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Title: Comparative relationships and chromosome evolution in switchgrass (Panicum virgatum) and its genomic model, foxtail millet (Setaria italica)

Author
item Daverdin, Guillaume - University Of Georgia
item Bahri, Bochra - University Of Georgia
item Wu, Xiaomei - University Of Georgia
item Serba, Desalegn - Samuel Roberts Noble Foundation, Inc
item Tobias, Christian
item Saha, Malay - Samuel Roberts Noble Foundation, Inc
item Devos, Katrien - University Of Georgia

Submitted to: BioEnergy Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2014
Publication Date: 7/30/2015
Citation: Daverdin, G., Bahri, B.A., Wu, X., Serba, D.D., Tobias, C.M., Saha, M.C., Devos, K.M. 2015. Comparative relationships and chromosome evolution in switchgrass (Panicum virgatum) and its genomic model, foxtail millet (Setaria italica). BioEnergy Research. 8:137-151.

Interpretive Summary: Driven by the need for greater energy security and a reduced impact of fuel consumption on the environment, there has been a growing interest in recent years to produce biofuels from cellulosic biomass. Switchgrass (Panicum virgatum L.), a perennial warm season C4 grass native to North America is one of the crops that was identified in the 1990s as a potential feedstock for the production of cellulosic biofuels because of its high biomass yield, low nutrient and water requirements and adaptation to marginal lands [1-3]. The objectives of this research were (1) to integrate several of the published switchgrass genetic maps into a consensus map with an increased marker density that can be used to validate the sequence-based genetic map and in practical breeding applications and (2) to employ the consensus map in a comparative analysis with the foxtail millet genome sequence.

Technical Abstract: A switchgrass (Panicum virgatum L.) consensus map was developed that combined data from two mapping populations and integrated recombination data from both parents of this largely obligate outcrossing species. The consensus map consisted of 1,321 loci and spanned 2,122 cM. An analysis of the distribution of genic and genomic markers across the length of a linkage group showed that genic markers were relatively overrepresented in distal regions, while genomic markers were relatively overrepresented in pericentromeric regions. Furthermore, genic markers located in distal and pericentromeric regions identified orthologs in the genome of the closely related species foxtail millet (Setaria italica (L.) P. Beauv.) at a similar rate, but fewer orthologs were found for genomic markers that mapped to pericentromeric regions compared to distal regions. This suggests that genomic markers that map to distal regions are more likely to be derived from genic regions than those that map to pericentromeric regions. A comparative analysis between loci on the switchgrass consensus map and their orthologs in the foxtail millet genome showed that the two species varied by at least nine inversions and one reciprocal translocation. Extending the comparative analysis to sorghum demonstrated that the majority of the rearrangements occurred in the foxtail millet genome in the past 13 million years. The switchgrass - foxtail millet comparative map provides a guide of the rearrangements that need to be taken into account when using foxtail millet as a surrogate for switchgrass in genetic analyses.