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Open Access Highly Accessed Open Badges Research article

Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass

Hugh A Young1, Gautam Sarath2 and Christian M Tobias1*

Author Affiliations

1 Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA

2 USDA Central-East Regional Biomass Center, 137 Keim Hall, East Campus, UNL, Lincoln, NE, 68583, USA

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BMC Plant Biology 2012, 12:117  doi:10.1186/1471-2229-12-117

Published: 26 July 2012



Karyotypes can provide information about taxonomic relationships, genetic aberrations, and the evolutionary origins of species. However, differentiation of the tiny chromosomes of switchgrass (Panicum virgatum L.) and creation of a standard karyotype for this bioenergy crop has not been accomplished due to lack of distinguishing features and polyploidy.


A cytogenetic study was conducted on a dihaploid individual (2n = 2X = 18) of switchgrass to establish a chromosome karyotype. Size differences, condensation patterns, and arm-length ratios were used as identifying features and fluorescence in-situ hybridization (FISH) assigned 5S and 45S rDNA loci to chromosomes 7 and 2 respectively. Both a maize CentC and a native switchgrass centromeric repeat (PviCentC) that shared 73% sequence identity demonstrated a strong signal on chromosome 3. However, only the PviCentC probe labeled the centromeres of all chromosomes. Unexpected PviCentC and 5S rDNA hybidization patterns were consistent with severe reduction or total deletion of these repeats in one subgenome. These patterns were maintained in tetraploid and octoploid individuals. The 45S rDNA repeat produced the expected number of loci in dihaploid, tetraploid and octoploid individuals. Differences observed at the 5S rDNA loci between the upland and lowland ecotypes of switchgrass provided a basis for distinguishing these subpopulations.


Collectively, these results provide a quantitative karyotype of switchgrass chromosomes. FISH analyses indicate genetic divergence between subgenomes and allow for the classification of switchgrass plants belonging to divergent genetic pools. Furthermore, the karyotype structure and cytogenetic analysis of switchgrass provides a framework for future genetic and genomic studies.

Bioenergy; Switchgrass; Cytogenetics; CHIAS IV; Perennial biofeedstocks; Dihaploids; Renewable energy; Polyploidy