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CONTRIBUTOR(S): Mark Burnell, Amy Jennings,

Genetics and genomics – an introduction

Genetics and genomics – an introduction

Genomics can help farmers to make more informed choices about breeding their stock and so achieve greater profitability, faster.


Charolais bull
©Mo Kemp

Introduction

DNA (deoxyribose nucleic acid) are molecules, arranged as double helical chains, which carry the genetic coding of an animal.

A Gene is a section of DNA (there are about 23,000 genes known in the cow, only 10% of all the DNA!).

Genetics: the study of heredity, concerning a single gene or many with complex interactions.

Genomics: the science of studying and mapping the genomes (the DNA).

A Genome, is an animal’s entire genetic code contained as chromosomes (arranged as 30 pairs).

Chromosome: a structure made up of DNA molecules. These are in pairs, and are inhereited, one from the mother and one from the father.

Genotype: the entire genetic constitution of an individual which expresses the phenotype (physical appearance) of the animal. This includes both recessive and dominant genes.

Phenotype: the outward appearance of an animal in all of its anatomical, physiological and behavioral characteristics, as dictated by genetics and the environment.

What is the relevance of genomics to cattle breeding?

Genomics has been used to study the genetic component of disease as well as characteristics associated with productivity such as growth rate and milk production.

If you took the same sire and the same dam and bred them, there are >1 quintillion possible variations in offspring genome. This is because ‘gene shuffling’ leads to unequal amounts of genetic material from the sire and dam in the offspring. This has traditionally made it hard to predict which characteristics a calf may have, eg future milk production, with any accuracy.

Genomic testing identifies exactly which genes are present and so predicts the likely performance with greater accuracy than using tools such as pedigrees. This gives us a lot more certainty when predicting which traits an animal will have (often around 60-70% compared to 20-30% with pedigree/parent information). Potential stud bulls can therefore be selected as calves with reasonable (70%) reliability rather than go through the long process of progeny testing.

Genomics offer the opportunity for a producer to select for traits that suit their production requirements and aims, or for resistance to diseases that cause a particular problem in their herd or flock.

Examples of desirable phenotypes/traits include:

  • More efficient production, such as higher feed efficiency (lower maintenance requirements).
  • Reduced greenhouse gas emissions for yield.
  • Increased milk production.
  • Change in the proportion of milk components.
  • Improved fertility.
  • Reduced susceptibility to inflammation of the udder (mastitis) leading to reduced somatic cell count.
  • Increased longevity (predicted life span).

What about breeding reliability?

Traditional methods of decision making when breeding cattle include the following:

Random breeding

This does not provide an ability to select for traits required by the farmer (0% reliability). However, it will still result in evolution of sorts, as those individuals that are successful within their environment are likely to survive longer to produce more progeny.

Visual selection

This gives us a very low reliability as the information relies on judgement and personal opinion. However, this method has resulted in the large diversity of breeds we currently farm across the world that are often well adapted to their environment and usage.

Pedigree selection

This method has the potential to offer 20-30% reliability for trait selection. Bear in mind that correct parentage is not always known, but can now be checked relatively cheaply using DNA methods.

Genomic predictions

These provide us with ~68-70% reliability. A genomic prediction derives from the genes that are present in the animal itself. These provide a measure of the genetic potential of the individual. This genotype will interact with the environment to result in a phenotype (the actual performance of the animal).

It is important to note that assessing the animal’s actual performance still achieves the best accuracy, eg daughter proven bulls can have 99% reliability if there are sufficient daughters on the ground. This takes time however, by which younger (and on average better) bulls will be being born. Genomics provides the greatest degree of reliability for selection of dairy heifers.

Why should a dairy business consider using genomics?

Dairy businesses have always been improving using the above (traditional) methods of breeding reliability. Genomics allows us to make these improvements and progress more quickly to utilize maximum breeding reliability (initially via genomically tested bulls).

The ‘Farmers Equation’: Rate of genetic gain = (Accuracy x Selection Intensity x Genetic Variation)/Generation Interval.

Generation Interval = average age of parents. It is better to calve at 2 years old than 3 years old and better to use young bulls. Therefore, breed your youngest animals (heifers) to produce herd replacements and use (a number) of young genomic bulls.

Selection Intensity = the lower the proportion of animals selected as parents, the higher the selection intensity. Rank your heifers according to genomic testing. Don’t breed replacements from the bottom end.

Accuracy = square root of reliability. Genomic testing at 70% v pedigree at 30%).

In summary, for a high rate of genetic gain we need to be making reliable breeding decisions which involves selecting only those animals of desired attributes to produce the next generation. (traditional breeding ‘sped up’! Genomics also allows farmers to establish parentage. More than 10-15% of animals will not have the correct parentage as recorded on farm!

What about genomic testing calves?

Genomic testing gives you options to rank your calves.

By genomic testing your calves, you can:

  • Use ET/IVF on the top animals, use the “poorer” animals as recipients.
  • Use sexed semen on the top animals to try and maximize replacement number.
  • Breed the bottom ranking animals to beef to avoid propagating he undesirable genetics.
  • Select the most appropriate bull for each animal (make sure you always consider calving ease as part of your selection).
  • Save on rearing costs and space by selling the calves that you don’t need.
  • By just taking a hair or tissue sample from an animal you can find out a huge amount of information (depending on the test) including:
    • Potential milk yield and constituents including casein types.
    • Health and performance parameters such as fertility, cell count, calving ease, TB susceptibility.
    • Conformational traits such as stature, chest width, teat placement etc.
    • Genetic conditions: some animals may be carrying genetic conditions, even though they do not suffer with problems themselves. It is best to know about these animals. We are not necessarily trying to not breed these animals but just make sure they are not mated with another carrier – as that is when problems will manifest themselves.
    • Inbreeding: average inbreeding level within UK herds is 3.5%, and >5% in the US. >6.25% tends to be the line that we aim not to cross.
    • Parentage verification: this can produce more issues than you think… more than 10% of animals will not have the correct parentage recorded on some dairy units.

Will it pay off?

Increased genetic gain

More profitable cows. Improvements in genetic gain is always additive year on year.

Change in breeding management bringing in other income

Opportunities for the production of beef calves? Sale of heifer calves?

Youngstock

Fewer calves reared will save on rearing costs. Decreased stocking density- underlying health benefits.

What are the risks?

As with anything, there can be risks and these need to be investigated and weighed up. Selection for a single trait can lead to accidental selection for undesirable traits and this is worth bearing in mind and monitoring. A holistic approach must be adopted. Genetic selection cannot correct for poor management.

In conclusion

Genetics are an important part of how a cow performs and with the latest technology it is possible to know your herd better than ever. Genomics has the potential to improve your stock quality and profitability. Well managed systems can test and select the female component of their herd, leading to rapid genetic progress in the direction you want.

Genomics is not a magic bullet! Good husbandry and management will always be essential.

There are many companies now offering genetic testing and genomics services.

Speak to your veterinarian to find out if it is applicable to your farm business.

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