Scripts for analyzing Paspalum vaginatum GBS data

Seashore paspalum (Paspalum vaginatum Swartz) is a halophytic turfgrass
and emerging genomic model system for the study of salt tolerance in
cereals and other grasses. Despite recent interest and an increase in
available tools, little is known about the diversity present in wild
populations of P. vaginatum and its close relative P. distichum. Variation
in ploidy, clonal propagation, hybridization, and subgenome composition
appear to occur in the wild and may interact to influence geographic
patterns of adaptation, particularly in response to environmental salinity
levels. Using 218 accessions representing >170 wild collections
from throughout the coastal southern United States plus existing USDA
germplasm, we employed genotyping-by-sequencing, cpDNA sequencing and flow
cytometry to identify genetic differentiation and ploidy variation. Within
P. vaginatum, there are two morphologically distinct ecotypes: the
fine-textured ecotype is diploid and appears to reproduce in the wild both
sexually and by clonal propagation; in contrast, the coarse-textured
ecotype consists largely of clonally-propagating triploid and diploid
genotypes. The coarse-textured ecotype appears to be derived from
hybridization between fine-textured P. vaginatum and an unidentified
Paspalum species. These clonally propagating hybrid genotypes are more
broadly distributed than clonal fine-textured genotypes and may represent
a transition to a more generalist adaptive strategy. The triploid
genotypes vary in whether they carry one or two copies of the P. vaginatum
subgenome, indicating multiple evolutionary origins. This variation in
subgenome composition shows associations with local ocean salinity levels
across the sampled populations and may play a role in local adaptation.