Pick the best parents for profit

When selecting bulls, the best way to achieve genetic improvement in offspring is selection based on EBVs or an index, Dorian Garrick writes.

Managers tend to seek out and make changes that improve their profit. Most normal management interventions such as changing feeding levels, choosing the date the bulls go out, the date for weaning the calves, vaccinating the animals, or applying anthelmintic treatments, are done at the level of the whole herd, or at least to all the animals of a particular age class.

Farmers should always be considering management interventions that are practical, proven, and cost-effective. This includes those that have short-term impact and others that may provide benefit over longer timeframes.

Animal phenotypes are the technical description for those characteristics that we can see or that we can measure on an animal.

Farmers like certain phenotypic outcomes such as fast growth rates, docility, easy calving, disease resistance and longevity. They do not like other phenotypic outcomes such as slow growth rates, temperamental behaviour, difficult calving, susceptibility to diseases, or failure to rebreed in a timely fashion.

Collectively, the profitability of the farming system is determined by the value of the phenotypic performance of each individual animal, summed across the value of all the products from the animals on the farm, minus all input costs.

Within any group of animals of the same age and managed in the same mob and treated alike, there will still remain significant variation. We refer to this variation as phenotypic variation. It does not include differences in performance between animals that are in different mobs.

Phenotypic variation, observed within a mob, will always be less than the variation observed across animals from different mobs, farms, or years.

Most management practices do not influence the variation within a mob, except for drafting outliers and providing preferential treatment to make them more alike. This practice is commonly applied to body condition score, where fat cows are put on poorer pastures and skinny cows are provided better quality and higher feed allowance.

Genetic improvement

Assuming a farmer is managing their animals in the most practical and cost-effective way, the biggest opportunity for further improvements in profitability of that farming system is through genetic improvement.

An individual animal does not exhibit genetic improvement, as its genetic merit was defined at conception and does not change over its lifetime. Genetic improvement occurs in any year when the average genetic merit of the animals that are allowed to become parents is higher than the average genetic merit of all the candidates that were available for consideration.

In a well-managed improvement scheme, the average genetic merit of every successive crop of calves is better than the average genetic merit of the previous crops. Genetic merit drives phenotypic performance in any management circumstance, and the technical term used to describe the true genetic merit is the breeding value (or BV).

An astute farmer seeking improvement in their farming system, would include consideration of genetic merit of their replacement bulls and replacement heifers, along with due consideration of all the other management practices available.

In practice, we cannot observe the BV or true genetic merit of an animal. The most reliable approach to estimating the BV, known as the EBV, is from a well-managed and carefully conducted progeny test.

Since the genetic merit of the progeny of a bull (or cow) is determined by the half of the genome they inherited from their sire, plus the half of their genome they inherited from their dam, it makes sense that an above-average sire assessed on hundreds or thousands of progeny from different mates, will be easily recognised as being superior.

In a large well-managed progeny test, the EBV can be simply computed as twice the average superiority of the offspring, adjusted for non-genetic factors such as contemporary group effect, date of birth, and age of dam. The “twice” multiplier reflects the fact that offspring only inherit half of the genome of the parent.

Bull too old

By the time we wait for progeny test information, a sire is typically too old to be of much interest. A bull cannot normally be used as a sire until he is a yearling, and after a 282-day gestation, the sire will be two years old when his progeny are born.

In the case of reproductive traits, it will take another two years before the daughters become mothers and can begin to be assessed for maternal traits. At best, a progeny test sire would be five years old before he can be selected from a progeny test for maternal performance and be widely used to produce commercial offspring.

In the case of carcase traits, these can be assessed on offspring harvested about 18 months of age. So the progeny test results will be available before the sire is four years old, but typically not soon enough to be selected from progeny test results to produce commercial calves before five years of age.

Most selection therefore must take place without the most reliable source of information which comes from a progeny test.

The traditional approach for early selection was to base the EBV on performance information collected on the candidate of interest. This might sometimes be based on phenotypes for the actual trait of interest, such as calving

ease, weaning weight or yearling weight, but is more commonly based on correlated traits.

In the case of carcase EBVs, the correlated traits are usually measures of muscularity or fatness obtained from real-time ultrasound machines. The use of an animal’s own performance measures to infer or estimate its genetic merit, creates somewhat of an enigma.

This is because the genetic merit or BV causes the phenotypic performance, not vice versa. Lots of factors determine phenotypic performance, not just genetic merit.

A sire with above-average genetic merit will produce a crop of offspring that are typically above-average relative to offspring of other sires that might have been bred with the same mates. However, an individual with an above-average genetic merit can exhibit below average individual performance, and an individual with below-average genetic merit can exhibit above-average individual performance.

Conversely, an individual with above average phenotypic performance or appearance, might produce offspring that are below-average for that particular trait. The strength of the relationship between genetic merit and individual performance can be quite strong, for traits like gestation length or mature size, or can be quite weak for traits such as reproductive performance during first lactation.

Animal breeders refer to the strength between genetic merit and phenotype using the term “heritability”.

Using SNP chip technology

Genomic information can be used to improve the accuracy of estimating the BV of young animals and is typically collected using SNP chips. Many of these chips contain about 50,000 genomic features and are therefore referred to as 50k SNP chips. Just like progeny testing, the effective use of SNP chip technology requires large databases of information on animals with phenotypic data.

Provided a DNA or tissue sample has been collected, it is a simple matter to buy genomic information on that animal to build the size of the database of animals with phenotypic and genomic information. However, it is not nearly as straightforward to buy phenotypic information.

It is not possible to go back in time and collect phenotypes other than those that were already collected. This led a colleague from Edinburgh to once remark that “in the age of genomics, phenotype is king”.

This does not mean we should use phenotype to make selection decisions regarding the likely performance of offspring of a potential sire or dam. That decision will be most accurate when it is based on EBVs, or on an economic index constructed by combining EBVs for traits that influence income or expenses.

For the commercial farmer buying bulls, genetic improvement of successive crops of offspring is best achieved by bull selection, based on EBVs or an index. For a bull breeder, selection ensures that each crop of sale bulls is better than the previous crop with respect to the offspring they produce on the farms of the bull buyers. That selection relies on the widespread collection of phenotypes comparing the relative performance of all the animals within every mob on the bull breeding unit. Those phenotypes are used along with pedigree and genomic data to generate EBVs that represent the best predictions of relative performance in the next generation.

Choosing the best animals to use as parents, based on EBVs, can make measurable and cumulative improvements to farm profitability.

• Dorian Garrick is Massey University professor of animal breeding and genetics.