Potato Infinium SNP Platform

This set of files correspond to sequences and SNPs used in the SolCAP 8300 Infinium Chip.

Potato Transcript Assemblies Corresponding to the Candidate Genes Submitted by the Community - A file of the sequences used for the candidate genes that were placed on the SolCAP 8300 Infinium Chip.

Potato Infinium SNP Annotation - A file with all SNPs on the SolCAP 8300 Infinium Chip with their annotation.

Potato Infinium Manifest File - The manifest file describes the SNP or probe content on the SolCAP 8300 Infinium Chip.

Potato Infinium Cluster File - SolCAP 8300 Infinium Chip cluster file generated by SolCAP using two 4x mapping populations, a 2x mapping population, and a set of diverse lines.

Potato Infinium SNP Chip 5 Cluster Boundary Positions - Dosage cluster calling boundaries for the 5,031 SNPs whose dosage boundaries could be determined. NA indicates that the boundary for a specific marker class (AAAA, ABBB, AABB, ABBB, BBBB) could not be clearly determined. Marker class theta boundaries could only be determined for the marker classes that were present across the two 4x mapping populations, one 2x mapping population, and set of diverse lines that were used to identify the cluster boundaries. This file in conjunction with theta values exported from genome studio can be used to convert a matrix of theta values into dosage genotype scores (AAAA, AAAB, AABB, ABBB, BBBB). It should be noted that the dosage model is highly reliant on thermodynamic and florescence consistency, which can vary with temperature and using this model can add additional error to your genotype calls. Manual curation of your cluster boundaries is recommended.

Coded Potato Infinium GenomeStudio Project - This folder contains coded samples from two 4x mapping populations, a 2x mapping population, and a set of diverse lines that was used to generate the cluster file above. There is also a file potato_infinium_snp.txt in this folder that contains comments about the quality of the SNPs (GOOD, QUESTIONABLE, SEGREGATION, BAD). The designation SEGREGATION indicates that the segregation ratios for at least one of the populations did not match the expected ratios given the parental genotypes.

Potato diversity panel 3 cluster genotype scores - Genotype scores for 6,373 single nucleotide polymorphism markers on 250 lines using a diploid model (AA, AB, BB).

Potato diversity panel dosage genotype scores - Genotype scores for 3,763 single nucleotide polymorphism markers on 250 lines using a dosage model (1x – A and B; diploid AA, AB, and BB; tetraploid AAAA, AAAB, AABB, ABBB, and BBBB).