Generation of a Switchgrass Consensus Map and Its Comparative Analysis with Foxtail Millet

Switchgrass (Panicum virgatum L.; 2n = 4x =36) is a native perennial warm season (C₄) grass that has been identified as a promising species for bioenergy research and production. The switchgrass genome sequence has been assembled into 319,670 contigs with an L50 of 5.7 kb (www.phytozome.org).  Genome sequence assembly remains a challenge due to the heterozygosity, tetraploidy and relatively high repeat content of switchgrass. Anchoring of the switchgrass contigs to the classically constructed switchgrass genetic maps has been difficult due to the relatively low marker density of the individual maps. However, the Joint Genome Institute has recently sequenced the progeny of one of the mapping populations, and used this data combined with information from the assembly of the genome sequence of P. hallii, a close relative to P. virgatum, to order the switchgrass sequence contigs (assembly v1.1; www.phytozome.net).  We have integrated three published genetics maps to generate a switchgrass consensus map consisting of 1212 markers that can be used as an independent tool to validate the sequence-based map.  We also conducted a comparative analysis of our integrated map with the foxtail genome sequence. Foxtail millet diverged some 13 million years ago from switchgrass and was sequenced in 2010 as a model for switchgrass.  Our results show that switchgrass and foxtail millet differ by at least eight chromosomal inversions and one translocation. Extending the comparative analyses to other grasses showed that all rearrangements occurred in the Setaria genome after its divergence from a common ancestor with switchgrass.