Genetic linkage

Genetic linkage

Genetic linkage across herds and years is critical to breeding programs which utilize Breeding Values (BVs) to provide a measure of genetic worth.  Linkage through the use of common sires (i.e. same sires used between farms and/or years) allows for statistical adjustment of environmental differences between farms (or years) in performance of progeny. This adjustment of environmental effects means that all animals in a well linked analysis can be directly compared.  Without good linkage the relativity of BVs produced between years or herds cannot be established and year-to-year or herd-to-herd data cannot be directly compared.

DEERSelect linkage graphs
DEERSelect provides genetic linkage graphs each time a new across-herd analysis is run.  These graphs show how well linked the different herds within the analysis are for specified trait groups (e.g. growth, reproduction or velvet).  Linkage is a measure of the genetic 'connectiveness' of the herds within that DEERSelect analysis.  Linkage values greater than 0.25 represent poor linkage while values less than 0.1 represent very good linkage.  Some traits which are harder or more expensive to record, such as reproduction, generally have fewer records and, hence, poorer linkage.  Linkage can also be lost over time (>3 years) if link stags are not used across years and farms.  This is something that needs to be always considered and maintained by the sharing of sires (mainly by AI).

How is the deer industry improving linkage?
Good linkage does require a certain scale of breeding programme to allow for the exchange of genetics.  Accordingly, the scale of the New Zealand deer breeding (stud) industry makes it difficult to maintain high quality linkage. This is one of the main reasons behind the establishment of the Deer Progeny Test (DPT).  The DPT directly links herds by running progeny of different sires from different herds in the same environment (contemporary group).

How can a breeder improve linkage?
Breeders can improve their own linkage by:

  • contributing genetics to the DPT
  • purchasing genetics directly linked to the DPT
  • purchasing genetics linked to other herds (ideally from well recorded sires) and generating at least 25 progeny in their DEERSelect recorded herds
  • having their herd’s genetics (ideally through AI) used to generate a large number (greater than 25) of progeny in another herd

Example of across-herd linkages

genetic linkage diagramIn the diagram below there are seven herds involved: six individual herds and the DPT herd.   The coloured sires in the DPT herd each form different sets of linkages, and because of these links all of the black animals outside the DPT herd can be compared in DEERSelect.  These links are across-herds, primarily around the DPT.  However the concept is essentially the same across years.

Herds A, B and C are all linked by the blue sire.  The blue sire is also directly linked to the DPT herd, so A, B and C are also linked to D, E and F.  By herds A and B using the blue sire from herd C they did not have to directly contribute to the DPT to take advantage of the good linkage the DPT offers.  Herds E and F contribute a sire (pink and orange respectively) directly to the DPT, so through the DPT and the blue stag they are linked to all herds. 

Herd D has purchased a new unrecorded sire (purple).  The progeny of the purple stag born in herd D can be directly compared with all the other herds, due to the links formed by the green stag in the DPT.



Example of a Linkage graph

This graph shows the linkage (or ‘connectiveness’) of deer stud herds in DEERSelect for growth traits. Farms that cluster to the left show good linkage. However, farm 8127 (bottom) is not linked to any other her