Education - A Guide To Genetic Indexes

Genetic indexes have been part of the cattle breeding industry for over 25 years yet even today, many of us feel unfamiliar with their use and unsure of their exact meaning. In this guide, we go back to basics on some of the most regularly used indexes, and explain some of the common dairy cattle breeding jargon.

What is a genetic index?

A genetic index is a measure of an animal's ability to transmit its genes on to the next generation. These could be genes for production, for conformation, for a combination of the two, or for any other heritable trait that can be measured. It is important to understand that a genetic index is not a measure of a physical trait in an animal, which is technically known as it’s phenotype (e.g. coat colour, stature, milk production etc), but is a reflection of its genotype (i.e. its genetic make-up). This distinction is important to understand, since many cows could produce high quantities of milk, but their high production may be more a function of their management regime than their genotype. A genetic index therefore makes the best estimate possible of an animal's ability to transmit a quality, by discounting the effects of its management regime and other environmental factors. 

How is a genetic index calculated?

For male dairy animals, genetic indexes are calculated largely from the performance of daughters, with adjustment made according to the production levels and management of the herds in which they are milking. However, other factors also come into play, including the genetic indices of other relatives of the bull (particularly his sire).
For a female dairy cow the same principles apply but naturally, the animal's own performance is also an important component of the genetic index.

A summary of the main information used to calculate an index is as follows:

  • The animal's own performance (if available)
  • The performance of progeny
  • The genetic index of the sire
  • The genetic index of the dam
  • The genetic indices of all other known relatives

As more information becomes available for the animal itself, so the importance of the ancestor information declines.

Genetic index for production

PTA - The Predicted Transmitting Ability (PTA) is probably the most commonly used index and forms the basis of many other indices in the UK. It is primarily a genetic index for production - specifically the components of milk (weight), fat (weight and per cent) and protein (weight and per cent). PTAs are calculated for males and females. An example PTA for a bull could be expressed as follows:

384 kg milk
24.1 kg fat
+0.13% fat
17.4 kg protein
+0.07% protein
Reliability 78%.

This bull's daughters are expected to give, on average and in their first lactation, 384 kg more milk, 24.1 kg more fat and 17.4 kg more protein than cows whose sire has a PTA of 0 kg milk, 0 kg fat and 0 kg protein. The reliability figure is a reflection of the number of daughters that have contributed to the bull's proof and their distribution across herds. When published for bulls, reliability ranges from 50% to 99%. The higher the reliability, the more likely is the proof to be an accurate reflection of the bull's true transmitting ability. It is therefore recommended that bulls of low reliability are not used on a widespread basis within any one herd.
As with all genetic indexes, it is important not to directly compare PTAs from more than one country. These should be expressed on a UK scale when they can be easily compared.

PTA 2005 - Currently the PTA is termed PTA2005, the 2005 denoting the year in which the base, or average cow production was measured. It is less important to understand the principles of base change, than it is to be aware that PTA2005's must never be directly compared with PTA2000's (their predecessor). 

Genetic index with economic weightings

PIN - Profit Index (PIN) is an economic index derived from the production PTA. It is expressed as a financial value in £s and reflects the expected increase in revenue per lactation for each daughter, relative to an animal with a PIN of zero. The formula for PIN has been calculated to reflect expected future milk prices; the amount of feed energy required to produce each component of the milk; the cost of quota and the cost of cooling and transporting milk.
Although pricing systems for milk can now vary widely (ranging from 'white water' contracts to high protein milk for cheese manufacture), any economic index has to reflect the economic situation predicted to exist five years ahead when the offspring of matings currently being planned are having their maximum effect on a herd. All indications are that the current PIN formula reflects these predictions.

PLI - Profitable Life Index (PLI) is a very similar economic index to PIN, but it recognises that milk production is not the only factor to influence profitability, but that herd life also has an important part to play. The core of its formula is the same as PIN, but added to this is a weighting for Lifespan.

Lifespan - The Lifespan value itself is measured directly from actual daughter survival and from certain type traits. The type traits with the strongest association with Lifespan (major reasons for involuntary culling decisions) are leg and foot composite, mammary composite and somatic cell count. Locomotion is used where available for UK tested sires to replace leg and foot composites. Fertility is another major factor involved in culling decisions and the new Fertility Index was incorporated into overall £PLI in August 2006.

Genetic indexes for type

TM or PTAT - Type Merit (TM) or Predicted Transmitting Ability for Type (PTAT) is a genetic index for conformation, which indicates a sire's ability to transmit his genes for physical traits on to the next generation. It is not a measure of the sire's own type, but is calculated from the linear scores of daughters and how far from the breed ideal the daughters score in comparison to their dams and contemporaries for each trait.
Type Merit is expressed on a scale of around -3 to +3, with both extremes denoting a likelihood of movement. A few exceptional animals will fall outside this range. These figures are known as standard deviations and indicate how far the animal is from breed average.

Pedigree indexes

The Pedigree Index has been developed by Holstein UK to provide an estimate of a young animal's genetic potential before it has any production information of it’s own. The effective use of the index enables breeding decisions to be made at an early age and can therefore reduce heifer rearing costs. The Pedigree Index is based on the average of the parents' genetic merit, but in the absence of parent information, indexes from further back in the pedigree are used. Pedigree Indexes can be calculated for almost any index, ranging from the basic PTA to the more complex economic indexes or even type indexes. Naturally, the Pedigree Index is less reliable than the genetic index the animal receives after it has production information of its own. It should therefore be used with the appropriate caution. The reliability of Pedigree Indexes generally ranges from about 20 to 40%.

Other indexes

Confusion often arises over the term Production Index, indicated on milk records, which is in fact not a genetic index, but an indicator of a female's actual performance (based on weight of fat and protein) in any lactation within a herd. This is adjusted to a heifer equivalent and corrected for age and season of calving. The average Production Index of any herd is always 100. This is often a useful method to determine prospective replacement breeders within any system.