Table 1. Parentage SNP selection criteria for use in globally diverse breeds of sheep.
Criteria | Benefits |
Concurrent membership on OvineSNP50 Bead Array (autosomes) | Increased standardization |
Highly informativea in at least 36 ISGC breed groups and a U.S. sheep panelb | Increased PE and PI |
Concurrent membership in any of four parentage SNP setsb | Increased standardization |
Only two nucleotide alleles observed | Improved assay design |
Not part of an insertion or deletion polymorphism | Increased testing accuracy |
Absence of large blocks of repetitive DNA nearby | Increased quality controlc |
Unique map location | Increased testing accuracy |
Even distribution of parentage SNPs (approximately 15 Mb) | Reduced allelic association |
Nearby polymorphisms identified in 166 sheep and 50 breedsd | Increased testing accuracy |
Parentage SNP region correctly amplified by PCR in a U.S. sheep panel and verified by Sanger sequencing | Increased testing quality control |
Consistent Mendelian inheritance patterns in 95 tetrad familiese | Increased test validation |
MAF greater than or equal to 0.3 in the specified group.
See Materials and Methods for description of sets.
Large blocks of repeats (>1 kb) in nearby sequence precludes the production of unique 750 bp PCR fragments for Sanger sequencing, and thus hinders independent validation of genotypes.
Nearby SNPs and indels identified within approximately 350 bp of the parentage SNP.
Described in Materials and Methods.