Expected and Unexpected Patterns of Chromosomal Inheritance from Resequencing of Tetraploid Switchgrass

Switchgrass (Panicum virgatum L.) is a large-stature, stress-tolerant North American Tallgrass Prairie species being developed as a bioenergy crop. It is primarily outcrossing, consists of upland and lowland ecotypes, and is typically polyploid. The main objectives of this project are to produce 1) sequence of reduced diversity genotypes to support the switchgrass genome project and 2) a high-quality, uniform variant catalog to support switchgrass improvement efforts. In this project, 48 genotypes of switchgrass have been resequenced via shotgun sequencing, with ~60 Gbp of 150 bp paired-end reads generated per genotype. Resequenced genotypes consist of lowland tetraploids (33), uplands (11, including 4 octoploids), and lowland-upland hybrids (4). Two of the lowlands possess upland chloroplast sequences, consistent with hybridization across the ecotypes in situ. Sequencing confirmed that three genotypes have greatly reduced heterozygosity relative to the reference, including a dihaploid, and two third-generation selfed genotypes. The data show approximately the expected crossover frequency upon selfing. Preliminary analysis has found that many of the genotypes, including some wild accessions, possess large regions that are homozygous between the sister chromatids. Low heterozygosity regions are also apparent in other switchgrass genotypes characterized by exome capture. This suggests the possibility of 1) rampant nondisjunction during chromosomal segregation, 2) the opportunity to study/isolate homozygous alleles in these regions, and 3) improving breeding program diversity by incorporating genotypes with variation in these regions. The data provide a deep characterization of the genetic differentiation between individuals and within ecotypes that might be leveraged to improve switchgrass as a bioenergy species.