A Pipeline for Robust Marker Calling from Infinium SNP Arrays for Diploid Crops

Single-nucleotide polymorphisms (SNPs) markers have been recognized as the marker of choice in genetic studies due to their suitability for high throughput genome-wide genotyping. Several SNP genotyping platforms and related software for genotype calling are commercially available, including Illumina’s Infinium platform and Genome Studio software.

Although SNP genotyping is highly automated, a common approach for filtering of the well performing markers has not been published yet. Moreover, the application of a 20K array on diploid apple learned that around 7% of the markers were incorrectly called. All this made the genotyping a time-consuming procedure with an unnecessary high error rate.

We present a semi-automatized Excel based pipeline for SNP filtering and calling using Genome Studio derived data as input. This pipeline efficiently distinguishes robust, problematic and truly monomorphic markers. It also resolves erroneous callings that are due to paralogous loci, null alleles, or to additional SNP at the primer site. The final set of SNP markers are grouped according to their segregation pattern and and adjusted to JoinMap format. Completion of the pipeline takes just 2-3 hours. The pipeline has been calibrated on three mapping populations and has been applied on another 20 populations. It showed to be highly efficient, as 99.7% of the resulting polymorphic markers mapped easily.

This work was performed in the framework of the EU-FruitBreedomics project, a central goal of which is to accelerate and increase the efficiency of Rosaceous cultivar release through the delivery of molecular markers that are of use for marker assisted breeding.