Hereford Cattle Society Implement Single-Step BREEDPLAN Analysis

Additional Enhancements Also Released

Feb 2023

The Hereford Cattle Society (HCS) has become the next breed society in the UK to incorporate genomic information into their BREEDPLAN genetic evaluation. This represents one of several significant enhancements delivered to the HCS with the release of their January 2023 BREEDPLAN analysis.

Members of the HCS have invested considerably in the collection of 50K SNP genotypes for registered cattle, with the HCS subsequently deciding to provide greater return on this investment by including this information in their BREEDPLAN evaluation. SNP data is now being used along with pedigree and performance data to calculate BREEDPLAN EBVs and accuracy “in one step”. This applies to all traits in a multi-trait model combining birth, growth, fertility and carcase traits. As such, SNP data provides additional information in these calculations by accounting for the true genomic relationships among animals and how the SNP information relates to the performance records for each trait in the analysis. An important feature of the Single-Step BREEDPLAN approach is that complete use is made of the high density of genotypes recorded by HCS members. This currently amounts to over 12,000 animals with over 50,000 SNPs per genotype now being included in the BREEDPLAN evaluation.

There are advantages that come with genomics and the Single-Step BREEDPLAN model. When young animals are genotyped at an early stage in life, they can achieve higher levels of EBV accuracy earlier in life – especially for traits expressed later in life – than is possible with a conventional (non-genomics) BREEDPLAN model. This equates to greater accuracy of selection decisions, at an earlier stage in the growth of animals, for members of the HCS. Furthermore, for breeders with small herds, accuracy levels are often limited by small contemporary group sizes even when pedigree and performance records are available. If calves are genotyped, however, they can accumulate additional information – and accuracy – via their relationship to the wider genotyped and performance recorded population.

An advanced algorithm for accuracy calculations was also implemented in the Single-Step BREEDPLAN evaluation provided to the HCS. This algorithm represents a “world first” approach to modelling SNP effects in accuracy calculations, given the high density of genotypes that are used in the BREEDPLAN evaluation.

In addition to genomics, a new set of genetic parameters were also introduced to the HCS with the release of their January 2023 BREEDPLAN analysis. As populations change over time and as performance recording practices change – especially for traits that are either less common in their levels of recording (e.g. because of cost) or for newly-introduced traits which are still gaining uptake among beef cattle breeders – it is necessary to regularly update the genetic parameters used in the calculation of EBVs. In relation to the HCS, the number of records available has increased considerably since the first BREEDPLAN evaluation was introduced. The re-estimation of genetic parameters was finalised in 2022, with test evaluations completed to understand the impact of the new parameters on BREEDPLAN EBVs and accuracy reported for the HCS. With the implementation of updated genetic parameters in January 2023, the parameters used in the BREEDPLAN evaluation reflect the on-going investment in data collection by HCS members.