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  • Title: Genomics - an update

  • Category:

  • Date: Monday, 23 January 2017


Picking genetics during the artificial breeding season works on the assumption that, when it comes to breeding and production efficiency, farmers want new generations of replacement cows to outperform the previous generation.

This comes largely down to good sire selection. 

Arguably still in its infancy, genomic selection of bull calves is finally getting traction in New Zealand, where benefits for LIC’s  sire selection processes are emerging, and better alignment between (forecasted) genomic worth and (realised breeding) worth is the expectation.

Genomically-selected bulls have been marketed by LIC for eight years, with mixed results in the first several years. Here, we offer an insight into progress that’s been made by LIC since 2013.

Using milk and TOP (traits other than production) information from a bull’s daughters, it takes LIC seven years to get an accurate estimate of a bull’s genetic merit, commonly referred to as breeding worth.

Only after that ‘progeny test’ period will the bull’s genetics become commercially available to the nation’s dairy farmers. This is the traditional method of ‘proving’ a bull’s value as a breeder of dairy cow replacements.

But genomic selection, using latest science methodology, offers the industry an attractive alternative proposition.

“What we want to do is get a reliable estimate of genetic quality at a bull’s birth, rather than having to wait seven years (for daughter information),” says Bevin Harris, LIC science leader.

Bevin leads LIC’s development of its genomic selection tool.


How the tool works

“The really cool thing is that, when I say ‘reliable estimate’, it doesn’t have to be as reliable as progeny testing,” Bevin continues.

“Because, if you save seven years, you can actually forgo a little bit of reliability and make greater levels of genetic improvement, just  by using the slightly less reliable bulls at a younger age.”

That’s the essence of genomic selection.

Genomic selection hones-in on a series of DNA markers that control the key traits dairy farmers are interested in (for example, fertility, fat, protein, udder support).

“The idea is that we use DNA from young animals when they’re born, and derive a better estimate of their BW than we’d get from the parent average BW, bypassing progeny testing in the process,” Bevin says.

“We do this by using their DNA, specifically the DNA markers.

“So some markers are associated with genes that control the traits we are interested in. If we get a marker that’s associated with a positive trait, we can work out whether that animal is going to be any good.”


What's been the hold up?

The method is working well in almost all dairy industries around the world, but progress has been slower in New Zealand and a few Scandinavian countries.

“We (New Zealand, Norway, and Finland) have large cow populations, but our industries also feature multiple breeds and cross-breeds,” explains Bevin.

“When you’ve got one population, for example, exclusively Holstein – like in the United States, it seems to work much better.

“When you start crossbreeding, you start splitting up the associations between the DNA and the traits, so you get a lot more admixture in the genome.

“It’s a matter of really driving the science forward and having the ability to gain a good understanding of how to take account of the crossbreeding within the genomic predictions – that’s the really important component in getting this thing really firing.”

There are aspects of the technology that are firing.


Recent progress

Five years ago, bull calves for LIC’s Sire Proving Scheme were selected exclusively on ancestry records.

Now, rather than merely selecting 200 male calves to be raised and tested from LIC’s Newstead bull farm, the co-operative ‘pre-selects’ a list of 2000 male calves.

These comprise calves from cow families that have sound conformation traits, and are deemed as the most-efficient producers in New Zealand.

Before leaving the farms they are born on, LIC is able to run all 2000 young sires through DNA testing, Bevin says.

“We run them across the DNA chip (looking for key ‘marker’ traits). So we take the top-200 or 250 (from the initial list of 2000), for the Sire Proving Scheme.

Sire acquisition managers will visit farms throughout the country to eyeball the 200 to 250 bull calves (and their dams) before confirming their place in the Sire Proving Scheme.

“That’s a really big change from what LIC used to do,” Bevin says, “which was select our top-200 based purely on the parent average (the BW index).”

Although parent average is still a significant factor, the genomic selection tool complements the process and Bevin maintains bull composition is slightly different under the improved pre-selection method: “There’s much more choice, a wider range of bulls,” Bevin says.

“Looking at a list of 2000 sires allows us to open the way for a small number of animals that might not have otherwise come on the radar.

“We can use the knowledge that a bull has good genomic values compared to his parent average, which gives the bull a greater probability of having a successful outcome from progeny testing.

“We’re also doing more embryo transfer work. This helps, for example, if you take two identical full brothers who have identical parent averages: You can use the DNA information to show differences – one might have better associations in the traits we’re interested in, so we’ll take him.”


What about the girls?

The co-operative is also using a lot more heifers to generate elite bulls.

Previously, LIC had to wait until cows were milking to get an idea of how good they were, before using them as mothers of bull calves.

Nowadays LIC gets samples of the hiefers’ DNA, generating breeding values before the heifers have calved: “So that speeds things up again (intensifying the selection); we’re turning generations over,” Bevin says.


Promising signs

In 2013, LIC made a significant change in the method behind genomic selections, including the mathematics behind it: “What we’re trying to do is to improve the stability of the difference between what we say the animal’s going to be (based on DNA information) and what it finally comes out at (when daughter information comes through).

Ideally the numbers would be the same, Bevin says.

“We don’t want to over-promise on the genetic level of these animals, or over-promise on the accuracy we think we’re getting from the genomic Breeding Worths.

LIC is also using a different system to calculate the association between genomic markers and the traits farmers are most-interested in: milksolid production, fertility, and survival.

Looking at bulls that had their progeny-test results coming through in 2014 and 2015, Bevin says their original genomic predictions (using the improved calculations) appeared to be ‘holding up’ as more daughter information became available.

“Pre-selection is working, and we’re seeing results in the RAS List right now.

“Instead of having a group of sires below zero (ie. falling short of initial genomic predictions when daughter proofs emerged), they’re not there anymore,” Bevin says.

“In other words, the ones that inherit poor genes from their Mums and Dads are less likely to be progeny tested.”

If improved rates of genetic gain are achieved, more-profitable cows for farmers will result, Bevin says.

“The other benefit, from a company point of view, is that if we’re getting improved rates of genetic gain, we’re getting more top bulls on to the RAS List than our competitors.”

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