Haplotypes affect herd fertility

22 Sep, 2018 04:00 AM
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Figure 1: What happens when two animals carrying the JH1 haplotype are joined.
To reduce the frequency of haplotypes ... farmers should look at only using JH1-free bulls.
Figure 1: What happens when two animals carrying the JH1 haplotype are joined.

]The latest round of Australian Breeding Values (ABVs) has been released, and with the use of genomics, the dairy industry is moving towards the 'perfect cow' faster than ever before. It's wonderful to see breeds making progress towards increasingly productive, healthier and structurally sound animals.

Genomic testing is a great example of science in action. Scientific breakthroughs in genetics not only help farmers to achieve their goals faster, but they can also help everyone understand how to get there safely. Risk management is a less glamorous topic than accelerated progress, but it has always been one of the foundations of profitable farming.

With this in mind, I want to talk about haplotypes. In 2011, scientists discovered a sequence in Jersey DNA that significantly affects fertility - something they called the JH1 haplotype. Haplotypes are groups of genes that are inherited together from a single parent. In this case, the JH1 variety is defective. It can't produce an important protein that is needed for life.

Luckily, most animals (including humans) have two copies of each gene, with one inherited from each parent. So if an animal is a carrier for the JH1 haplotype, it still has one working copy, which is able to compensate. This means that there is little impact on that animal's performance.

The problem occurs when a carrier is joined to another carrier. Copies of the genes recombine randomly in the embryo and there is an equal probability for one of four possible combinations - two where the copies are different (Aa or aA - known as 'heterozygous') and two where they are the same (AA or aa - 'homozygous').

If the embryo is homozygous for the non-JH1 haplotype - that's great news, the calf is in the clear.

If it is heterozygous, it becomes a carrier - which won't affect that animal's performance.

But if it is homozygous for the JH1 haplotype, the embryo will die.

This means that a quarter of these pregnancies are lost within 60 days of insemination - which appear as lowered conception rates.

If a farmer has been unknowingly using JH1 positive bulls for many years, the frequency of the JH1 gene in their cows will have risen steadily. A calf with two carrier parents has a 66 per cent chance of being a carrier itself and only a 33 per cent chance of being JH1-free. Even if a calf has one non-carrier parent, it has a 50 per cent chance of being a carrier and only a 50 per cent chance of being JH1-free.

So if a farmer used a JH1 carrier bull in the past, it's likely that a proportion of its daughters in the herd are carriers.

How significant is this problem within the Australian dairy industry?

The good news is that a study done by Australian scientists in 2011 showed that the frequency of the JH1 haplotype in Jersey bulls was only 6.5 per cent, with 35 out of 540 bulls testing positive. The bad news is that a study done in the United States found that the frequency was 23.4 per cent, and in the past seven years, the number of bulls imported from the US has only been rising. Individual farms also tend to use a large number of straws from a small number of bulls, so the frequency in the sire population does not necessarily reflect the frequency in calves born on a particular farm.

The ugly news is that another haplotype, which affects fertility (JH2) was discovered in 2014.

Holstein-Friesians aren't exempt either, with six known haplotypes (HH1 to 6) found so far. However, these haplotypes occur at a lower frequency than JH1 at present.

How can a farmer tell if this affects them?

If farmers are seeing cows mysteriously come back on heat within two months of a seemingly successful joining, or if they have an unexpectedly high percentage of cows tested in-calf early that then calve late, it may be worthwhile checking the herd's pedigrees for carriers.

How do farmers know which animals are carriers?

Animals can be directly checked for carrier status using genomic testing. For AI bulls, haplotype status can be seen using Displayabull on the Datagene website. Or alternatively, ask a breeding consultant to check sires.

What can farmers do next?

If farmers would like to reduce the frequency of these haplotypes in their herd, then they should look at only using bulls that have a JH1-free status. However, it can still be tempting to use extremely high-performing bulls that are carriers. If these are used, it would be a good idea to join them to non-carrier cows. [lastpar]Conception rates for that joining will not be reduced, but half of the offspring will be carriers whose future joinings will need to be carefully managed.

For more information, see Technote 16 on the Datagene website or have a friendly chat with a breeding consultant and/or AI technician.*Ee Cheng Ooi is a dairy veterinarian and fertility researcher in Northern Victoria. All comments and information discussed in this article are intended to be of a general nature only. Please consult the farm's vet for herd health advice, protocols and/or treatments that are tailored to a herd's particular needs.

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