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Pedigree Reconstruction with Genome-Wide Markers in Potato

Jeffrey B. Endelman, Cari A. Schmitz Carley, David S. Douches, Joseph J. Coombs, Benoit Bizimungu, Walter S. De Jong, Kathleen G. Haynes, David G. Holm, J. Creighton Miller Jr, Richard G. Novy, Jiwan P. Palta, David L. Parish, Gregory A. Porter, Vidyasagar R. Sathuvalli, Asunta L. Thompson, G. Craig Yencho
American journal of potato research 2017 v.94 no.2 pp. 184-190
Solanum tuberosum, breeding, breeding programs, data collection, genetic distance, genotyping, germplasm, paternity, pedigree, pollen, potatoes, single nucleotide polymorphism, tetraploidy
Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 719 tetraploids was genotyped with an Infinium SNP array, yielding 5063 high-quality markers. Based on pedigree records, the dataset contained 198 parent-offspring trios, of which 182 were consistent with the marker data. For 13 of the 16 trios with a pedigree error, the true parent was identified in the population. By comparing the additive relationship matrix calculated from pedigree with the genetic distance calculated from markers, an additional 24 pedigree modifications were proposed, including the paternity of several varieties developed with bulk pollen. To ensure accurate pedigree records are published in the future, we recommend that new varieties be SNP genotyped and checked against this dataset.