Ploidy estimates with genome-wide heterozygosity
For GBS-genotyped samples that vary in ploidy, measures of genome-wide heterozygosity can potentially be used as a complement to flow cytometry for identifying ploidy variation (Gompert & Mock, 2017). This approach is based on the rationale that if all reads are mapped to a diploid reference genome, any subgenome differences in polyploids will be recorded as ‘heterozygous’ loci. At increasing ploidy levels, each additional subgenome will introduce more differences and increase the number of heterozygous locus calls. This approach can also be used to identify diploid hybrids, which are identifiable as showing a quantum increase in heterozygosity with no associated increase in genome size based on flow cytometry. We employed these strategies to assess ploidy variation in the Paspalum samples, focusing on genotypically unique accessions with the highest sequence coverage. Genome-wide heterozygosity was calculated as the individual inbreeding coefficient (F) with the het function in plink (Purcell et al., 2007).