A total of 103 SSR markers and 4 chloroplast markers developed in Noble Foundation were used for PCR amplification. Samples were then genotyped using an ABI 3730 capillary sequencer at the Plant Biology Department of Noble Foundation. All genotypes were manually checked and cleaned using Genemapper. Base pair scores were converted to binary scores with the presence of a PCR product scored as 1 and 0 for its absence. Preliminary results using 27 SSR markers revealed a total of 50 alleles with an average of 2 alleles per marker per genotype. Hierarchical cluster analysis using Ward’s minimum variance (R package) grouped the individual genotypes into four clusters representing different accession origins. Additional marker data will be included for further analysis.