What is genomics?
? The term genomics refers to a whole host of technologies that use information about DNA and DNA sequences.
In sheep breeding we are talking about the use of genomic selection in which we use sequence information from the DNA of individual animals to generate genomic breeding values that help us identify sheep that will be most useful in a breeding programme.
To calculate genomic breeding we first have to establish the association between thousands of small differences in the DNA of individual animals and the differences in their performance.
We can use these relationships to improve predictions of breeding values of future animals based on information about their DNA.
This has the advantage of being available to us very early in the animal’s life, before we have to decide whether to sell the animal or keep it for breeding, and it gives us information on maternal traits even in ram lambs.
What are the benefits of using genomics over EBVs?
? It is unlikely genomic breeding values (GBV) will be used to replace EBVs. Instead the genomic information is likely to be used alongside performance records to improve the accuracy of EBVs for traits that have low accuracy.
How far away are we from it in the sheep sector?
We hope to have genomic breeding values for some of these traits, such as meat quality, available to use in our breeding decisions within the next five years.
How can it be used in the sheep sector?
? Genomic breeding values will be particularly useful for traits that are currently hard to record in the live animal (such as disease resistance and meat quality), only expressed in one sex (such as prolificacy and mothering ability) or measured late in an animal’s life (such as longevity).
This will involve first building up thousands of detailed records of the traits we want to select for in our breeding populations by using “old-fashioned” performance recording. Alongside this we will need to genotype animals using an SNP chip, which is a way of identifying thousands of very small differences in the DNA of sheep right across their whole genome.
This will allow us to develop the prediction equations that we can use to calculate genomic breeding values.
We will then use these prediction equations to help improve the accuracy of breeding values in our breeding programme.
How accurate is it?
? The use of genomic information will only have marginal effect on the EBVs for easily recorded traits such as growth rate and ultrasonic scanning information, but could significantly increase the accuracy of other traits such as mothering ability, lamb survival and longevity, making these traits easier to improve in our breeding programmes.
Genomics may be an alien word for many sheep producers, but it is a term that is going to become more important if the
However, producers should not let their unfamiliarity with genomics prevent them from embracing the new technology, says sheep farmer
“It’s definitely not technology for tomorrow – it’s happening right here, right now,” he says.
Genomics enables an animal’s genetic potential to be predicted from a young age by comparing its DNA with an “SNP chip”, which is produced using a bank of genetic information representative of the national population. This allows rams to be used at a younger age, rather than waiting for progeny testing.
However, to use genomics, any animal tested must have a genetic link back to the reference population, in this case the CPT flock.
The background on genomics
It’s for this reason the Hodgkins family, who sell breeding stock to commercial producers from their Wairere NZ Romney flock in West Sussex, have been able to start using genomic technology.
Their 3,400 head flock is of
“We first became interested in genomics when my dad and I heard geneticist Dr
“Dr Ball said the northern hemisphere was years behind because there was not the massive recorded data in the
“But that got me and my dad thinking, as we had 100%
Wairere flock set-up
The Hodgkins are using genomics in their nucleus flock containing 1,700 ewes.
In 2012 all stud rams in this flock had a DNA 50K SNP chip sample taken, meaning all progeny born to these rams in 2013 have been evaluated with genomic estimated breeding values as well as normal EBVs. These are the first sheep in the
He explains that in the 5,000 head central progeny testing flock in
“For example, if they identified 50 sheep with the highest EBV for growth rate in this population, the DNA for each of these sheep could then be compared to see which areas of the genome were common across each of those 50 top growth rate sheep.
“Once the gene combination responsible for that particular trait had been identified, other sheep could be tested to see if they carried this gene combination for growth.”
Benefits of genomics
“By combining DNA information with actual recorded information, accuracy levels can jump between 5% and 15%. The range in accuracy depends on how heritable some of the traits are,” he says.
“This animal, 08147, came back as being in the top 5% for fat yield and top 10% for meat traits, which was just exceptional. The phrase ‘trust and verify’ sums up what genomics is all about. You trust some of the traits, but genomics just allows you to verify, giving you the confidence to use ram lambs and speed up the genetic gain.”
When the stud rams were tested at the end of 2012, the 50k SNP test cost about £240 an animal. However, offspring from those stud rams can be tested with a cheaper test because half of their DNA is already known, bringing down the cost.
“The higher the SNP chip number, such as 50,000, the more specific the test, as the DNA is being analysed in 50,000 segment sections. However, there are cheaper genomic tests such as the 5K SNP chip that can be used when one of the parent’s DNA is already known and this only costs £40 an animal,” explains
From next year the family will start selling high-value rams with a full DNA breakdown to show customers what genesets the animals are carrying.
“If we were to mate all of our best rams with all of our best ewes we would end up with a smaller genetic pool. So we make sure our rams tup a group of ewes of mixed ability.”
The groups remain in a single-sire group for one cycle and then they remove the rams, amalgamate three groups and add in a Hampshire.
If the Hampshire picks up a ewe, which is easily determined by the colour of the lamb’s face, then that ewe will drop out of the elite group and won’t be part of the performance-recorded flock.
This year 1,700 ewes were performance recorded, with 1,700 non-performance recorded in the commercial flock.
In order to continue verifying the data, accurate recording is vital. In the 1,700 elite recorded ewe flock the Hodgkins measure eight-week weight, and 21-week weight. Maternal score given at birth, along with lambs ultrasound-scanned for back fat and eye muscle, are also recorded.
“We lamb outside so recording data has to be made easy, says
“Although we are looking at both maternal and terminal traits, at the end of the day we are looking at producing a maternal ewe.
“Mothering traits are key to everything, if you don’t have a ewe with high survivability, good fertility and good milking ability, then you are not going to have a fast-growing lamb.”
“Genomics is certainly something that will help drive our business as it will give the commercial buyer more confidence.
“Commercial buyers are looking for animals that can work off forage. We get lots of repeat custom and already 90% of our females have been sold for 2014.
“Genomics is not changing the genes, it is just helping speed up natural selection. It isn’t something that couldn’t be done in 10 years using pen and paper, it’s just helping us progress quicker,” he adds.
More on this topic
Read more on genomic use in the sheep sector
? Tenanted 560ha farm
? Sell breeding rams and ewes
? Animals not sold or retained for breeding are sold finished
? Switched from a Mule-based flock in 2000 to one of New Zealand Romneys
? Since 2005 a breeding programme has been in place to increase the amount of
? In 2006 they teamed up with
? Imported first rams in 2007 and since then have flown over 24 rams from NZ
? More than 3,000 100% NZ Romneys run under
? Largest Signet recorded flock in
Genetic technology is something the
Genomics can write success in your flock’s DNA
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