Understanding the “New” Angus BREEDPLAN Analysis

April 18, 2018 12:21 pm

December 2017 heralded a new era for the genetic evaluation of Angus cattle in Australia with the implementation of a new and improved approach for incorporating genomic, or DNA information into the calculation of Estimated Breeding Values (EBVs).

The new approach, utilising single step analytical software, simultaneously utilises genomic, pedigree and performance information, placing appropriate emphasis on all available sources of information, to generate the best possible prediction of each animal’s breeding value.

By comparison to previous versions, the new approach for incorporating genomic information into the calculation of EBVs for Angus cattle included a number of new features, including modifications to:

  • the manner in which genetic relationships between animals are determined
  • the method by which genomic, or SNP effects are estimated
  • the way in which genomic information contributes to the EBVs of relatives
  • the relative emphasis that is given to genomic information
  • the EBVs for which genomic information is considered

This article provides some further background regarding the first new feature, being modifications to the manner in which genetic relationships between animals are determined, and attempts to give Angus breeders an insight into what to expect when obtaining EBVs for their animals from the “new” Angus BREEDPLAN analysis.

Understanding Mendelian Sampling

Before discussing the new approach, it is firstly important to review the way in which genes are passed from one generation to another.

Most people will be familiar with the concept that an animal possesses two copies of each gene, with one copy inherited from each parent.

When an animal becomes a parent, only one copy of each gene is passed onto each offspring, resulting in four different combinations of the gene being possible in the offspring.

This is illustrated in Figure 1, with the chance factor describing which half of a parent’s genes are passed on to their offspring referred to as “mendelian sampling”, named after the scientist who developed the concept in 1822, Gregor Mendel.

 


Relationships Between Animals

Considering what is known about how genes are passed from one generation to the next, it is possible to use pedigree information to estimate the expected genetic relationship, or expected proportion of genes in common, between relatives.

Some common examples of the expected relationship between an individual and its relatives are illustrated in Table 1.

However, in practice, the transfer of genes from one generation is a bit more complicated, so while animals inherit 50% of their genes from their sire and 50% of their genes from their dam, there is some variation in the actual genetic relationship that is observed between animals and their relatives.

For the more technically minded, this variation is due to the fact that genes are not transferred in isolation but as part of a chromosome, the manner in which chromosomes are separated during meiosis, and the exchange of chromosome segments that can occur during this process (a phenomenon known as “crossing over”).

In the case of an animal’s relationship with their full siblings, on average, an animal will have a genetic relationship of 0.5 with each full sibling, as described in Table 1, but the actual relationship between the animal and each individual full sibling may vary. This is illustrated in Figure 2, with the genetic relationship between the animal and its individual full siblings ranging from approximately 0.4 to 0.6.

The same variation is the actual versus expected genetic relationship applies to all different classes of relatives, such as parents, grandparents and great-grandparents. For example, while an animal will, on average, have a genetic relationship of 0.125 will each great-grandparent, it may have a closer genetic relationship to individual great-grandparents than others.

Modifications to Approach for Determining Relationships in Angus BREEDPLAN

The availability of genomic technology now enables the genetic relationship between an animal and each relative to be estimated more precisely in the calculation of EBVs.

Previously the relationship between an individual animal and other animals in the Angus BREEDPLAN genetic evaluation was estimated by pedigree alone, and consequently, assumed an animal had the same relationship with each of its relatives.

For example, in the case of full siblings, the genetic evaluation assumed the animal had a genetic relationship with each of its full siblings of 0.5.

The new analysis approach uses genomic information, in association with pedigree, to more precisely estimate an animal’s genetic relationship with other animals in the genetic evaluation.

In the example of full siblings, as described in Figure 2, rather than a relationship of 0.5, the genetic evaluation now estimates the actual relationship between an animal and each individual full sibling, when calculating the animal’s EBVs.

Consequences for EBVs

The new approach for determining the relationship between animals has several consequences for the EBVs that are calculated for Angus animals.

Angus breeders may notice:

  • while in most cases there will have been no change, the EBVs for some individual animals, particularly those with genomic information, may have changed considerably by comparison to the EBVs calculated previously.
  • there may now be considerably more variation observed between the EBVs of full and half siblings, such as embryo transfer calves from the same flush, or progeny of the same sire.
  • the EBVs of progeny may be less aligned to the EBVs of their parents, particularly if the genomic information is showing the progeny has a genetic relationship with its parent/s that is considerably different to 0.5.
  • the influence that a pedigree error has on the EBVs calculated for an animal is greatly reduced, as the genomic information will demonstrate the relationship between the animal and the respective “erroneous” ancestor is negligible, and the “erroneous” ancestor’s information will no longer incorrectly contribute to the animal’s EBVs.
  • the information from an animal that is unrelated by pedigree but who shares genes in common will contribute to the calculation of an animal’s EBVs.

Importantly, the improvement in the way genetic relationships between animals are determined within Angus BREEDPLAN will result in EBVs being calculated that provide a better prediction of an animal’s breeding value, particularly for animals with genomic information available.

To further discuss the modifications to the manner in which genetic relationships are determined in Angus BREEDPLAN, please contact Angus Australia’s Breed Development & Extension Manager, Andrew Byrne, on (02) 6773 4618 or andrew@angusaustralia.com.au.

 

 

 

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