Example
We applied our novel approach to a freely available data set. FruitBreedomics' apple dataset was used to demonstrate some of the techniques that we are uniquely implementing. We used apple SNP array dataset provided by Dr. Muranty.
Apple dataset
A total of 1425 diploid individuals with their complete pedigree information was analyzed with the Axiom®Apple480K array. A set of 253 K SNPs were used to conduct analysis.
Highlight - NO MANUAL MANUPULATION OF DATAFILE
We used BED files provided by Muranty et al. and filtered entire dataset based for MAF=0.47 and ended up using 6895 SNP markers for further analysis.
Initial ME checking: "0" errors
Missing calls - 208,211 (0.18%)
After implementing two iterations our novel marker phasing and imputation pipeline, 24 duos and 59 trios MSEs were detected, which were further identified, deleted and imputed without any manual work. At the end, there were "0" MSE in the dataset.
Discovery of New Pedigree Relationships
We applied propriety methods to estimate various degrees of relationships in the datasets.
Newly discovered relationships are 50% identical-by-descent (IBD) i.e., there is an immediate parent-child relationship (first degree), and age data from breeding programs can determine which one is parent and which one is progeny.
In the network plot -
Color gold - Grand Parent
Color Green - Parents
Color Cyan - Seedlings (Two groups)