Integrating genetic maps and physical genome maps is extremely valuable for map based isolation, comparative genome analysis and as anchors for genome sequencing projects. The DOE (Department of Energy) Joint Genome Institute (JGI) has sequenced plant genomes of candidate bioenergy crops such as sorghum (Paterson et al. 2009) and the model grass Brachypodium (International Brachypodium Initiative 2010). Both plants have been used as references for switchgrass, however sorghum last shared a common ancestor with switchgrass more than 20 million years ago while Brachypodium last shared a common ancestor with switchgrass more than 50 million years ago. The genome of a much closer switchgrass relative—foxtail millet (Setaria italica)—is described recently (Bennetzen et al. 2012; Zhang et al. 2012). All three genomes, along with those of switchgrass sequenced by the JGI are publicly accessible at www. phytozome. net. The genus Panicum also includes diploid species closely related to switchgrass such as P. hallii. Meyer et al. (2012) sequenced, assembled and annotated the transcriptome of a lowland ecotype P. Hallii var. Filipes, using 454-FLX Titanium sequencer. Totally 1.26 million EST reads were produced, and 15,422 unique genes identified. A majority of contigs (77%) and 34% of singletons matched ESTs from switchgrass (Meyer et al. 2012). In addition, a switchgrass bacterial artificial chromosome (BAC) library containing 147,456 clones and covering the effective genome approximately 10 times are established, and the average length of inserts in BACs is 120 kb (Saski et al. 2011). Moreover, two BAC libraries with 16 times genome equivalents of switchgrass were constructed, and each library comprised 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated) (Sharma et al. 2012).

In parallel, molecular linkage maps composed of various molecular markers including RFLP, SSR and STS (Missaoui et al. 2005b; Okada et al. 2010, Liu et al. 2012) have been constructed in switchgrass. For a more complete genome assembly and analysis, and to take full advantage of linkage map resources, it is of great importance to combine switchgrass genetic maps with physical map information. This can be accomplished by connecting genetic mapping data to BAC clones, which is a well established approach in rice (Chen et al. 2002), wheat (Sourdille et al. 2004), sorghum (Klein et al. 2000), and ryegrass (Lolium perenne, King et al. 2002), but has not been employed in switchgrass on a genome-wide basis.

Identification of Genome Structure

Tetraploid (2n=4x=36 chromosomes) and octoploid (2n=8x=72) are two major ploidal forms in switchgrass, while diploid (2n=2x=18), hexaploid (2n=6x=54), decaploid (2n=10x=90), and 12-ploid (2n=12x=108), and aneuploids were also reported (Lu et al. 1998; Costich et al. 2010, Young et al. 2010; Zalapa et al. 2011). Most of lowland switchgrass is tetraploid and octoploid lowland switchgrass has been discovered recently (Zhang et al. 2011b). Upland ecotype encompasses primarily octoploid and tetraploid plants although the former is more frequent than the latter. Using single dose molecular markers, one study inferred tetraploid switchgrass is an autotetraploid with a high degree of preferential pairing (Missaoui et al. 2005b), and another study indicated switchgrass has a near complete preferential pairing in disomic inheritance (Okada et al. 2010). The mode of completely disomic inheritance was further revealed by using about 500 co-dominant markers, which distributed on whole genome (Liu et al.

2012) . Recently Triplett et al. (2012) sequenced five low copy nuclear loci and two chloroplast loci and clarified that switchgrass was an allopolyploid originated from hybridization of two close diploids. The "A" subgenome of switchgrass is likely derived from an ancient species which was a close

relative to the current species in section Rudgeana of Panicum genus, while "B" subgenome is not identified yet (Triplett et al. 2012). The subgenomic differentiation in switchgrass was confirmed by karyotype analysis of a diploid individual (Young et al. 2012), which were selected from the progeny of a cross between two lowland tetraploid cultivars, ‘Kanlow’ and ‘Alamo’ (Young et al. 2010).