An R package for SNP marker-based parent-offspring tests.
BACKGROUND
With the advancement of genotyping technologies, whole genome and high-density SNP markers have been widely used for genotyping of mapping populations and for characterization of germplasm lines in many crops. Before conducting SNP data analysis, it is necessary to check the individuals to ensure the integrity of lines for further data analysis.


RESULTS
We have developed an R package to conduct a parent-offspring test of individuals which are genotyped with a fixed set of SNP markers for further genetic studies. The program uses monomorphic SNP loci between parents and their progeny genotypes to calculate the similarity between each offspring and their parents. Based on the similarity of parents and individual offspring, the users can determine the threshold level for the individuals to be included for further data analysis. We used an F5-derived soybean population of '5601T' x PI 157440 that was genotyped with 1,536 SNPs to illustrate the procedure and its application.


CONCLUSIONS
The R package 'ParentOffspring' coupled with the available SNP genotyping platforms could be used to detect the possible variants in a specific cross, as well as the potential errors in sample handling and genotyping processes. It can be used in any crop which is genotyped with a fixed set of SNP markers.
Hussein
H
Abdel-Haleem
Pengsheng
P
Ji
H Roger
HR
Boerma
Institute of Plant Breeding, Genetics and Genomics & Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd,, Athens, GA 30602, USA. zli@uga.edu.
Zenglu
Z
Li