Development and analysis of an 20K SNP array for potato (Solanum tuberosum): An insight in the breeding history

P.G. Vos, J.G.A.M.L. Uitdewilligen, R.E. Voorrips, R.G.F. Visser, H.J. van Eck

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

A 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.
Original languageEnglish
Pages (from-to)2387-2401
JournalTheoretical and Applied Genetics
Volume128
Issue number12
DOIs
Publication statusPublished - 2015

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Solanum tuberosum
Breeding
Single Nucleotide Polymorphism
potatoes
history
breeding
cultivars
Genotype
introgression
genotype
Genetic Phenomena
genetic variation
vpr Genes
Founder Effect
founder effect
Tetraploidy
Population Genetics
genotyping
tetraploidy
gene frequency

Cite this

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title = "Development and analysis of an 20K SNP array for potato (Solanum tuberosum): An insight in the breeding history",
abstract = "A 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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Development and analysis of an 20K SNP array for potato (Solanum tuberosum): An insight in the breeding history. / Vos, P.G.; Uitdewilligen, J.G.A.M.L.; Voorrips, R.E.; Visser, R.G.F.; van Eck, H.J.

In: Theoretical and Applied Genetics, Vol. 128, No. 12, 2015, p. 2387-2401.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Vos, P.G.

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