19Genotyping-by-sequencing (GBS) potentially offers a cost-effective alternative for SNP 20 discovery and genotyping. Here, we report the exploration of GBS in tetraploid potato. 21Both ApeKI and PstI/MspI enzymes were used for library preparation on eight diverse 22 potato genotypes. ApeKI yielded more markers than PstI/MspI but provided a lower read 23 coverage per marker, resulting in more missing data and limiting effective genotyping to 24 the tetraploid mode. We then assessed the accuracy of these SNPs by comparison with 25SolCAP data (5,824 data points in diploid mode and 3,243 data points in tetraploid 26 mode) and found the match rates between genotype calls was 90.4% and 81.3%, 27respectively. Imputation of missing data did not prove very accurate due to incomplete 28 haplotype discovery, suggesting caution in setting the allowance for missing data. To 29further assess the quality of GBS-derived data, a genome-wide association analysis was 30 performed for flower color on 318 clones (with ApeKI). A strong association signal on 31 chromosome 2 was obtained with the most significant SNP located in the middle of the 32 dihydroflavonol 4-reductase (DFR) gene. We conclude that an appropriate choice of 33 enzyme for GBS library preparation makes it possible to obtain high-quality SNPs in 34 potato and will be helpful for marker-assisted genomics. 35 36 Keywords: genotyping-by-sequencing, potato, complexity reduction, genome-wide 37 association mapping, marker-assisted genomics. analysis (Kolech et al. 2016) and linkage disequilibrium analysis (Vos et al. 2017). 54However not all of these SNP markers can actually be used successfully in a given 55 experiment as they may not be polymorphic or may present a low minor allele frequency 56 (MAF) in a given population. For instance, a study based on the Infinium 8303 array 57 found 6,373 usable SNPs in a diploid calling mode and 3,763 usable SNPs in a 58 tetraploid calling mode within a diversity panel comprising 250 clones (Hirsch et al. 59 2013). Another work conducted on a collection of 350 tetraploid cultivated potato 60 varieties found 4,239 usable SNP markers, in tetraploid mode, after removing SNP 61 markers that mapped to multiple locations and SNP markers having more than 20% 62 missing data as well as SNP markers whose minor allele frequency was less than 5% 63 Vos et al. 2015Vos et al. , 2017. 66Another drawback of such highly parallel SNP genotyping platforms is that they typically 67 carry a high cost per sample for first-time or small-scale users. In contrast, approaches 68 that enable the simultaneous discovery and genotyping over the entire genome are 69 becoming an appealing alternative. For instance, an optimised RAD-seq approach was 70 reported in potato (Jiang et al. 2016). Similarly, genotyping-by-sequencing (GBS) 71 approaches offer a highly cost-effective alternative for simultaneous SNP discovery and 72 genotyping (Elshire et al. 2011; Poland et al. 2012; Sonah et al. 2013). Moreover, GBS 73 provides other advantages such as red...

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