Genomic testing helps to make right decision, more often

from Herefords Australia - Winter 2023

Vale - William Kenneth “Cowboy” Godbolt

around records

The inclusion of genomics in the Hereford BREEDPLAN analysis means data from all sources, pedigree, performance and DNA now gets used simultaneously to give the highest possible accuracy estimated breeding values (EBVs).

This in turn means we are making the right choice about which animals have the best combination of EBVs to breed from more often.

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 allowing Hereford breeders to manage this relationship by identifying animals carrying 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 effectively. Genetic progress for the breed shows current calves can be expected to be 0.6kg lighter at birth but nearly 12kg heavier at 600 days of age than calves born 10 years ago.

With the Hereford reference population now around 30,000 records for birth weight and early live weight traits, Hereford breeders now have access to higher accuracies EBVs for these traits.

Because higher accuracy means we are making the right choice more often we are seeing an improvement in the rate of genetic progress with genetic trends demonstrating the breed has maintained its rate of progress for growth at the same time as increasing the rate of improvement for birthweight since the use of genomics was implemented.

However, it is important to understand that every time more data is included in the analysis for an animal, whether it is

CONTINUED PAGE 20 more performance/phenotypic data, more pedigree/relative’s 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 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 these animals carry and the genetic merit 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 see relatively minor 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 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 for further development are female fertility traits and carcase traits.

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 Department of Primary Industries, University of New England, and Meat and Livestock Australia, captures reference population data for a wide range of traits for multiple breeds, including Hereford, Angus, 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.