Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass

Authors: GRABOWSKI, PAUL - University Of Chicago; MORRIS, GEOFFREY - Kansas State University; Casler, Michael; BOREVITZ, JUSTIN - Canberra

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2014
Publication Date: 8/8/2014
Publication URL: https://handle.nal.usda.gov/10113/62383
Citation: Grabowski, P., Morris, G., Casler, M.D., Borevitz, J. 2014. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass. Molecular Ecology. 23:4059-4073.

Interpretive Summary: Switchgrass is native to the tallgrass prairie and savanna ecosystems of the central and eastern United States. It is highly valued as a component in tallgrass prairie and savanna restoration and conservation projects, and as a potential bioenergy feedstock. Using 98,042 DNA markers, we identified geographic patterns of variation associated with sand dune habitats, photoperiod and temperature, and humidity/rainfall gradients. We also identified plants that are descendants of ancient hybrids between upland and lowland ecotypes. These plants are of great potential value to plant breeders, geneticists, and restorationists as they learn why individual switchgrass plants have specific and sometimes narrow adaptation zones, as well as helping to create switchgrass populations that are resilient against impending climate change.

Technical Abstract: Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration, and natural selection. Switchgrass (Panicum virgatum L.) has strong ecotypic differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98,042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities, and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. While history, ploidy, and adaptation each influence genetic diversity individually, we also begin to discern signatures of interactions among these factors in shaping variation in switchgrass. For instance, we detect greater genetic diversity in lineages with higher ploidy beyond that expected by ploidy alone. This suggests that admixture promotes ploidy changes, which may aid in maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the interactions among mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of ecotypic adaptation in this species.