Location: Genomics and Gene Discovery
Title: Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass Authors
Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 11, 2012
Publication Date: July 26, 2012
Citation: Young, H., Sarath, G., Tobias, C.M. 2012. Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass. Biomed Central (BMC) Plant Biology. 12:117. Interpretive Summary: Collectively, these results provide a complete description of switchgrass chromosomes. Furthermore, results indicate genetic divergence between the distinct copies of its duplicated genome and allow for the classification of switchgrass plants belonging to divergent genetic pools. Furthermore, the chromosome structure and analysis of switchgrass provides a physical framework for genetic and genomic studies.
Technical Abstract: 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.