The total of the potato panel (183 genotypes) was genotyped using the new Illumina Infinium 12 K V2 Potato Array [24 (link), 25 (link)]. The V2 array contains 12,808 SNPs, the set of markers from the previous Infinium 8303 Potato Array and additional SNPs selected for genome coverage and on candidate genes and regions with resistant genes. The arrays were read using the Illumina iScan Reader with Infinium® HD Assay Ultra (Illumina Inc., San Diego, CA). Genome Studio 2011.1 software (Illumina, San Diego, CA) was used to assess initial sample quality. Tetraploid (5-cluster) genotyping was based on theta value thresholds, using a custom script from the Solanaceae Coordinated Agricultural Project-SolCAP [14 ]. Following 5-cluster calling, a filtering process was carried out to identify 4859 high-quality markers. These markers were used for further molecular analysis.
Infinium 12 k v2 potato array
Manufactured by Illumina
Sourced in United States
The Infinium 12 K V2 Potato Array is a high-density genotyping microarray designed for the analysis of genetic variation in potato samples. It features approximately 12,000 genetic markers, providing comprehensive coverage of the potato genome. The array enables researchers to efficiently conduct studies on genetic diversity, linkage mapping, genome-wide association, and other applications related to potato genetics and breeding.
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2 protocols using infinium 12 k v2 potato array
1
High-throughput Genotyping of Potato Germplasm
2
Genotyping Potato Samples Using Infinium Array
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Samples were assayed using the Infinium 12K V2 Potato Array on the Illumina iScan (Illumina Inc., San Diego, CA, USA). SNP genotyping and sample quality were analyzed with Illumina's GenomeStudio (v 1.0) software. Samples were genotyped as diploids (three-cluster calling) and as tetraploids (five-cluster calling). The samples were genotyped as diploids (AA, AB, and BB) using the GenomeStudio software auto-clustering feature and the SolCAP custom three-cluster calling file (Felcher et al. 2012) . The samples were also genotyped with five-cluster calling developed for tetraploids (nulliplex = AAAA, simplex = AAAB, duplex = AABB, triplex = ABBB, and quadruplex = BBBB). A custom Perl script was used for tetraploid genotype calling based upon theta value thresholds (Hirsch et al. 2013) . The triploid accessions were called as diploids and tetraploids as no algorithm for triploid calling has been developed. The SNP genotype data were filtered to exclude predetermined low quality SNPs (http://solcap.msu.edu/potato_infinium.shtml) and any loci with ≥10% missing data.
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