Genetic linkage

Deer Select provides genetic linkage graphs and linkage traffic light reports each time a new across-herd analysis is run. These documents 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' –a measure of the number of animals in common across the herds within that Deer Select analysis. 

Linkage values of 0 or less represent poor linkage and herds cannot be validly compared, while values greater than 0 indicate herds can be compared. A value of 1, 2 or 3 relates to the strength of the connections, with 1 being fewer animals and 3 being a greater number of connected animals. Connected animals are assessed over a three year period. For a trait to be linked requires a minimum of 30 animals in common with other connected herds. Linkage can also be lost over time (>3 years) if link stags are not used across years and farms regularly. This is something that needs to be always considered and maintained by the sharing of sires (mainly by AI).

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 was one of the main reasons behind the establishment of the Deer Progeny Test (DPT). The DPT directly linked herds by running progeny of different sires from different herds in the same environment (contemporary group).

Since the end of the DPT, herds have to manage connectedness themselves by sharing/exchanging common genetics. Using sire from another herd does not create connectedness unless that animal also has progeny, ideally in the same year in the source or other herds. This usually involves the use of AI for a sire to have progeny in more than 1 herd in the same year.

Breeders can improve their own linkage by:

• Using a sire in common with another herd- ideally in the same year
• Generating at least 20-30 progeny in their Deer Select recorded herds by these sires
• Having their herd’s genetics (ideally through AI) used to generate a large number (greater than 25) of progeny in another herd

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

Herds connecting on the left side of 0 (red line) are genetically connected and Indexes and Bvs can be directly compared. The 3, 2 1 0 on bottom scale refers to the strength of connectedness – with 3 being a lot of animals genetically in common and 1 fewer animals genetically connected. Herds with connections or no connections to the right of the red line (0) are not sufficiently connected to be validly compared with the other herds and values should be treated as “within flock” only. This means the animals will be ranked correctly within flock – but there are insufficent or no connectionst to allow for between herd corrections – so may not be correctly benchmarked relative to other herds.

The Traffic Light report presents the same information in a different way, with the number indicating the strength of connectedness (3,2,1, or 0) same as the graph above but includes :( icon warning that the connections are three years old and will be not next calendar year, or a :| warning that connections are two years old.

The Traffic Light report presents the same information in a different way, with the number indicating the strength of connectedness (3,2,1, or 0) same as the graph above but includes a :( icon warning that the connections are three years old and will be not next calendar year, or a :| warning that connections are two years old.