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Logo of bmcpsBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Plant Biology
 
BMC Plant Biol. 2012; 12: 117.
Published online Jul 26, 2012. doi:  10.1186/1471-2229-12-117
PMCID: PMC3492167
Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass
Hugh A Young,1 Gautam Sarath,2 and Christian M Tobiascorresponding author1
1Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
2USDA Central-East Regional Biomass Center, 137 Keim Hall, East Campus, UNL, Lincoln, NE, 68583, USA
corresponding authorCorresponding author.
Hugh A Young: hugh.young/at/ars.usda.gov; Gautam Sarath: gautam.sarath/at/ars.usda.gov; Christian M Tobias: christian.tobias/at/ars.usda.gov
Received February 23, 2012; Accepted July 11, 2012.
Abstract
Background
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.
Results
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.
Conclusion
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.
Keywords: Bioenergy, Switchgrass, Cytogenetics, CHIAS IV, Perennial biofeedstocks, Dihaploids, Renewable energy, Polyploidy
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