Introduction of Single-Step to Brahman GROUP BREEDPLAN
Publication of the first Single-Step BREEDPLAN analysis and release of Intramuscular Fat and Percent Normal Sperm EBVsApr 2020
Exciting times ahead for members of the Australian Brahman Breeders’ Association with the introduction of significant changes to the BREEDPLAN software used to calculate EBVs for Australian Brahman animals. These changes were applied in the April 2017 Brahman GROUP BREEDPLAN analysis and is now incorporated into the monthly analysis.
This has resulted from the implementation of a new approach for incorporating genomic information into the calculation of Estimated Breeding Values (EBVs) within Brahman BREEDPLAN. This technology is known as “Single-Step” BREEDPLAN and heralds a new age in BREEDPLAN genetic evaluation and the implementation of genomic selection for the Australian beef industry, and specifically the Brahman breed.
What is Single-Step BREEDPLAN?
Single-Step BREEDPLAN is a new genetic analysis where the pedigree, performance and genomic (DNA) information is processed and analysed all together. The single-step analysis is a significant improvement on the blending approach, in that it takes account of each animal’s actual genetic relationship based on its genotype with all other genotyped animals, including those in the reference population. In the blending approach, each animal with a DGV is assumed to have the same genetic relationship with the reference population. The reference population is the set of Australian Brahman animals that have genotypes (SNP data) and phenotypes (performance records) for a particular trait.
Overall, the most important effects of the switch to Single-Step BREEDPLAN are that:
- Genomic information will contribute to all EBVs that are calculated within the main multi-trait BREEDPLAN analysis.
- Animals that had previously obtained Blended EBVs will now show a range of accuracies in their EBVs for 200-Day Weight and Days to Calving. That range reflects the genomic relationship between the animal and the reference population, and will vary from animal to animal.
- The Days to Calving EBV now incorporates information from research data on two genetically correlated traits – first lactation anoestrous interval and heifer age at puberty. This data will ensure that the single-step analysis includes the same data previously used to derive the prediction equations and then to generate the DGV for Days to Calving.
- Unknown parents may be identified (provided the animals have genomic information available).
- Genomic information will contribute to not only the EBVs of the animal that has been genotyped, but will also contribute to the EBVs for the animal’s relatives (e.g. parents, progeny). This is unlike blending where the genomic value was only included into the individual’s own EBV (not its parents or progeny).
- With a traditional pedigree based approach, the relationships between animals within Brahman BREEDPLAN are determined by pedigree alone. For example, pedigree would predict that the genetic relationship between full siblings (i.e. animals with the same sire and dam) is 0.5. This means that full siblings are predicted to have 50% of genes in common when calculating traditional pedigree-based breeding values. Now in single-step the relationship between individuals is determined using their SNP genotypes and will vary from the previously assumed average relationship. In the case of full-sibs this may now vary from 0.35 to 0.65.
Other Changes to the Brahman Analysis
In addition to the introduction of the single-step technology, a number of other changes were introduced in the April Brahman BREEDPLAN analysis. These included:
- The calculation and reporting of the EBV for Carcase Intra Muscular Fat (IMF). Note that only IMF measurements derived from abattoir data are used in the calculation. Scan IMF measurements are not used in the Brahman analysis.
- The introduction of a new male reproduction trait, Percent Normal Sperm (PNS). PNS is measured as part of the bull breeding soundness evaluation (BBSE) at around 2 years of age. It is expected that sires with higher (ie more positive) PNS EBVs will produce sons with higher PNS compared to sires with lower (ie more negative) PNS EBVs.
- The elimination of the blending of DGVs. With the inclusion of the genotype information in the single-step analysis, it is no longer possible to blend the DGVs for 200-Day Weight and Days to Calving.
The Brahman BREEDPLAN analysis included significant changes:
- the introduction of the Single-Step BREEDPLAN software,
- the inclusion of additional traits, and
- the cessation of the blending of DGVs for 200-Day Weight and Days to Calving EBVs.