Developing a SNP Marker Set for Breeding and Genetics Applications in Cucumber

SNPs are powerful markers highly abundant across the genome. SNP genotyping can be automated resulting in lower cost and higher efficiency in routine applications. SNP calling were carried out in a mapping population of an advanced cucumber line highly susceptible to begomovirus infection and a landrace with high tolerance of begomovirus using three approaches: analysis of COSII fragments from parental lines and virus resistant F5 lines, genomic re-sequencing of one line and transcriptome sequencing of parental lines of the mapping population. Approximately 30,000 SNPs were discovered. From this set approximately 1,900 biallelic SNPs derived from unique sequences were selected. These SNPs are distributed on all 7 cucumber chromosomes. Approximately 1000 polymorphic SNPs between two parental lines are being used to generate a genetic map in a population of 164 RIL while a set of 120 SNPs are routinely used to ensure trueness-to-type and hybridity of commercial varieties and parent lines.  The SNPs will also be applied in identification and rapid introduction of novel genes into cucumber varieties and QTL mapping of interesting traits.