In response to enquiries from Herefords Australia members since the updates to the Hereford BREEDPLAN analysis in October, please find further information below on the update to the weighting used to combine genomic and pedigree relationship information and also the changes to the Calving Ease analysis.
Weighting between genomic and pedigree relationship information (Lambda) update
BREEDPLAN calculates EBVs by using an individual animal’s phenotypic measurement for a trait of interest as well as the phenotypes for all correlated traits. It also makes use of the phenotypic measurements from all known relatives. The size of the contribution of these relatives’ performance being determined by their relationship, or proportion of genes in common, with that individual.
Single Step BREEDPLAN further builds on this by using information about the relationship between animals from two different sources, pedigree records and genomics. To be able to do this the relationship information from the two different sources need to be combined. Since Hereford BREEDPLAN first moved to a Single Step analysis in 2017 this has been done using a weighting (known as Lambda) of 50% on both pedigree and genomic relationship information. More recent work conducted by AGBU has shown significant advantages in moving to a weighting of 95 per cent.
The diagram below shows an example of the different relationship information that can come from these different sources between an animal, his progeny and his grand progeny. It also shows how this information is combined both with Lambda of 50% and 95%.
What does this mean?
The change to a higher weighting on genomic relationship information means that all animals in the analysis, particularly those with genotypes, are getting higher accuracy EBVs. This in turn means that as a breed we are able to make faster rates of genetic progress.
This improvement has come from a much better understanding of the actual relationship between known relatives using genomics, allowing us to get better use of their phenotypes. But it also means that we now have a better understanding of the relationship between animals where no recorded pedigree links are available, again allowing better use of more phenotypes.
These changes have caused some relatively small changes to animals EBVs for traits that were already being analysed using the Single Step method.
What does this not mean?
This does not mean that genotypes are now more important than phenotypes. It does not mean that phenotypes only account for 5% of an animal’s EBV.
Phenotypic data is still being used in the same way in the BREEDPLAN analysis and is critically important. It is the relationship between animals that allows us to make use of other animals’ phenotypes that has been updated.
Calving Ease analysis update
In BREEDPLAN Calving Ease is analysed in a separate sub-analysis using calving difficulty scores, birth weight and gestation length. It has not previously been possible to use genomics as part of the Calving Ease analysis as appropriate methodology has not been available. A new model has now been developed and was implemented as part of the October Hereford BREEDPLAN analysis for the first time. Meaning that for the first time, genomic information is contributing to the calculation of Calving Ease EBVs by improving our understanding of the relationships between animals.
There have been other changes to the model that is used to calculate Calving Ease EBVs including improving how contemporary groups are formed. These updates bring Calving Ease into line with the rest of the analysis. These changes mean that more animals are now included in the Calving Ease analysis and there is significantly more data being used. This gives us access to much higher accuracy Calving Ease EBVs and means that will can make faster rates of genetic improvement for these traits.
Have animals changed in their ranking for Calving Ease?
These updates mean that we now see a greater range in Calving Ease EBVs within the Hereford breed and we also see updated rankings for animals within the breed. This has happened because of the high number of animals with Calving Ease data now in the analysis and a better understanding of the relationship between animals due to the use of genomics meaning that we get greater use of phenotypic data that is available for animals with common genes.
It is important to compare the updated EBVs for your animals to the updated percentile bands for Calving Ease to understand where your animals rank within the breed.
With more animals with Calving Ease EBVs, greater genetic variation being identified within the breed and higher accuracy EBVs, these changes will help Hereford breeders make faster rates of genetic improvement for calving ease.
For further information
If you would like further information about any of the updates please see the Hereford BREEDPLAN analysis updates article on the Herefords Australia website or contact the office.
If you would like more information about genomics and how it helps livestock breeders we recommend reading Demystifying DNA Technology.
