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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #314839

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content

Author
item Null, Daniel
item Cole, John
item Sun, Chuanyu - Collaborator
item Vanraden, Paul

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/17/2015
Publication Date: 7/12/2015
Citation: Null, D.J., Cole, J.B., Sun, C., Van Raden, P.M. 2015. Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):800(abstr. 647).

Interpretive Summary:

Technical Abstract: There is growing interest in cattle that are naturally polled, but the polled allele has a very low frequency. The best way to increase its frequency is by index selection, which requires known polled status for all animals. Laboratory tests for polled are used as data, and US and Canadian bulls with >=500 daughters and not designated as polled are assumed homozygous normal. Polled status is imputed for all other genotyped animals using these data. There are 2 mutations in the region around 1.7-1.9 Mb (UMD3.1) on BTA1 known to cause polled. The Celtic mutation is a deletion and an insertion, and the Friesian mutation a duplication. Both are located in a 75-marker window spanning 0.1-3.5 Mb on BTA1. An animal is heterozygous if it has either mutation, and is homozygous if both haplotypes contain polled, regardless of the mutation. This is consistent with -P and -PP coding in all breeds. Brown Swiss, Holstein, and Jersey polled haplotypes have frequencies of <1%, 0.71%, and <1%, respectively. The National Dairy Database has genotypes for only 678,848 of 39 million cows with records. Gene content (GC) for non-genotyped animals, the number of polled haplotypes in an animal's genotype, was computed using records from genotyped relatives. The GC are real-valued and range between 0 and 2. Prediction accuracy was checked by comparing polled status from recessive codes and animal names to GC for 1,615 non-genotyped Jerseys with known status. 97% (n = 675) of horned animals were correctly assigned GC near 0, and 3% (n = 19) were assigned GC near 1. Heterozygous polled animals had GC near 0 (52%, n = 474) and near 1 (47%; n = 433), although 3 animals were assigned a GC near 2. The expectation for GC is near 1 for heterozygotes, but can be lower if many polled ancestors have unknown status or when pedigree is unknown. In those cases GC may be set to twice the allele frequency, which is low. Some with -P in the name may actually be PP. All homozygous polled animals (n = 11) were assigned GC near 2. Polled status for non-genotyped animals can be accurately determined, and this method can be extended to other genes of interest.