STEPPING IT UP WITH SNPs

DNA parentage testing has traditionally been done with microsatellite markers. These markers are simple repeats in the DNA sequence, and the number of repeats present is highly variable. This high level of variability is what allows us to correctly assign DNA-based parentage using a relatively small number of markers.

Single Nucleotide Polymorphisms (SNPs) occur when there is a high amount of variation amongst individuals at a single position in the DNA sequence. There are millions of SNPs present across the cattle genome. Genotyping using SNP ‘chips’ can provide data on many thousands of SNPs at once, as opposed to the small 16 marker panel for microsatellites. 

As well being used for parentage verification, genotype data from SNP chips can be used to assess animal status for many single gene traits, such as myostatin status, or carriers of disease mutations such as arachnomelia and curly calf syndrome. They are also the technology that underpins genomic selection, which uses phenotype and genotype information on a reference population of animals to predict genetic merit in cattle at an early age.

Historically, the cost of SNP genotyping has been higher than that of microsatellite genotyping, however these costs have significantly decreased over time, and are now much more comparable. Moving from microsatellites to SNP-based parentage verification will provide many opportunities to accelerate breed development.

BRITISH SIMMENTAL MOVING ITS DNA SERVICE PROVISION TO SINGLE NUCLEOTIDE POLYMORPHISM (SNP) TECHNOLOGY IN 2021

In a progressive step, the British Simmental Cattle Society will move its DNA services in 2021 from the presently used Microsatellite (MS) technology to Single Nucleotide Polymorphism (SNP) technology.   

The work to make the transition has commenced with the aim being that the new service will fully commence from 1^st March 2021.   To explain this change as clearly and simply as possible, please see the following Q&A where we have anticipated what we think may be the most relevant and helpful questions:

Q:  Are there any other advantages or benefits that moving to the SNP technology may bring members?

A: Yes.  As above, the SNP technology will bring improved and more robust sire and parentage verification and is a move forward in technology.  The SNP technology will also give the ability to add more to a single test, a parentage plus polled test would be an example of this.  Both could be done at one test and as opposed to two separate tests at a greater cost.  Members will therefore, in such an instance, make a considerable saving.

SNP technology will also give the platform from which, if the Society chose to do so, major gene testing can be carried out for a range of such as health traits, traits of economic importance, and for work in genomics generally. 

be tested at the present prices.  The new pricing schedule will be applicable from 1st March and for samples received after that date.

If there are sale or ‘special’ situations where DNA testing is required then consideration will be given to this prior to March but it would be using the existing and in effect ‘old’ MS technology.

Q:  What challenges might the transition bring?

A:  We hope of course for the transition itself from MS to SNPs, and the DNA service provision thereafter, to be as smooth as possible.  It is likely, if not inevitable, that challenges will arise from time to time regarding such as ‘older animals’ and embryos in storage.  We hope that these will be at a minimum and each will have to be considered on their merits and as they arise.  Weatherbys have faced and successfully met similar challenges in other transitions, and whilst we are closer to the MS technology being phased out, we trust that this will also be the case during and beyond the Simmental transition also.   

Q: What about testing turn round times for SNPs

This is an important point.  The turn round time for DNA testing should be largely the same as at present i.e. from receipt of the sample, members should have results back within 4-6 weeks.  However, please note that the SNP process in itself takes 3 weeks from the time Weatherbys receive that sample, for samples to have DNA extracted and parentage tests carried out thereafter.   Therefore, particularly with reference to sale animals, samples will be required in plenty of time in advance of sale dates.  Where there are any problems or need for retesting following the initial sample being tested,  then at least three weeks is required for a second test beyond receipt of the sample at the lab.

Q: Are there any other suggestions for members in collecting samples?

A: Yes. If a member is selling/disposing of a bull that has had, or is due to have, progeny registered to him, then it would be good practise to collect a hair sample from the bull.  Identify the sample on the bag it’s put in, and keep in a drawer out of sunshine.  This could be very important in case the sample held and retrieved from Weatherbys is not good enough to be SNP profiled, or where a bull is having his first calves registered to him.     It would be sensible to take a hair sample in this manner from any pedigree breeding animal, male or female, that is being sold or disposed of, just in case there is a requirement for a DNA purpose, now or in the future.

Please note, hairs should be collected by plucking (not cutting) from the animal’s tail. This is preferable to hairs from the neck as the root follicles are bigger. It is recommended that 20-30 hairs are required per sample collected.

Q:  Will the Society be able to help with member queries around this transition now and beyond 1st March?

