Exploring the potential and limitations of genotyping-by-sequencing for SNP discovery and genotyping in tetraploid potato

Genotyping-by-sequencing (GBS) potentially offers a cost-effective alternative for SNP discovery and genotyping. Here, we report the exploration of GBS in tetraploid potato. Both ApeKI and PstI/MspI enzymes were used for library preparation on eight diverse potato genotypes. ApeKI yielded more markers than PstI/MspI but provided a lower read coverage per marker, resulting in more missing data and limiting effective genotyping to the tetraploid mode. We then assessed the accuracy of these SNPs by comparison with SolCAP data (5,824 data points in diploid mode and 3,243 data points in tetraploid mode) and found the match rates between genotype calls was 90.4% and 81.3%, respectively. Imputation of missing data did not prove very accurate due to incomplete haplotype discovery, suggesting caution in setting the allowance for missing data. To further assess the quality of GBS-derived data, a genome-wide association analysis was performed for flower color on 318 clones (with ApeKI). A strong association signal o...