Cotton High-throughput SNP Genotyping with the CottonSNP63K Array
Development of the CottonSNP63K Array was coordinated by Amanda M. Hulse-Kemp in David Stelly’s lab at Texas A&M University. Development was made possible also by the members of the International Cotton SNP Consortium effort who contributed ideas, time, potential SNPs, genotyping samples and/or array data to the effort. The contributions, array composition, development, performance and other descriptions of the Array will be detailed in refereed journal articles (submission expected in the first quarter of 2015, and electronic publication in mid-2015).
The standardized Illumina Infinium array contains 63,058 putative SNPs of which 45,104 are putative intra-specific SNPs for use within the cultivated cotton species, G. hirsutum, and 17,954 are putative inter-specific SNP markers for use with crosses of other cotton species with G. hirsutum. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis to provide high-quality data for 10,314 monomorphic probes and 38,822 polymorphic markers on the array. Pre-publication access to the generated cluster file is available HERE.
The panel will have varied uses, including genetic diversity analysis, genetic mapping, QTL analysis, candidate gene discovery, marker assisted selection, genomic selection and genome sequence assembly. Intra-specific SNPs were discovered and validated on germplasm lines that included Australian, US, Indian and Chinese varieties of Gossypium hirsutum. The technology allows for processing of sets of 24 samples over the period of three days. Additionally it is possible to add up to 20,000 attempted SNP assays to the standard set of public SNPs included on the array.
Illumina Infinium Platform
The Infinium platform detects SNP alleles by adding a fluorescence-labeled allele-specific nucleotide via single-base extension and subsequent detection of the fluorescent color. The Illumina Infinium chips are sophisticated silicon-based array devices. If you are interested to learn about the technology that drives the Infinium genotyping arrays, watch the following video: