Genetic indexes: the theory

An introduction to the basics of genetic indexes and PTAs (predicted transmitting abilities), why they are needed and how they’re calculated.

A genetic index is a measure of an animal’s ability to pass its genes on to the next generation. These could be genes for production, health, lifespan, conformation or for any trait that can be inherited and measured.

Although we’re most familiar with genetic indexes for milk, fat and protein, indexes are about far more than just production. Their application for non-production traits is becoming increasingly important in today’s health-and-welfare-conscious society.

Genetic indexes attempt to disregard the effects of environment and to strip performance down to the bare genetics. This means that a 12,000-litre cow from a high-input system can be compared with one in an extensive herd averaging 6,000 litres. Equally, bulls whose daughters are milking in different production systems can also be fairly compared. Before genetic indexes, there was no way of making such fair comparisons.

Every herd has strengths that farmers want to maintain and weaknesses they’re looking to address. Using genetic indexes, you can make accurate breeding decisions based on the predicted performance of a bull’s daughters.

To calculate a genetic index (often known as a proof), information is drawn from a variety of sources to produce the best possible estimate of an animal’s genetic worth. This includes information on the animal’s own performance, where appropriate, and on that of other family members.

An animal’s performance is a combination of genetics and environment, so allowances are made for age, lactation number, stage of lactation, herd performance and season.

For a bull, the most important component of his proof is his daughters’ performance. For a cow, the most important component, initially, is her own performance.

If a bull or cow is too young to have any daughter or performance information of its own, its genetic index is usually calculated from its own genotype (or gene set), measured from codes along each strand of its DNA.

Traditionally, an estimated genetic index for young animals has been called a pedigree index (or parent average), as information was based on the animal’s family or pedigree. However, these terms are used less since the advent of genomic indexes.

In all young animal indexes, their family and genomic information become progressively less important as the animal accumulates its own performance information (or from its progeny).

Information included in genetic indexes comes from:

• Milk records organisations – production and cell count information
• Breed societies – type and locomotion information
• A combination of the two – fertility and longevity

Calculating genetic indexes for production or production-related traits usually takes information from five lactations. Calculating genetic indexes for type or type-related traits typically relies on details of heifer classifications.

The accuracy with which genetic indexes are calculated is continually improving, thanks partly to the Test-Day Model (TDM).

In calculating a genetic index, TDM uses production information from every milk-recording test day, up to and including the fifth lactation. This has several advantages:

• It takes better account of management and environmental conditions affecting performance
• It provides earlier genetic information for bulls and cows

It allows a smoother transition to be made from the animal’s pedigree index, or genomic index, to its performance-based proof

In the UK, most genetic indexes are expressed as predicted transmitting abilities (PTAs), which predict the extent to which a trait will be passed on to an animal’s offspring.

PTAs don’t predict the offspring’s actual performance, which will vary widely depending on management, but instead they predict the amount of a trait the offspring will, on average, receive from its parents, compared with ‘average’ parents whose PTA is zero.

This principle applies to both male and female PTAs, and both to indexes based on actual and progeny performance and those based on family and genomic information.