Recessive haplotypes

We are now reporting recessives in the inbreeding checker, flagging matings that have a possibility of producing affected offspring, where the information is available.

Recessives only present a diseased phenotype when an animal inherits two copies - one from each parent. These variants remain silent in carriers, but when two carriers are mated, there is a risk of producing affected offspring. Identifying carriers is therefore important, yet challenging.

In some cases, the causative mutation is directly implemented in the SNP array (used for genomic evaluations), however, in other cases they need to be inferred from the surrounding genotype (haplotype).

Recessive diseases can cause a range of severe issues, affecting development, fertility, production - some can even be lethal. Understanding and tracking carrier status is essential for responsible breeding decisions and for reducing the incidence of harmful genetic conditions in dairy populations.

Holstein haplotypes

The table below details the haplotypes that we are currently publishing.

*Call rate is the percentage of carriers made through AHDB's recessive calling that matched other sources of recessive information. If this column is blank, the recessive calls are made exclusively by third-party data providers.

Processing data sources

Primary data

Many third-parties have been kind enough to supply their data from directly testing for recessive diseases. Where these have been supplied for an individual, these take priority over AHDB's data. Many of these test a wider range of traits and are supplied in regular data transfers from third-party suppliers. Please directly contact the test provider for more information on the testing process and reliability of calls made.

Currently, transfers are received from: Cogent, Genus, National Milk Records, Holstein UK, Interbull.

AHDB recessive calls

Where a direct recessive test is not available for an individual and when a genotype is supplied to AHDB for a genomic evaluation, we attempt to determine the carrier status for the recessives using the genotype.

In some cases, this is simply checking the causative SNP and making a direct call. In many cases, we do not receive the causative SNP from the genotype supplier, so we use imputation to predict the carrier status based on the surrounding genotype.

Importantly, this is not a direct test of the carrier status (unlike many third-party tests), but rather an estimate of the most likely given the information. The calls that are made through this process are validated against other tests where possible, and recessive calls are only published in this way if there is reasonable alignment with other, more reliable testing methods. See the table above for call rate values.

Although it is unlikely, it is possible that the recessive calls made in this way may change over an animal's lifetime. Usually this is because either an additional, different, genotype has been supplied for the animal, or as our genomic reference population grows the imputation slightly changes. 

Acknowledgement

We would like to thank Cogent, Genus, and National Milk Records for their support, cooperation, and enthusiasm to provide data and information for this project.

We would also like to thank Holstein UK for regular data supply.