Methods for Discovering and Validating Relationships Among Genotyped Animals

Abstract

Genomic selection based on single-nucleotide polymorphisms (SNPs) has led to the collection of genotypes for over 2.2 million animals by the Council on Dairy Cattle Breeding in the United States. To assure that a genotype is assigned to the correct animal and that the animal’s pedigree is correct, the pedigree parents are checked. As of January 2018, the sire was validated for 97% and the dam for 39% of the 2.2 million genotyped animals that passed edits. The genotype is compared with all other genotypes to detect unknown parent-progeny relationships or identical genotypes. If a parent is not confirmed, the grandsire is checked. If a grandsire is unknown or designated as unlikely, possible grandsires are proposed. If SNP conflicts for a parent-progeny pair are concentrated on a single chromosome, a chromosomal deletion or other abnormality is considered; 102 such cases have been detected. All comparisons consider the SNPs in common between the genotypes from the current 30 chip types. Comparison of each genotype with all others is a major and increasing consumer of computer resources. Because processing time has continued to increase, ways to reduce the time have been investigated. In 2012, a set of 1,000 SNPs that are present on nearly all chips was selected for preliminary screening. To further speed up processing, a set of 100 SNPs recently was selected based on minor allele frequency, call rate, and Mendelian consistency. Tests with the 100-SNP set showed that excluding cases with more than three opposite homozygotes could eliminate 99.7% of genotypes without eliminating any confirmed parent-progeny relationships. A continuing effort is required to maintain extensive checking and pedigree correction within the time available for processing incoming genotypes and applying updates caused by pedigree changes. In addition to grandsire checking when genotypes are loaded, maternal grandsire and maternal great-grandsire are checked and discovered using haplotypes from the imputation process as part of the genomic evaluation. For dams with unknown sires, the discovered maternal grandsire is assigned as her sire. The genotypes provide a rich source of information for validation and discovery of genetic relationships.