Speckle Park International (SPI) has worked collaboratively with staff at the Animal Genetics & Breeding Unit (AGBU) and the Agricultural Business Research Institute (ABRI) to incorporate genomic information into the calculation of Estimated Breeding Values (EBVs) within Speckle Park BREEDPLAN, using a method known as Single-Step. This major upgrade was implemented in the July 2023 Speckle Park BREEDPLAN evaluation.
Single-Step BREEDPLAN uses analytical software developed by AGBU, a joint venture of NSW Department of Primary Industries (NSW DPI) and the University of New England (UNE), funded by Meat and Livestock Australia Limited (MLA). The Single-Step BREEDPLAN evaluation utilises pedigree, performance and genomic information simultaneously. The evaluation takes account of each animal’s actual genetic relationship with all other genotyped animals, including those in the reference population. The reference population is the set of Speckle Park animals that have genotypes (SNP data) and phenotypes (performance records) for each particular trait.
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 SPI members.
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 SPI. 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 SPI. 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.
Utlimately, implementation of Single-Step BREEDPLAN for the Speckle Park breed provides SPI members with greater returns on their investment in the genotyping of seedstock cattle.