Potato (Solanum tuberosum L.) was originated and firstly domesticated in South America (https://cipotato.org/potato/). This crop occupies an important position in human consumption, with developing countries expanding its production by nearly 200 million t. from 1961 to 2016/18 (FAOSTAT 2020).
Modern potato breeding methods aided by genomic approaches provide means for shortening breeding cycles and increase the breeding efficiency across selection cycles. Therefore, pipelines with custom SNP subsets are a powerful tool for potato breeders.
The mid-density marker platform for potato genotyping contains 2,147 SNP markers, with an average density of 2-3 SNP/cM on all 12 potato chromosomes. The markers are a subset from the potato V3 Infinium array, which combines SNPs from the SolCAP (Hamilton et al., 2011, Felcher et al., 2012) and SolSTW (Uitdewilligen et al., 2013, Vos et al., 2015) projects. In addition, SNPs linked to the Ryadg and Rysto PVY resistance genes are included. The markers were selected based on their minor allele frequency (MAF > 0.1) in CIP and North American potato breeding germplasm and the quality of their dose response. Dose responsiveness was assessed by comparing the DArTag depth ratio Alt/(Ref +Alt) with the Illumina array signal ratio B/(A+B), and only markers with r2 > 0.6 were included in the final set. In the validation experiment, 90% of the genotype calls were supported by at least 40 reads; at this depth, about 10% of duplex genotypes are expected to be misclassified as simplex or triplex in a general population.
This panel can be used for potato genomic selection and diversity studies.
References:
- FAOSTAT (2020). Rome: FAO. http://www.fao.org/faostat/en/#data/QC
- Felcher K.J., Coombs J.J., Massa A.N. et al. (2012). Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoS ONE, 7(4):e36347. doi: 10.1371/journal.pone.0036347
- Hamilton J.P., Hansey C.N., Whitty B.R. et al. (2011). Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics, 12:302. doi: 10.1186/1471-2164-12-302
- Uitdewilligen J.G.A.M.L., Wolters A-M.A., D'hoop B.B. et al. (2013). A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE, 10(10): e0141940. doi: 10.1371/journal.pone.0141940.
- Vos P.G., Uitdewilligen J.G.A.M.L., Voorrips R.E. et al. (2015). Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history. Theor. Appl. Genet., 128: 2387–2401. doi: 10.1007/s00122-015-2593-y