Testing for Polled using Haplotypes

Paul VanRaden and Dan Null, AIPL

A haplotype test for Polled was introduced for Holsteins (HHP) in August, and a nearly identical test for Jerseys (JHP) could be added in September. In both cases, laboratory tests for Polled are included as data for genotyped animals, together with an assumed status of homozygous normal for USA and CAN bulls with at least 500 daughters and not designated as Polled. Using this data, Polled status is imputed for all other genotyped animals. A JHP file has been prepared and could now be examined by AJCA. AIPL could also develop a test for Brown Swiss (BHP), and the USA Brown Swiss office is preparing to send AIPL their Polled status, as AJCA did for the JHP test.

The dominant inheritance of polled / horned was discovered more than a century ago by USDA (Spillman, 1905), but exact genetic tests were not available until last year because at least 2 different mutations in the same genetic region around 1.6-1.9 Mbases (UMD3.1 map) on chromosome 1 cause the polled trait (Medugorac, 2012). The first mutation is called Celtic, where 10 base pairs at 1,706,051–1,706,060 are deleted and 212 base pairs of DNA from 1,705,834–1,706,045 are duplicated and inserted instead. The second mutation is called Friesian and has been fine mapped to a small haplotype region, but the exact causative QTL is not yet known. Both mutations are within the same 75-marker window that AIPL currently uses spanning from .1 to 3.5 Mbases on BTA1. Some haplotypes contain the Celtic mutation and others contain the Friesian mutation. An animal is called heterozygous if it has either and is called homozygous if both of its haplotypes contain Polled, regardless of which mutation (2 Celtics, 2 Friesians, or 1 of each). This is consistent with -P and -PP coding in all breeds.

Medugorac (2012) reported that the Friesian mutation was present only in Holsteins, but by examining haplotype similarity we found that the Friesian mutation actually has slightly higher frequency than the Celtic mutation in Jerseys. The Friesian mutation was introduced to Jerseys primarily via Fair Weather Bernard-P (USA634104) and Fair Weather Case-PP (USA633214) both born in 1978, whereas the earliest genotyped carrier of the Celtic mutation is Normsland Belle Boy-P (USA592073) born in 1960. Jersey pedigree files include Polled ancestors earlier than this (Herron, 2011), but those animals are not genotyped. Jerseys and Holsteins share fairly long sections of both the Friesian and Celtic haplotypes, but very little of either haplotype is preserved in the Brown Swiss breed, which may have a different mutation as noted by Medugorac (2012).

References for Polled:

Medugorac et al., 2012. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039477

Herron, J.E. 2011. http://www.polledjerseys.com/history.htm

Spillman, W. J. 1905. Mendel’s law in relation to animal breeding. Journal of Heredity. http://jhered.oxfordjournals.org/content/os-1/2/171.full.pdf

VanRaden et al. 2013. https://www.uscdcb.com/reference/changes/eval1308.htm