Santa Gertrudis Implement Single-Step BREEDPLAN

Mar 2021

The Santa Gertrudis Breeders` (Australia) Association (SGBAA) 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 Santa Gertrudis BREEDPLAN, known as Single-Step. This major upgrade will be implemented in the March 2021 Santa Gertrudis BREEDPLAN analysis.

What is Single-Step BREEDPLAN?

Single-Step BREEDPLAN is new analysis 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 analysis utilises pedigree, performance and genomic information simultaneously. The analysis 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 Australian Santa Gertrudis animals that have genotypes (SNP data) and phenotypes (performance records) for each particular trait. Currently the reference population for Australian Santa Gertrudis includes animals measured and genotyped in the CRC, along with animals genotyped and recorded in the Santa Gertrudis BIN program and current R&D projects (Repronomics) and several industry herds.

Overall, the most important effects of the implementation of Single-Step BREEDPLAN are that:

  • The evaluation requires high density SNP genotyping and those profiles are submitted to the BREEDPLAN genomic pipeline where they undergo extensive QA checking before being eligible for inclusion in the Single-Step run.
  • Genomic information contributes to all EBVs that are calculated within the main multi-trait BREEDPLAN analysis, resulting in an increased spread in the EBVs and an improvement in the accuracy in the EBVs. The amount of change depends on the size of the reference population for a given trait, and the relatedness of a genotyped individual to the existing reference population.
  • The Days to Calving EBV now incorporates information from research data on two highly heritable, genetically correlated traits – heifer age at puberty and first-calf cow anoestrous interval.
  • Single-Step may identify previously unknown pedigree (or multiple sire mated) of genotyped individuals, if their parent(s) have been genotyped.
  • Genomic information contributes mostly to the EBVs of animals with genotypes, but does also contribute to the EBVs of their ungenotyped relatives (e.g. parents, progeny).

Prior to Single-Step, the evaluation used relationships between animals within Santa Gertrudis BREEDPLAN that were determined by the pedigree provided. For example, the evaluation modelled a genetic relationship between full siblings (i.e. animals with the same sire and dam) of 0.5. This means that full siblings are predicted to share on average 50% of their genes in common. Whereas in Single-Step BREEDPLAN, high density SNP genotypes are used to determine the actual degree of relationship between individuals. In the case of full siblings, their relationship may vary from 0.35 to 0.65 depending on the number of SNP they share in common. Similarly, while pedigree may indicate that two animals are unrelated, they may actually share common genes and if genotyped, they will have a genomic relationship greater than 0.

The Single-Step analysis relies on the construction of the genomic relationship matrix (GRM) for a given breed. Important to this step is ensuring the animals entering the evaluation are from the given breed. Therefore, as part of the genomic pipeline QA checking, the genomic breed composition of an individual is determined. The GRM is only constructed for those animals that are ≥80% related to the existing population of genotyped animals in the breed. The software also identifies possible discrepancies in the society recorded pedigrees for genotyped animals. Breeders will be notified of these discrepancies and encouraged to re-sample animals to ensure DNA integrity and in some cases, pedigrees may need to be corrected by the SGBAA.

Other Changes to the Santa Gertrudis Analysis

In addition to the implementation of the single step method, a Shear Force EBV will be switched on in the March Santa Gertrudis BREEDPLAN analysis.

Shear Force EBVs are estimates of genetic differences between animals in meat tenderness. Shear force is measured as the force required (in kilograms) to pull a mechanical blade through a piece of cooked meat. It is based upon direct carcase measurements recorded in research projects. Shear force EBVs are expressed in kg, with lower (more negative) EBVs predicting lower shear force i.e. more tender meat.


The March 2021 Santa Gertrudis BREEDPLAN analysis included a major upgrade. Single-Step software has been introduced, meaning that genomic information, along with pedigree and performance data, will now be used in the calculation of BREEDPLAN EBVs for Australian Santa Gertrudis animals. Additionally, Shear Force EBVs have also been made available.

Any Santa Gertrudis breeder wishing to include genotypes in the Santa Gertrudis Single-Step BREEDPLAN analysis must submit DNA samples for genotyping via the SGBBA office. If DNA samples are not processed through the SGBBA office, then resulting genotypes cannot be included in the Santa Gertrudis Single-Step BREEDPLAN analysis.

If you have any questions regarding the changes to Santa Gertrudis BREEDPLAN, please contact Paul Williams or Tim Emery, TBTS Technical Officers for Santa Gertrudis. Paul can be contacted on 0427 018 982 or via email, while Tim can be reached on 0408 707 155 or via email You can also contact staff at Santa Gertrudis BREEDPLAN on (02) 6773 3555 or via email