Robert Hodgkins  -  Using genomic selection technology to advance the development of a ovine maternal breeding line

South of England Agricultural Society

31 year old Sheep farmer from West Sussex.

Locks Farm is a tenanted 1,400 acre farm, most of which is situated within the South Downs National Park. 90% of our grassland in permanent pasture and is the farmed under the South Downs ESA regime where no fertiliser or chemical is permitted, therefore there is very little we can do to manipulate or extend our grazing season.

Productivity of some of the swards would be considered very low – the ESA agreement stipulates an annual maximum stocking rate of 3 ewes per acre. The farm rises up to 783ft above sea level, and field contours range from flat ground at home to steep banks upon the downs.

We are large commercial family run sheep farm running 3000 plus NZ Romney ewes. The farm is a spread out unit (25 miles round trip to visit every flock) on good to mediocre grassland, land class 3-5. We operate a single breed, closed flock and take great care and interest in selecting future progeny to make shepherding as enjoyable and stress free as possible.  We are one of the largest Signet recorded flocks in the country, single sire mating and recording over 1500 ewes and there progeny per year.  We sell high quality, NZ Romney rams and females, this year we have sold around 110 2 tooth rams, and all of the breeding females (800+) we had for sale.

Back to school

2 day tripp to the University of New South Wales home of the sheep CRC

Posted by Robert Hodgkins on November 2, 2012

Appears in Livestock, Technology

Recording and estimating breeding values (EBV)

As a very quick introduction:

 sheep breeders know that their flock’s performance and therefore the money the flock makes them is an expression of both the genes the animal is carrying and the nutrition and management the animal receives, therefore different animals farmed on the same ground using the same management techniques will make you different amounts of money.

Some will require less feed to reach a certain lean weight (don’t you have friends who seem to eat whatever they like and don’t get fat.) Some will produce bigger framed animals that you can pack more meat on (in general tall parents produce tall children)   etc.

Typically a Ram covers around 100-120 ewes per year with a 5-6 year working lifespan meaning he would have around very conservatively 800 offspring in his life.  On my farm I want those offspring to have genes from the ram equivalent of Usian Bolt rather than Johnny Vegas!

To make sure I avoid the” Johnny” rams I need as much information as possible: so growth rates (birth, 8 week’s old, and 20 weeks old then throughout its life) and muscle size and fat depth via ultra sound measurements. I then need to ensure that that lamb did not just get very good nutrition and so I need to compare it to all its cousins to ensure the figures it has are really what it deserves, this figure having hopefully excluded environmental factors by comparing it across its peers is known as its estimated breeding value.

Each animal has several EBV’s not only for growth rate (that was just an easy example) but for  a wide range of variables likely to affect your bottom line for example internal parasite resistance, litter size, body fat %, body muscle % and mothering ability to name a few. All these EBV’s are blended together to create one overall value for that animal.

So to summarise I could take  a Johnny ram put him on a diet make him lift some weights while at the same time taking the Usian ram and feeding him junk food and sitting him on a sofa all day. If you were then buying a ram by “eye” you would choose Johnny – because he would look better. Only by looking at the EBV values would you know to choose Usian.

In England this type of recording system is called Signet, in Australia the equivalent called Lambplan.

Lambplan has 3 main indices within it, a terminal index, a dual purpose index and a maternal index.  All indexes are cross-breed meaning you can compare for example White Suffolk’s to Border Leicester’s the Cross breed analysis was very interesting and I think something the UK desperately needs to adopt if we want to make profitable gains within our industry.  It seems insane that with around 73 million sheep Australia can make do with 3-4 indices that are non-sheep breed specific. But the UK with around 20 million sheep seems to need a different index for each breed (and sometimes different indexes within breeds!!) All this seems to achieve is to protect English breeders by meaning that customers cannot compare different systems against one another.

 Also interesting was how much use Australian farmers use “linked sires” programs. This is where older rams with known recorded progeny are exchanged between farms and the progeny in the new environment recorded, by comparing the progeny’s EBV’s correction factors for environment and management can be taken into account in the EBV’s, meaning a higher accuracy can be achieved even when comparing farms against one another.

Australian farmers also have much greater use of “linked sires” programs where older rams with known recorded progeny are exchanged between farms and the progeny in the new environment recorded, by comparing the progeny’s EBV’s, correction factors for environment and management can be taken into account and farms on hard ground will not be penalised within the overall breed analysis. 

In short the whole Australian attitude towards recording seems to be a lot more focused towards true benchmarking themselves against their peers with a lot more openness and a willingness to adapt to best practices,  meaning a much more healthy and profitable industry.

Genotyping and Genomic selection

This is where the Southern hemisphere really starts to pull away from us in the North! Genomics is the study of the DNA of sheep and its use in selection of the very best sheep, so for example by submitting a sample of ear tissue for analysis a detailed look at the genome structure of that animal via a SNP chip can be done which will tell you the genetic potential of that animal. So to go back to our analogy rather than spend a lot of money and time on raising both “Johnny” and “Usain” for many years to determine who is best, one simple test at birth will tell me all the information in terms of EBV’s that I need to know. I can then with a high degree of confidence get rid of Johnny the ram straight away.

Australia have genotyped and are able to offer genomic breeding values on the following breeds:

  • Poll Dorset
  • White Suffolk
  • Border Leicester’s
  • Merinos

They have approximately 5000 measurements from each breed as a reference population and on average are recording around 1000 animals per year to ensure that the genomic calibration remains accurate. The tests are currently subsidised to around $50 per animal. There is very little correlation between breeds, so the genes indicating high weight gain on a Merino will not be the same as for a Poll Dorset. This technology is currently around 12-18 months away from commercialization and I believe it is no exaggeration to say it will transform the industry. By having a genotype of the animal you can now select for hundreds of different variables that would be very expensive to test for in a traditional system, MLA (Meat and Livestock Australia) have done huge amounts of work on the genome linking key traits from there reference group back to certain areas of the genome an example would be the “eatability” of lamb meat and comparing different sires they now have gene markers in place for intramuscular fat content (how much fat is in the meat), shear force (how difficult the meat is to cut – its tenderness) Iron and zinc content of the meat and many others.  MLA intends to sell this to the industry by creating a "star system" for its meat. Meat that has come from a sire known to produce expentionally tender lamb very low in intermuscular fat will be gradded at 5 stars and have a premium price attached to it.

Genomics also allows selection based on physical attributes of the animal that would be beneficial for the farmer. An example would be the amount of wool around the back end – lots of wool on the backend leads to more dagginess.

Genomic selection will have a big impact on flocks that do not do any recording, as one $50 test will tell you the same information that has taken another farmer $1000’s of dollars of recording and effort.  But herein lies the current problem facing the industry.  For the genomic testing to be accurate it needs the information from recorded animals every year to remain calibrated but how do you get people to stay recording when genomic tests can be done so cheaply? Several options are on the table including paying farmers for that recorded information via the levy system or giving them free SNP chips.

But of course on recorded flocks the SNP chips use will be limited to improving the accuracy of EBV figures (by around 3-10% depending on what figure you are looking at) or improved selection of very young rams to take forward or used as tool to determine difficult to measure traits.

In Summation: Genomics allows selection of breeding stock based on internal very difficult to measure points at a very early point in its life and from what i have seen the uk is at least 10 years behind where we will soon need to be in order to compete globally with our lamb exports!

Sincere thanks to everyone at the UNE, the work they are doing is incredible.



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