Absolutely.  The Society’s staff will be working hard to ensure the ‘new’ service is rolled out as smoothly as is possible and to help members with queries and problems.  Many members will remember Bloodtyping being the standard technology.  The livestock industry then transitioned to Microsatellites.  This move to SNP technology is the next and further step forward in the provision of DNA services. 

can truly overcome the influence of poor genetics. The benefits of genetic improvement are both cumulative and permanent, so good breeding decisions will continue to pay dividends in the herd over many years, and the use of estimated breeding values (EBVs) across the agricultural industry has led to huge gains in productivity and profitability in the past 50 years. As the industry has gained more knowledge on the use of these tools, we are now able to continue that improvement in productivity while maintaining health and welfare traits.

In this article we take a closer look at Simmental genetic improvement since 2000, to discover how the breed has improved over time, and how more effective use of EBVs could speed up progress and add value within the breed.

Genetic index trends

Looking at the trend in index values for the Simmental breed since 2000 (Figure 1), we can see that the breed has made progress in terms of both the Terminal Index, and the Self Replacing Index. The breed averages (Mean EBV) for the Terminal and Self Replacing index have each increased by over 50%. For each index, animals that were within the top 10% of the breed in 2000, would find themselves in the bottom 20% of the breed by today’s standards. 

The Simmental has a recognised reputation for being an easy calving breed, and this may become an increasing challenge to take sight of and maintain if the current genetic trends for birth weight and direct calving ease continue. 

Both the calf and the dam have an effect on overall calving ease, the calf through its size and shape (the ‘direct’ component), and the dam through her pelvic size and shape (the ‘maternal’ component). The calving ease daughters EBV is made up of the maternal genetic component, plus ½ of the direct genetic component for calving ease. The increase we see in calving ease daughters over time will be driven by the maternal genetic component of this EBV. 

The other potential challenge is the EBV for mature cow size, where we see the breed average EBV increasing by over 1kg per year. Despite larger cows generally producing progeny with higher carcase weights, these gains are outweighed by higher cow maintenance costs, and decreased fertility. The question of “how heavy is too heavy” is discussed in more detail on page 80.

Data since 2000 shows that the general strategy employed in breeding Simmental cattle is to select animals whose genetics reflect the breed average or better (Table 1). The breed has therefore taken the important first step towards good genetic progress, by not breeding from animals whose genetics are below average.

Although it’s a great first step, using the breed average as your selection threshold for breeding will set an upper limit to the amount of progress over time. If the breed continues to use “above average” as their selection threshold, while other breeds push towards breeding only animals from (for example) the top 20% of the breed, there is a high risk of the breed being left behind in terms of performance. 

To really ignite genetic progress in the breed, and ensure that the Simmental retains and kicks on it’s place in the UK beef market, then there is a challenge to hold your breeding cattle to higher standards of performance, and target only the top 25% of animals for use in breeding.   

At the moment it may not be as easy as you would like to identify these higher performing animals. As with so many things in life, “If you can’t measure it, you can’t manage it”. The best way to identify the best genetics within the Simmental population is to encourage widespread performance recording among pedigree breeders. 

Take home messages:

• Aim high, not average (select within top 25% of breed)
• Performance record wherever possible “If you can’t measure it, you can’t manage it”)
• Keep an eye on maternal performance
• Know your market, and breed animals that will excel for yourself and your customers

*The British Simmental Cattle Society uses the Breedplan system which is one of the most widely used beef recording systems in the world. Breeders submit weight and performance data to the Society which is in turn sent to ABRI, the providers of Breedplan, who generate the EBVs across a range of maternal and terminal traits. EBVs are calculated and updated on a monthly basis and fed back to members. Herd costs to performance record starts at £120 per annum.  If you are a BSCS member and wish to begin performance recording your herd, please email information@britishsimmental.co.uk and request a Breedplan membership pack.

cows benefit the modelled farm through higher cull cow revenue, and by producing offspring with higher carcase revenue and quality. However, heavier cows have higher costs in terms of maintenance feed and replacements, and they also suffer from a decrease in fertility, potentially producing less offspring in their breeding lifetime. Heavier cows also require more land than lighter cows, resulting in a reduced stocking density on farm. Once you combine all of these factors, the cost of production is higher for heavier breeding females and therefore profitability is worse. 

Assuming that this dataset is a representative sample of the UK Simmental herd, this would suggest that in 2013, over 50% of mature cows weighed more than the optimum 685kg, and as the genetic potential for larger mature cow weight increases, the percentage of mature Simmental cows over the optimum mature weight is likely to be higher than 50% today. The profitability of the national herd is therefore lower than it could be.

To increase herd profitability, there is a strong argument of the importance that this trend for heavier cows is reversed. As mature weight is a heritable trait, we can use genetic improvement techniques to help take aim at the current trend.

