Genomic testing of females steps up a gear with PrecisionDNA


Genomic indexes took the UK by storm when they were first published in this country for Holstein sires. Since that day in April 2012, farmer confidence has steadily built, to the extent that today, young genomic sires represent over 70% of all dairy insemination's.

But sires are just half of the breeding equation and today, the smart money is on genomically testing females. This practice is rising in popularity amongst progressive dairy producers, who are boosting their profits with the additional knowledge the service provides.

Just as Cogent has been at the cutting edge with other breeding technologies – most notably SexedULTRA 4M – the company is also leading the way with genomic testing. Like other genomic tests, their service, branded PrecisionDNA, measures the DNA of the females in a herd, and provides a genomic Predicted Transmitting Ability (PTA) across a cross-section of traits.

However, what sets PrecisionDNA apart from other genomic tests is the level of detail it is able to provide.

Rudolph Linde, business development manager with Cogent, explains: “We have been able to bring the most advanced 70K SNP-chip to the UK market, which provides a level of detail and reliability producers haven’t been able to access before.

“In practice, this means they will not only receive the full breakdown of each animal’s genomic Predicted Transmitting Ability, but it will also identify most economically important haplotypes and recessive genes.”

This means the farmer will know, with a greater degree of accuracy than ever before, whether the animal carries undesirable as well as desirable genetic traits.

And whilst the undesirable traits may simply be carried with no detrimental effect to the female concerned, it’s vital not to double them up in an unsuitable mating.

Carriers of defects such as BLAD (bovine leucocyte adhesion deficiency), CVM (complex vertebral malformation), DUMPS (deficiency of uridine monophosphate synthase) and Mulefoot will all be identified, as too will negative haplotypes which could affect fertility.

Conversely, positive traits can also be identified such as which alleles are present for the milk proteins, A2A2 kappa-casein or beta-casein.

Obtaining the information

The first step in the process begins with a tissue sample taken from the animal’s ear. Once this is converted to a genotype – which takes place in the laboratories of Cogent’s US-based sister company, Genetic Visions – the information is interpreted in the UK by EGENES (Edinburgh Genetic Evaluation Services). The final step in the process is the calculation of a Predicted Transmitting Ability for the young animal, published as an official UK index by AHDB Dairy.

Affordability

“A distinct difference between PrecisionDNA and other genomic tests is that our own company handles the technology, up to the point at which the index is calculated,” says Mr Linde. “It is this which has controlled our costs and made the medium-density SNP-chip affordable to the farmer.”

Reliability

A further bonus of the 70K chip is the reliability of the resulting PTA.

“Genomic PTAs will always be more reliable than the Parent Average indexes they replace,” says Mr Linde. “But upgrading to a 70K chip, increases reliability further.

“A Parent Average [or Pedigree Index] would typically have a reliability of around 30-35 per cent, and that’s without accounting for errors in parent identification,” he says. “But using the 70K chip, we can increase that reliability to 65-70 per cent, depending on which trait we are measuring.”

The upshot is that dairy producers have a far more accurate idea of the genetic potential of their heifers from as early as a few weeks old.

Understanding the information

An obstacle to genomic testing farmers have sometimes incurred has involved the presentation of the genomic data.

“This hasn’t always been easy to interpret, so at Cogent, we’ve designed a simple graphical presentation of the results for easy understanding,” he says. “There’s a fully interactive portal which allows the user to not only compare females within the sample population, but also to benchmark against the national breed. And added to this, is the availability of Cogent breeding advisors who are trained to help with interpretation.”

Acting on the results

The key to success in genomic testing is taking appropriate action with the results, continues Mr Linde.

“Genomic testing only delivers a return on investment when the resulting information is correctly interpreted and utilised, resulting in sound management decisions,” he says.

The three main actions which could be taken are as follows:

1. Assuming a surplus of replacement heifers, the genetically inferior animals could be sold, before they incur any rearing costs, also resulting in increased selection intensity.

2. The genetically inferior animals could be bred to beef, while the genetically superior animals could be bred to SexedULTRA 4M dairy semen, to increase genetic gain.

3. More reliable and informed breeding decisions could be made by correctively mating to sires which complement the female’s genetic profile, so correcting any weaknesses and avoiding undesirable recessive traits.

