The inclusion of genomics in the single-step BREEDPLAN analysis has meant that the selection decisions about which animals have the best combination of EBVs to breed from can be done with a higher accuracy.
Selecting for higher growth rates is an important profit driver for Hereford breeders but is usually related to higher birth weights, which in turn has an impact on calving ease.
Birth weight (BWT) EBVs are an important tool that allow Hereford breeders to manage this relationship by identifying animals that carry both the genes for moderate birth weight and the genes for good growth rates.
The genetic trends for the breed over the past 10 years show Hereford breeders have been using these tools very effectively. BWT has decreased on average from +4.5 kg down to +3.9 kg for the current drop, while 600 day Weight has increased from +67.1 kg to +78.7 kg.
With the Hereford reference population now around 30,000 records for birth weight and early live weight traits it is possible to see animals with EBVs for those traits with accuracies greater than 55% (depending on relationship to the reference), based solely on genotype information.
There have been some cases where breeders have raised concerns as there have been significant changes to some animals’ BWT EBVs following genotypes being included in the BREEDPLAN analysis.
It is important to understand that every time more data is included in the analysis for an animal, whether it is more performance/phenotypic data, more pedigree/relatives information, or more genomic data, it is telling us something more about the genes that animal carries. Therefore, it is possible that its EBVs may change to some degree to better reflect the most up to date information about the genes they carry.
Changes in BWT EBVs show no bias
There has been a significant amount of work done to investigate changes caused by the inclusion of genotypes. Test analyses run by ABRI both with and without genotypes have shown that, as expected, some animals BWT EBVs remain reasonably stable, some go down and some go up. Importantly, there was no significant systematic bias created in either direction by the inclusion of genomic information.
Further analysis showed that there are many SNPs (Single Nucleotide Polymorphisms – or locations on the DNA where we can identify variation) that have some level of association with birth weight in Hereford cattle.
It was found that out of these SNPs there were 5 or 6 SNPs that were significantly associated with larger changes in BWT EBVs. The animals that had demonstrated the largest changes in BWT EBV when genotypes were included were shown to have been carrying unfavourable variants of multiple SNPs that have a significant impact on birth weight. It is the combination of the impact or ‘dose’ from each of these SNPs that has led to the larger changes.
This gives us much more specific information about the genes that these animals carry and the genetic merit that they are likely to pass on to their progeny.
Single step BREEDPLAN improves accuracy
Because there had been structured R&D projects done in the past to develop a reference population, Herefords Australia was one of the first breeds in the world to move to a Single-Step BREEDPLAN analysis in October 2017.
The implementation of Single-Step BREEDPLAN has meant higher accuracy EBVs for all animals in the evaluation, with greater improvements for animals that have been genotyped.
The biggest impact is for young animals that have limited (or no) other information available (older animals that already have high accuracy EBVs based on their own performance and progeny performance will typically not see further increases in accuracy with the inclusion of a genotype).
Reference populations critical to genomics
The use of genomics to calculate EBVs relies on having a reference population, a group of animals that have been measured for the traits of interest and that have also been genotyped.
Herefords Australia currently has a very sound reference population for birth weight, live weights and ultrasound scan traits as well as gestation length and male reproductive traits. The key focus areas currently for further development are female fertility traits and carcase traits.
If we have an effective reference population, we can then genotype other animals out in the industry and estimate their genetic merit based on their genomic relationship to the reference population.
The factors that influence the accuracy of genomic EBVs (GEBVs) include
- The size of the reference population, i.e. how many animals with both phenotypes and genotypes
- The heritability of the trait – the lower the heritability, the more records are needed in the reference population to get the same accuracy
- The relationship between the animals you are genotyping and the reference population. Higher relationship = higher accuracy.
The Herefords Australia reference population is developed using information collected through a number of channels including structured R&D projects such as the BIN (Beef Information Nucleus) project and Southern Multi Breed project; animals in stud breeders’ herds that have been genotyped as well as phenotyped as part of normal practice (usually limited to relatively easy to measure traits); and data captured on commercial animals i.e. co-operator herds.
The Southern Multi-Breed Project, a joint project between Herefords Australia, NSW DPI, UNE and MLA, captures reference population data for a wide range of traits for multiple breeds, including Hereford, Angust, Wagyu, Charolais, Shorthorn and some Brahman.
These include traits from fertility to birth, growth rate, carcase, feedlot performance, net feed intake and methane measures, with the aim of building a data set that enables BREEDPLAN analyses for more than one breed at a time.
This would enable a breeder to buy bulls with the best EBVs irrespective of breed type, and give Hereford breeders the ability to benchmark cattle against animals from other breeds as well as their own.