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Dataset for: Potato genotyping using Infinium Potato Array SNPs.

International Potato Center Dataverse OAI Archive

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Title Dataset for: Potato genotyping using Infinium Potato Array SNPs.
 
Identifier https://doi.org/10.21223/P3/AAIHVZ
 
Creator Bonierbale, Merideth
Lindqvist-Kreuze, Hannele
 
Publisher International Potato Center
 
Description 103 tetraploid breeding clones were genotyped using the SolCAP Infinium Potato SNP Platform containing 8300 SNP. The objectives of the study were to examine in this set of germplasm: (i) the genetic substructuring and (ii) the association of SNP markers with late bligh resistance phenotype. The DNA of the germplasm was extracted at 2012 at CIP and submitted for genotyping to Michigan State University on a service contract. The normalized allele signal ratio (normalized X divided by the sum of normalized X and normalized Y) was calculated using Illumina GenomeStudio software and exported in csv format. A custom R script was used to call and filter the genotypes. Each SNP was run through the CodomMarker function of the fitTetra R package. Each sample was categorized into one of five possible tetraploid genotypes (AAAA, AAAB, AABB, ABBB, or BBBB). Markers were filtered allowing for at maximum 5% missingness.
 
Subject Agricultural Sciences
SNPs
Tetraploid potato
Linkage mapping
Association mapping
Polymorphism
 
Language English
 
Contributor Administrator, CIP
International Potato Center
CGIAR Research Program on Roots, Tubers and Bananas (RTB)
David de Koeyer, Agriculture and Agri-Food Canada (AAFC)
Project: Solanaceae Coordinated Agricultural Project (SolCAP): Infinium Potato SNP Platform
 
Relation Potato Infinium SNP Platform: This set of files correspond to sequences and SNPs used in the SolCAP 8300 Infinium Chip: http://solcap.msu.edu/potato_infinium.shtml
 
Type xls