Answers to farmer questions on a genetic defect seen in some calves sired by Matrix
24 Sep 2012
Farmers may have read articles in the media about a genetic defect seen in some of the calves of an LIC bull called Matrix.
This Q&A gives you the facts about what happened, why and what we’ve done about it.
If you have any more questions, please direct them to Clare Bayly, LIC Communications Manager email@example.com.
How and when did this genetic defect start?
As the bull matured he was seen to be unusually hairy but there was nothing to raise any concern about subsequent impact for his daughters.
Halcyon sired 95 daughters across 44 LIC Sire Proving Scheme herds and two sons, Matrix who came into the 2010 DNA Proven team as a late replacement and Maverick who was sampled in 2010 Sire Proving.
Halcyon was never used commercially. Maverick has been sampled and does not carry the mutation.
Halcyon’s Sire Proving Scheme daughters calved in spring 2011. Nothing unusual was noticed about them (by the farmers or breed society TOP Inspectors) but concerns were raised when herd testing showed that some were not producing milk. Investigation revealed that these effects were seen in around half of Halcyon’s daughters which were also hairier than normal.
When did LIC begin investigating the issue?
What did LIC do?
The DNA from both groups was sent to the United States for genotyping just before Christmas 2011. The results came in over the holidays and we began analysing the data.
By early February 2012 we had narrowed things down to 1 of the 30 bovine chromosomes which might have contained the defective gene.
Our analysis showed that one group received a piece of the chromosome while the others received the other chromosome pair on around 5% to 10% of the chromosome. We then had to go into the region of the chromosome and see what genes were sitting in this area. (There are around 5-10 million base pairs and 100 genes in this region of the chromosome).
Our scientific team knew about a gene which has a major role in lactation and is also known to create a hairy phenotype in humans when disrupted, and we thought this was probably the gene causing the problem – we just had to sequence it.
The gene was sequenced in Halcyon and some affected and unaffected heifers and we found the base pair that differed between the two groups. That was in March 2012.
Some farmers have said that it took too long for LIC to advise farmers about the genetic defect.
The inability of some daughters to lactate resulted in LIC Scientists begin an urgent analysis. This involved tracking down the specific causative mutation among 3.2 billion base pairs arriving at a conclusion in March 2012. Once we knew what was causing the problem, we immediately contacted farmers who had used Matrix.
We understand farmer frustration but 5 months is incredibly quick compared to the years it would have taken before LIC began its investment in biotechnology.
It’s worth noting that, even a few years ago, achieving this breakthrough in identifying the cause of the defect would have taken years – not months.
LIC’s research and development is peer reviewed by the independently appointed BoviQuest Science Advisory Board (SAB) which acknowledged the speed with which our R&D team tracked down this genetic mutation.
(SAB Membership - Dr Dorian Garrick of Iowa State University, previously Massey University, Dr Howard Jacob of the College of Wisconsin and Dr Russell Snell of Auckland University).
When did LIC contact farmers?
We have maintained contact with all farmers who used Matrix semen, meeting some on farm to better understand their experiences and concerns, and also provided them with a comprehensive overview of what happened, where, when and how.
Why won’t LIC pay compensation to farmers who have heifers with the genetic defect?
The LIC Shareholder sub-Committee of the Board (made up of farmer Directors) made a recommendation to the LIC Board that compensation should not be offered because the defect occurred naturally and spontaneously and was not discovered until after the inseminations were carried out.
Genetic defects are a fact of life – in any animal species (including humans). No genetics company in the world has been known to compensate in similar circumstances.
LIC’s focus has been on equipping farmers with the necessary information to identify and remove affected animals to avoid further cost and to rid the industry of the genetic defect for good.
A substantial investment has been made by the Cooperative in research and the provision of tissue collection and genotyping service for hundreds of herds at no charge.
What is now known as the Halcyon Defect has been added to the list of genetic defects which all LIC sires are tested for – meaning this defect will not occur again within our bull teams.
Why is LIC now making a gesture of goodwill?
The majority of farmers we have talked with understand that genetic defects of this nature are extremely rare and compensation should not be paid, but support a gesture of goodwill to affected farmers.
What is the gesture of goodwill?
How was the gesture of goodwill calculated?
Note : Around 60% of inseminations create a pregnancy, 52% of the resulting offspring are male, 48% female. Around half the female offspring have the genetic defect.
Will all farmers receive the same credit, regardless of whether they reared affected calves, or culled them?
When did LIC stop selling Matrix semen?
Have Matrix and his sire, Halcyon, been culled?
Was Matrix’s promotion page removed from the LIC website?
Have any affected animals been exported?
How often do these spontaneous genetic defects occur?
Most defects involve a ‘recessive’ mode of transmission. This requires the mating of carrier bulls and cows, and even then, the defect is observed in only 25% of progeny. That is why internationally well known defects, such as BLAD, Factor X1, DUMPS, citrillanemea, mulefoot and CVM are seldom observed on-farm.
Genetic defects are a fact of life, but their occurrence is random making it difficult to identify animals which are ‘different’. Advances in genomic testing, however, remove any doubt – once concerns are raised DNA analysis enables scientists to track down genetic defects in a shorter timeframe than has ever been possible.
Does LIC remain confident in DNA Proven bulls?