ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2015
Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Research progress on genomic selection breeding technology for crops.Protoplasma · 2026Review
- SNPoptimizer: a scalable genetic-algorithm framework to derive minimal discriminatory SNP panels from large genotyping datasets.Molecular breeding : new strategies in plant improvement · 2026Article
- Starch and tuber traits of diploid potato lines B26 and B100 and their hybrids.BMC plant biology · 2026Article
- The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus.The New phytologist · 2026Article
- Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding.The plant genome · 2026Article
- Tracing modern breeding introgressions in European potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Leveraging unmanned aerial vehicle derived multispectral data for improved genomic prediction in potato (Solanum tuberosum).The plant genome · 2025Article
- The phased pan-genome of tetraploid European potato.Nature · 2025Article
- SpudDB: a database for accessing potato genomic data.Genetics · 2025Article
- Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis.The plant genome · 2024Article
- Diploid inbred-based hybrids: fast-forward breeding approach in potatoes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Review
- Tailoring Genomic Selection forGenes · 2024Review
- QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing.G3 (Bethesda, Md.) · 2024Article
- Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.The plant genome · 2024Article
- Modern Breeding Strategies and Tools for Durable Late Blight Resistance in Potato.Plants (Basel, Switzerland) · 2024Review
- Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.).The plant genome · 2024Article
- Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice.Rice (New York, N.Y.) · 2024Article
- Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato.Frontiers in plant science · 2024Article
- Potato soup: analysis of cultivated potato gene bank populations reveals high diversity and little structure.Frontiers in plant science · 2024Article
22 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
key messageA 20K SNP array was developed and a comprehensive set of tetraploid cultivar was genotyped. This allowed us to identify footprints of the breeding history in contemporary breeding material such as identification of introgression segments, selection and founder signatures. A non-redundant subset of 15,138 previously identified SNPs and 4454 SNPs originating from the SolCAP project were combined into a 20k Infinium SNP array for genotyping a total of 569 potato genotypes. In this study we describe how this SNP array (encoded SolSTW array) was designed and analysed with fitTetra, software designed for autotetraploids. Genotypes from different countries and market segments, complemented with historic cultivars and important progenitors, were genotyped. This comprehensive set of genotypes combined with the deliberate inclusion of a large proportion of SNPs with a low minor allele frequency allowed us to distinguish genetic variation contributed by introgression breeding. This "new" (post 1945) genetic variation is located on specific chromosomal regions and enables the identification of SNP markers linked to R-genes. In addition, when the genetic composition of modern cultivars was compared with cultivars released before 1945, it appears that 96% of the genetic variants present in those ancestral cultivars remains polymorphic in modern cultivars. Hence, genetic erosion is almost absent in potato. Finally, we studied population genetic processes shaping the genetic composition of the modern European potato including drift, selection and founder effects. This resulted in the identification of major founders contributing to contemporary germplasm.
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