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Parent and grandsire discovery in a rapidly expanding collection of genotypes.

G. Wiggans




Parent and grandsire discovery in a rapidly expanding collection of genotypes.
G. Wiggans*. Council on Dairy Cattle Breeding Bowie, MD.

For genomic selection based on SNP, the Council on Dairy Cattle Breeding (Bowie, MD) has collected over 3.9 million genotypes. In 2019, over 67,000 genotypes were added monthly on average. To assure that a genotype is assigned to the correct animal and that the pedigree is correct, parents are verified, and each genotype is compared with other genotypes to detect unreported parents or progeny or a duplicate genotype. To speed this discovery, a set of 4,668 SNP was defined based on their presence on nearly all genotyping chips, parent-progeny consistency, and minor allele frequency. Assessment is done after 96 and 1,000 SNP so that comparison can stop if a relationship is unlikely. If both parents are confirmed, only genotypes from potential relatives born < 500 d earlier are checked to detect duplicates. Each SNP genotype is represented by 2 bits rather than 1 byte to save storage space. Because discovered relationships are recorded based on genotype-specific identification, they are unaffected by the assignment of the genotype to a different animal. This process improves efficiency by comparing 2 genotypes only once, using sequential memory access when doing comparisons, and limiting discovery to just once a day to reduce setup time. The design allows use of the presence of progeny and date loaded to exclude comparisons with genotypes unlikely to be related. When a parent is not confirmed, the grandsire may be designated as unlikely using the same SNP set. For unlikely and unknown grandsires, discovery is done weekly based on haplotype matching, which relies on imputation done for weekly evaluations. This haplotype analysis also discovers other relationships, which can provide a check on SNP-based discovery. These changes in discovery method were developed to address the ever-increasing computing time needed as the number of genotypes in the US genetic evaluation system rapidly grows. The new discovery design is expected to enable a continued high level of genotype validation and relative discovery for many years as the genotype collection expands.

Keywords: dairy cattle, parentage discovery, genotype validation.