KASPar: An Efficient and Cost-Effective Technology for SNP Genotyping in Cotton

Cotton is the world’s most cultivated natural fiber and oil seed crop. Lack of reference genome sequence and tetraploid nature of cultivated cotton pose numerous challenges to develop SNP markers. While in silico SNP detection algorithms such as AutoSNP and QualitySNP can provide candidate SNP information based on SNP quality and confidence scores, validation of these SNPs is still an expensive process. In order to reduce the cost of SNP validation and genotyping in cotton, we have utilized KASPar (KBiosciences, Hoddesdon, UK), a cost-effective single-plex SNP genotyping technology. KASPar assays were designed for 150 candidate SNPs using Primer Picker software (http://www.kbioscience.co.uk/primerpicker/). The Assay consists of three unlabeled interrogation primers that include two allele specific primers to target SNP and one common primer. KASPar data obtained from a FRET capable plate reader with relevant filters for FAM and VIC flourescence were plotted to determine the genotype clusters. The genotyping results and efficacy of this cost-effective SNP genotyping system for marker development and marker-assisted selection in crops will be discussed.