“The many farmers who are already making genomic testing work in their herds, are taking one or all of these actions,” says Mr Linde.

What are the benefits?

The increase in genetic gain obtainable through genomic selection has been worked out by independent geneticists. They say the gain is dependent on three factors:

1. The intensity of selection;

2. The genetic variation across the trait;

3. And the reliability of the genomic evaluation.

Using this knowledge and the so-called ‘Breeder’s Equation’, it has been calculated that a typical 300-head herd with a replacement rate of 25 per cent (plus 10 per cent over-production to allow for mortality and selection) can achieve an additional response to genomics of 81.51kg milk per lactation and 301.59kg milk over the lifetime of the cow.

Margins

This extra production has a value in extra margin of £3,315.95 per cow (Promar Milkminder costings, December ’18). Once the cost of the genomic testing is deducted, the financial benefit to be gained from the extra milk production alone is £1,240.95 in the 300-cow herd, in just the first round of genotyping.

Added to this, are the health, fertility and other traits which can equally be improved and bring further financial benefits, depending on selection policy.

Genetic gain

In a practical farm situation, progressive farmers who have adopted genomic testing are typically also using SexedULTRA 4M (high purity sexed female semen) to breed their highest genetically valued females. This strategy has been calculated to increase the Profitable Lifetime Index (£PLI) of the resulting generation by £60.10. This compares with an increase of £40.81 using sexed semen and traditional (non-genomic) PTAs, or £28.62 if using traditional, conventional and traditional PTAs.

Cumulative

“However, as is the nature of genetics, the major benefit will be seen further down the line,” remarks Mr Linde. “Because genetic gain is additive and cumulative, any decision affecting the next generation will be passed down and potentially further improved in generations to come.”

Furthermore, the benefits to be gained from genetic improvement are independent of both the reduction in rearing costs to be gained from removing the lower genetic merit heifers from the herd at a young age and the financial benefit of combining genomics with the use of SexedULTRA 4M to produce high value beef-cross calves from the genetically inferior portion of the dairy herd.

“As is the case in any business, information is power and progressive dairy farmers are using the knowledge they gain from genomic testing to empower their breeding and management decisions and improve their profitability,” says Mr Linde.

Panel:

Busting genomic jargon

DNA – Deoxyribonucleic acid is a genetic blueprint containing the instructions for the development and function of life.

Gene – The basic unit of inheritance which comprises a segment of DNA which codes for a particular amino acid.

Allele – A form or version of a gene, such as an allele for either red or black in the coat colour gene.

Recessive allele - An allele which only has an effect when two copies are inherited – one from each parent. Most harmful alleles are recessive.

Genome – The entire complement of the animal’s genetic material.

Genotype – The measure of an animal’s genetic makeup. This measurement is taken by Cogent’s sister company, Genetic Visions, based in Wisconsin, USA.

Phenotype – The observable physical traits of an animal (such as stature or milk yield) which is determined by both its genetic makeup and environmental influences.

Reference population – A population of several thousand animals whose actual performance (phenotype) and genotype are compared to establish relationships between the two. From these relationships, a SNP-key can be devised.

SNP (Single Nucleotide Polymorphism) – A measurement of genetic variation at one position on a strand of DNA, which can be used to describe an animal’s genotype.

SNP-chip – A simultaneous measure of many different SNPs. A high-density SNP-chip measures more than 500,000 SNPs and a low-density chip measures around 3,000 SNPs. A 70,000 SNP-chip is considered to be medium density.

SNP-key – A key (also called a prediction equation) which translates an animal’s genotype, as measured by the SNP-chip, into a genetic index such as a genomic Predicted Transmitting Ability. In the UK, this key is calculated by EGENES (Edinburgh Genetic Evaluation Services) on behalf of AHDB Dairy, who publish the animal’s PTA, making the figure an official UK evaluation.

Haplotype – A group of SNPs or alleles located close to each other, which are usually inherited together. Haplotypes can have positive, neutral or negative effects, and some which are negative can impair fertility or cause embryonic death.

The Breeder’s Equation – an equation proposed by Falconer and Mackay (1996) which defines the genetic gain which can be made at different levels of selection intensity, genetic variance and reliability.

Reliability – a figure assigned to a genetic index which gives an indication of how likely it is to change as more information is added to its calculation

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