Synteny of the Switchgrass Linkage Map with Sorghum, Rice, and Foxtail Millet Genomes.

Polyploidy and outcrossing strongly influence genetic diversity and the ability to detect loci controlling biomass traits in switchgrass (Panicum virgatum). The Potential of genes to diverge and evolve new functions is also influenced by the meiotic behavior of chromosomes in polyploids leading to segregation as a single locus or duplicated loci. Switchgrass linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome.  This is a first step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 cM and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homoeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages.