R Software Program for Conducting Parent-Offspring Test Using SNP Markers.

With advancement of high-throughput genotyping technologies, high-density SNP markers have been widely used for genotyping QTL mapping populations and for characterizing germplasm lines in many corps. Before conducting the SNP data analysis, it is desirable to check the individuals to ensure the integrity of samples for further data analysis. We have developed a computer program written in R language to conduct a parent-offspring quality control test of individuals which are genotyped with a fixed set of SNP markers for further genetic studies and breeding efforts. The program uses monomorphic SNP markers between parents as an input file to calculate similarity between each offspring and their parents. Based on the similarity of parents and individual off-spring, the users can determine the threshold level for the individuals to be included for further study or data analysis. We used an F5-derived soybean population of ‘5601T’ x PI 157440 which was genotyped with 1536 SNP markers on Illumina GoldenGate platform to illustrate the procedure and its application. The R code can be used in any crop which is genotyped with a fixed set of SNP markers.