Identification of clonal replicates
The filtered GBS dataset was characterized by 127,282 SNPs in 218
accessions. Principal component analysis (PCA) and application of
genetic similarity threshold criteria to identify clonal replicates (see
Methods; Supporting Information, Fig. S1) revealed a large number of
genotypically identical accessions (Supporting Information, Table S1).
For the coarse-textured P. vaginatum ecotype, only 12 unique
genotypes were detected among the 148 accessions, with just three
widely-distributed genotypes accounting for >85% of the
accessions. This indicates that extensive clonal propagation occurs in
wild populations of this ecotype. Somewhat greater genotypic diversity
was found in the fine-textured ecotype, but extensive clonality was
still present; 24 unique genotypes were identified in 55 accessions.
Four out of eight genotypes in the wild-collected fine-textured
accessions were represented by multiple clonal replicates. For P.
distichum , there were four unique genotypes in the collection of 15
accessions, two of which were unique to our wild collections. The final
SNP dataset for all genotypically unique samples across both species,
including wild-collected and USDA samples, totaled 40 genotypes (Table
1). Together these results suggest that clonal propagation occurs
extensively in wild P. vaginatum and P. distichumpopulations.