Genomics – a need-to-know guide (May 2021)

Genomics is a term that producers will be familiar with, particularly when it comes to selecting young sires. But this alone provides only half the picture, and the technology is now being adopted to make informed heifer-breeding decisions.


TEXT SARAH ALDERTON



Q: What is genomics?


A: Genomics is technology that looks at the DNA of an animal to accurately predict its future appearance, performance, and a range of other useful management information.



Q: How does it work?


A: Geneticists have identified thousands of small sections of DNA (markers) in the bovine genome, which are related to poor or favourable traits in an animal. These markers are referred to as SNPs. These SNPs can be detected and used to highlight whether an animal is going to have favourable or unfavourable genetics for certain production and health traits, including milk yield, fat and protein content, and mastitis.


Producers traditionally select sires or replacement heifers by looking at the productivity of each animal (and their offspring, if available) and data collected from the animal’s parents, which gives a parent average value. But this is prone to significant errors and makes the incorrect assumption that DNA is inherited from each parent in equal measure.


For example all full siblings will have the same parent average figure for any given trait, but we know from experience that siblings can vary hugely in both appearance and performance.


Q: Why use genomic testing?


A: Genomics reliably predicts how an animal will perform in its environment by examining the slight differences in the genes the animal has inherited from each parent. On average, it would take production data from eight years to obtain the same reliability provided by one genomic test. By genomically testing young females, producers can make accurate selection and breeding decisions right from day one. This increases the rate of genetic gain and ensures time and money is only invested in animals that are more likely to be profitable during their lifetime.


Q: How reliable is genomics?


A: It’s more accurate compared to selecting animals using parent averages, but the exact figure will depend on the trait or index. Taking milk yield as an example, genomic testing predicts with about 70% reliability how an animal will perform. This compares to about 35% reliability when using parent average. The parent average reliability is also dependent on accurate parentage recording. Correcting parentage using genomics shows that, on average, one in 10 heifers is recorded as having the wrong sire or dam. For these heifers, the reliability of the parent average figure will be much closer to zero.


Q: How does it differ from the figures in the free AHDB herd genetic report?


A: The free AHDB herd genetic report gives a good insight into where a herd or cohort of animals is in comparison to national averages. But for individual animals, we will only be looking at parent average figures initially. And these have much lower reliability than a genomic result. Once each heifer has been genomically tested, her figure will be updated in the AHDB report to show her more reliable genomic results.


Q: How many animals should be tested?


A: When looking to make any heifer group selection decisions, it is important to test all heifers. This is because when narrowing down a group to test, whether that’s done by eye or using parent averages, heifers with a much better (or worse) genetic potential than their parent average predicts could be missed. The only exception to this would be for heifers that will be sold or bred to beef, regardless of genetic potential.


Q: At what age should heifers be tested?


A: Calves can be genomically tested as soon as they are born. The earlier they are tested, the sooner producers can make use of the data. For example when selling surplus heifers, if they have been genomically tested, it’s easy to accurately identify those that should be retained and those to sell. Selling any surplus heifers early will save shed space and feed costs. And time can be better spent looking after higher genetic merit replacements.


Testing can be done at any age, including adult cows. But we recommend testing heifers before 11 months old, or at least eight weeks before they’re served. This is because it takes between four and five weeks for test results to come back, and time is then required to look at the data and make breeding decisions.


Q: What does the test involve?


A: A hair or tissue sample is required. A tissue sampling unit (TSU) allows you to take a tiny ear notch from any animal of any age. This can be taken using a standalone TSU or as part of the official tag pair. The sample is then sent to the laboratory for testing.


Q: How is the genomic data used?


A: The key to using genomic data is to not become fixed on individual traits. It is important to pick and then trust an index (a group of traits that contains the traits that fit your breeding goals). Indexes allow gains to be made on a range of traits at the same time, while keeping the process easy to implement by providing one single figure for each animal. Cherry-picking individual traits could result in selecting animals that are good for those specific traits, but have significant weaknesses in other important areas.


CLARIFIDE Plus provides the Dairy Wellness Profit Index (DWP), as well as eight other industry recognised indexes. DWP is based on a range of traits that affect health, fertility and production. These all determine an animal’s profitability. DWP also describes more genetic variation in profitability than other indexes, allowing for faster progress toward greater lifetime profitability. It balances selection across a range of economically relevant traits, as producers seek to identify and breed the most profitable cow that can meet current and future environmental and production demands.


Three times a year – in April, August and December – the top 100 Holstein animals tested using CLARIFIDE Plus are ranked on DWP. This shows where animals rank and could be used as a marketing tool when selling surplus heifers. Producers can view the top 100 UK Holstein females ranked on DWP at www.clarifide.co.uk.


Producers are under increasing pressure to become more sustainable, particularly as support payments are removed. Breeding is the foundation of every herd and by using genomics producers can accelerate the genetic progress in their herd by accurately selecting genetically superior animals.

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