Extensive genetic diversity present within North American switchgrass germplasm

Authors: EVANS, JOSEPH - Michigan State University; SANCIANGO, MILLICENT - Michigan State University; LAU, KIN - Michigan State University; CRISOVAN, EMILY - Michigan State University; BARRY, KERRIE - Joint Genome Institute; DAUM, CHRIS - Joint Genome Institute; HUNDLEY, HOPE - Joint Genome Institute; JENKINS, JERRY - Joint Genome Institute; KENNEDY, MEGAN - Joint Genome Institute; KUNDE-RAMAMOORTHY, GOVINDARAJAN - Joint Genome Institute; VAILLANCOURT, BRIEANNE - Michigan State University; ACHARYA, ANANTA - University Of Georgia; SCHMUTZ, JEREMY - Joint Genome Institute; SAHA, MALAY - Noble Research Institute; KAEPPLER, SHAWN - University Of Wisconsin; BRUMMER, E - University Of California, Davis; Casler, Michael; BUELL, C - Michigan State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2017
Publication Date: 3/2/2018
Citation: Evans, J., Sanciango, M.D., Lau, K.H., Crisovan, E., Barry, K., Daum, C., Hundley, H., Jenkins, J., Kennedy, M., Kunde-Ramamoorthy, G., Vaillancourt, B., Acharya, A., Schmutz, J., Saha, M., Kaeppler, S.M., Brummer, E.C., Casler, M.D., Buell, C.R. 2018. Extensive genetic diversity present within North American switchgrass germplasm. The Plant Genome. 11:170055. doi:10.3835/plantgenome2017.06.0055.
DOI: https://doi.org/10.3835/plantgenome2017.06.0055

Interpretive Summary: The development of switchgrass into a dedicated biomass crop for conversion to bioenergy requires extensive evaluations of many sources of seeds in the search for the best plants. Essentially, all of North America, east of the Rocky Mountains and south of the coniferous forest, is a potential source of plant material. DNA technologies are being employed to assist in screening these materials (germplasm) to identify and classify various groups of materials. Using 1.9 million DNA markers, a total of 140 different sources of switchgrass were classified into seven groups which represent potentially seven different sources and types of genes for use in switchgrass improvement for different regions, i.e., seven different gene pools. Detailed analyses of diversity indicated that northern types have undergone a massive reduction in genetic diversity, while southern types still contain sufficient diversity to be of value to breeding programs outside the southern USA. These results will be extremely useful to switchgrass breeders throughout North America.

Technical Abstract: Switchgrass (Panicum virgatum L.) is a perennial, native North American grass currently grown for ecological restoration and forage purposes that has potential as a biofuel feedstock crop. Switchgrass is present in two primary ecotypes: upland, found in the northern range of switchgrass habitats and present in tetraploid and octoploid populations; and lowland, found in the southern reaches of switchgrass habitats and composed primarily of tetraploid populations. Previous studies focused on a diversity panel of primarily northern switchgrass. To expand our knowledge of genetic diversity in a broader set of North American switchgrass, we generated exome capture sequence data for an additional 632 individuals that are primarily lowland which, when combined with the 537 individuals previously analyzed, represent 140 populations (72 lowland, 67 upland, 1 mixed), and a total of over 5 Tb of sequence data. We used these data to identify over 37 million single nucleotide polymorphisms (SNPs) of which 1.9 million high-confidence SNPs were used for downstream analysis of genetic diversity and population structure. Using these SNPs, we identified seven separate population groups (four upland groups, three lowland groups) within the switchgrass populations sampled which provide wide representation of native North American switchgrass diversity. Assessment of population structure and genetic distance analyses readily revealed moderate genetic differentiation between the lowland and the upland populations, with extensive genetic diversity within lowlands relative to the uplands, consistent with reports of a genetic bottleneck in upland switchgrass. Analyses of nucleotide diversity revealed a high degree of genetic diversity relative to rice, maize, soybean, and Medicago, consistent with the outcrossing mode of reproduction and polyploidy in switchgrass.