Karyotype Variation in Switchgrass is Indicative of Subgenomic and Ecotypic Differentiation

The herbaceous, perennial grass Switchgrass (Panicum virgatum L.) represents a major lignocellulosic feedstock for renewable bioenergy production in the United States and abroad. Little is understood about genome organization in this polyploid species which encompasses distinct Upland and Lowland ecotypes. We conducted a cytogenetic study to establish a standard karyotype for switchgrass chromosomes (n=9) and to answer questions about ecotype and subgenome variation. Size differences, condensation patterns, and arm-length ratios were used to identify individual chromosomes. Fluorescence in situ hybridization (FISH) using rDNA probes (45S, 5S), maize CentC, and a native switchgrass centromeric repeat (CentSWG) further distinguished individual chromosomes, but also indicated patterns of subgenome and ecotype divergence. Unexpected CentSWG and 5S rDNA hybridization patterns were consistent with complete loss or severe reduction of the number of repeats in one subgenome. These patterns were maintained throughout the ploidy series, from dihaploid (2n=18) to octaploid (2n=72). In addition, differences observed at the 5S rDNA loci between the Upland and Lowland ecotypes of switchgrass provided the basis for distinguishing these subpopulations. We will discuss how FISH analysis can distinguish switchgrass plants belonging to divergent genetic pools and aid in ecotype distinction. The karyotype structure and cytogenetic analysis of switchgrass allows for the classification of individual chromosomes (n=9) and provides a framework for future genetic and genomic studies.