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

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 genetic and adaptive 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. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.

Genome wide association analysis in a mouse advanced intercross line

“…GBS is a reduced-representation genotyping method (Elshire et al 2011;Grabowski et al 2014) that we 392 have adapted for use in mice and rats (Parker et al 2016;Fitzpatrick et al 2013). We extracted DNA 393 from spleen using a standard salting-out protocol and prepared GBS libraries by digesting DNA with the 394 restriction enzyme PstI, as described previously (Parker et al 2016).…”

Biomass Yield Heterosis in Lowland Switchgrass

“…The two ecotypes are very different in terms of adaptation and morphology (Bouton, 2007). Molecular analysis has also indicated the presence of natural hybrid types between upland and lowland ecotypes (Grabowski et al, 2014). The two widely grown populations of lowland ecotype are 'Alamo' and 'Kanlow'.…”

A framework for incorporating evolutionary genomics into biodiversity conservation and management

“…From hundreds of millions of dollars for the first draft of the human genome in 2001, the sequencing required to assemble a reference genome for a species now costs just a few thousand dollars. Economical sample preparation strategies reviewed in [51][52][53] now enable high-throughput genomics studies even without a reference genome [54]. "Home-brew" methods for sequencing library preparation [55,56] have reduced persample cost and prices of commercial kits have followed a similar downward trend.…”