Peter G. Vos, Jan G. A. M. L. Uitdewilligen, Roeland E. Voorrips, Richard G. F. Visser, Herman J. van Eck

Theoretical and Applied Genetics; December 2015, Volume 128, Issue 12, pp 2387-2401

Abstract

Key message

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.

Abstract

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.

Fig. 1

SNP Resources. Venn diagram of SNPs used for development of the SolSTW array (Orange). SNPs originated from the 8303 SolCAP array are indicated in purple, SNPs originated from Uitdewilligen et al. (2013) are indicated in blue and SNP from Hamilton et al. (2011) are indicated in green. This figure does not display 87 SNPs included in the SolSTW array, which have been described by both the SNP discovery studies (Uitdewilligen et al. 2013 and Hamilton et al. 2011) (color figure online).