The Genomics of Environmental Adaptation in Panicum hallii, a Diploid Model for the Biofueld Crop Switchgrass

In this study we have characterized variation across the genome of the wild grass Panicum hallii, a model species for the bioenergy crop switchgrass (Panicum virgatum). We identify SNP and structural variation within the genome using a set of deeply re-sequenced lines aligned to the recently completed P.hallii genome (v2.0). Similar to switchgrass, P. hallii occurs as two ecotypes: a xeric adapted upland variety (var. hallii) and a mesic adapted lowland variety (var. filipes). To begin to understand the genes underlying adaptive differences, we present the results of multiple genome scans and SNP outlier analyses between the two subspecies. We compare our results with loci identified in recent eQTL and allele specific expression studies. Our results yield a set of candidate genes and polymorphisms linked with ecotypic adaptation in P. hallii, which can be compared with the forthcoming results of QTL mapping for improvement traits in switchgrass.