Steps to optimise mature cow weight

1. Where available, make use of selection indexes that have penalties applied to breeding female mature weight EBVs; this controls the increase in mature weight, associated with selection for early growth
2. Weigh breeding females regularly and compare this to the weight of the calf they produce at weaning. It is aimed that a cow should produce 45% of her weight at weaning. Sign up for performance recording so that the data can be shared with Breedplan and used in genetic evaluation.
3. Don’t retain heifers from your biggest cows in the herd, mature weight is heritable. 
4. Buy sires where it is possible to assess the size/weight of the breeding females, and gather more intelligence about the genetic merit of the males for growth, mature weight and other genetic merit estimates
5. Communicate with commercial farmers to understand the needs in the context of breeding female mature weight, with an understanding that bigger is not always better.

These EBVs are calculated using data from BCMS, processors and breed societies, giving high accuracy figures for bulls that have had progeny slaughtered. For young bulls, EBVs can still be calculated using data from their relatives, such as their parents and grandparents. These figures will get more accurate when their own progeny reach slaughter age. The processor data currently covers 40 per cent of the national kill and almost 3 million carcase records for both purebred and crossbred animals have been used in the latest genetic evaluation.

The heritability tells us what proportion of variation we see in a phenotypic trait is down to genetics. For the new carcase traits, over 40% of variation we see is a result of genetics, so making use of these new EBVs will greatly accelerate improvement in carcase characteristics.

Understanding the new carcase traits 

This set of EBVs is derived directly from commercial data, and should therefore be of high interest to commercial producers as well as the pedigree sector.

CARCASE CONFORMATION

Definition: An EBV predicting carcase conformation at a given slaughter age.
Calculated from: Records of carcase conformation based on the EUROP classification system, provided by UK processors.
Unit of measurement: Carcase conformation scores converted to a 45 point score. A conformation grade (e.g. R to U) spans about 9 points.
Interpretation: Skerrington Superstar has a carcase conformation EBV of +0.02. On average, he will produce progeny whose carcase conformation is equivalent to that from a bull with a carcase conformation EBV of 0. A bull with a carcase conformation EBV of +9 would produce progeny that have conformation half a grade higher than a bull with a conformation EBV of 0.

AVERAGE DAILY CARCASE GAIN (ADCG) 

Definition: An EBV predicting daily gain in the carcase.
Calculated from: Carcase weight, date of birth and date of slaughter.
Unit of measurement: Kilogrammes (kg)
Interpretation: Skerrington Superstar has an ADCG EBV of +0.04. On average, the daily carcase gain of his progeny will be 0.02kg greater than progeny from a bull with an EBV of 0.

All five EBVs are expressed on two bases, native and continental, so EBVs for Simmental cattle can be compared directly with other continental beef breeds.

What does this mean for Simmentals?

Currently ranked #1 continental breed for age at slaughter

Based on data from the December 2020 evaluation on continental breeds, the Simmental breed ranks number one in terms of average EBV for days to slaughter, with an average EBV of -5.13 days. This average is currently significantly lower than the other continental breeds. The genetic trend for days to slaughter has a shallow downward slope, meaning that Simmental breeders are successfully breeding animals that finish at an earlier age, but there’s still plenty of room for more progress.

We do see high levels of variation in all five traits for all breeds, which combined with the high heritabilities means there is good scope for carcase improvement in every breed. To maintain the current breed advantage in terms of days to slaughter, Simmental breeders should make use of these new EBVs when making selection decisions to help accelerate genetic gain.

“Why is the average progeny performance half of the EBV value?”

The EBV is the measure of the genetic merit of the bull. He contributes 50% of his genetics to his progeny, therefore the average progeny performance is 50% of the EBV value.

“Will such small increases in conformation and fat class really make a difference?”

Example shows small benefits (less than half a grade) for conformation and fat class. It’s important to remember that genetic improvement is both cumulative and permanent, so even small improvements will add up over generations to produce higher performing animals.

“How reliable are the new EBVs?”

As with the BREEDPLAN EBVs, the new carcase trait EBVs have an accuracy value associated with them. The higher the accuracy value, the more reliable the result. EBVs are only published for animals where the accuracy for all five traits is over 30%. 

How can you help to make these EBVs better?

The production of these EBVs relies on sire details being recorded on passports to be able to identify genetic links between bulls and recorded progeny. In the latest genetic evaluation (December 2020), there were 5 million carcase records that could not be utilised because the sire was not recorded in BCMS, so genetic links could not be made. We are urging farmers to make sure they record known sires when registering animals with BCMS as this is the best way to improve the range and accuracy of these EBVs. As well as recording all known sires for your own herd, please encourage buyers of stock bulls to do the same. Increasing the level of sire recording will allow us to identify genetic links between cattle and improve the accuracy