Technical information - selection

Basic Genetics

by Alex Ashwood

BRAHMAN NEWS MARCH 2009 Issue #162

Throughout the history of breeding cattle, beef producers have successfully improved the quality of cattle and increased the profitability of their business through selection and genetic improvement. “Genetics, however, is a extremely complex and evolving subject” Nevertheless, studies have shown that the application of basic genetic principles can have a major impact on the quality of the herd and the productivity of the beef enterprise.

Furthermore, since stud breeders are largely responsible for the production of seedstock they have a significant influence on the quality of cattle available to the beef industry. Subsequently, further knowledge of basic genetic principles may allow a better understanding of selection tools and programs available to stud and commercial producers.


With minor exceptions, each animal receives half of its genes from its sire and half from its dam.

Thousands of pairs of genes exist in each animal but since only one member of each gene pair comes from each parent the particular combination of genes is determined purely by chance.

Some reproductive cells will contain more desirable genes for economically important traits (ERT’s) than others and the union of reproductive cells (eggs and sperm) containing high proportions of desirable traits (functional and ERT’s) results in a superior animal.

“The random combination of genes creates widespread differences in the offspring”

Some individuals will be genetically superior, some average and others inferior. The selection of genetically superior animals provides the opportunity for the introduction of qualitative (simply inherited) and quantitative (multigenetic) traits that lead to herd improvement.

Qualitative Traits

Examples of simple traits in beef cattle include hair colour, horned v’s polled and various inherited abnormalities. Very rarely do these traits involve environmental interactions (eg drought conditions have no bearing on polled v’s horned cattle).

The principle of inheritance of qualitative traits can be demonstrated through the polled v’s horned traits where two alleles at a single locus control the presence or absence of horns (Diagram 1). The allele for polled (P) is dominant to the horned allele (p) although the dominance is apparently not complete and sex linked modifying genes can also intervene (eg scurs).

Polled v’s horned trait shows how alleles interact in a trait with dominance. Bull (a) is homozygous dominant which means it has two polled alleles (PP). Cow (a) is homozygous horned (pp) which means she has horned alleles and 100% of the offspring will be heterozygotes (Pp). If heterozygous heifers (Pp) are mated to the horned bull (b) it would result in 50% heterozygous polled (Pp) and 50% homozygous horned (pp). If the heterozygous polled heifer (Pp) are mated to the heterozygous bull (c) there would be three possibilities: 25% homozygous polled (PP); 50% heterozygous polled (Pp) and 25% homozygous horned (pp). The ratio would be 25%: 50%: 25% and the phenotypic ratio would be 75%:25% polled to horned.

With Brahmans the situation is more complicated with the presence of the scur gene. Scurs is another type of inheritance interaction which is sex linked. Sex influenced trait expression occurs when phenotypes are different with the same gene type. In male cattle, the scur allele is dominant and in the female it is recessive. Thus, if a male or female are homozygous at the scur loci, then they will be scurred. If they are heterozygous at the scur allele, then the males will be scurred but the female not. *Readers are referred to the Brahman Journal, June 2003 to obtain further information on the inheritance of scur (Sc) and aflican (Af) genes.

Quantitative Traits

As the name implies multiple traits involve many genes and the environment also plays a major role in the phenotypic expression (appearance and/or performance).

“Quantitative traits are more difficult to predict than qualitativew traits”

Sometimes the animals phenotype provides limited information about the genotype. For instance, bulls with the same genotype raised on inland pastures v’s coastal pastures can result in noticeable differences in the phenotype expression for size and carcass weight which needs to be considered when evaluating bulls from different environments.

Most quantitative traits are measurable ie they are continuous traits which means there are numerous possibilities for the phenotype expression of the trait. Therefore, the genetic improvement of quantitative traits (eg muscle definition and growth pattern) poses quite a challenge. Meeting these challenges, however, is very important because many of the economically relevant traits (ERT’s) such as carcass yield meat characteristics, feed efficiency and tenderness are inherited quantitatively.


Correlated Traits

The correlation between traits measures the tendency to vary in the same direction (positive correlations) or opposite correlations (negative correlations).

The maximum positive correlation is+1.0 indicating that both traits vary in the same direction unit for unit. A correlation of 0 means that the two traits are completely independent. The largest possible negative correlation is -1.0 indicating that the two traits vary unit for unit in opposite directions.

“Both phenotypic & genetic correlations are important”

The genetic correlation is that portion of the correlation between two traits that is due to inheritance.

The effect of one trait on the other trait can be complimentary (positive) or disadvantageous (negative). For instance, as selections are made for increased birth weight, weaning weights and yearling weight are increased. Vice versa, as selections are made to decrease birth weights, weaning & yearling weights are usually decreased.

The phenotype correlation is simply the correlation between phenotypes eg there is a positive correlation between body size and body weight whilst there is often a negative correlation between large frame score and early maturity.

Phenotypic correlations are usually influenced by inheritance and environment eg large frame score and reduced reproduction efficiency in low nutritional environments. The implications of genetic correlations for some traits are shown in Table 1.


Birth Weaning Yearling Milking Ability Calving Ease Mature Size
Birth weight + + + 0 - +

+ + + - - +

+ + + - - +
Milk yield 0 * * + 0 0
+ positive - negative 0 no relationship * influenced by high milk yield EBV


Heritability estimates (statistical ratios) are used to define genetic change or phenotypic variations due to additive genes that contribute to differences of individuals in a given population.

For instance, weaning weight has a medium-high heritability of 0.30 – 0.50 which means that 30-50% of the difference between weaner cattle are caused by additive genes. If a trait has low heritability (eg reproduction) this indicates that there is a low involvement of additive genes and/or that the environment has a much larger influence on the trait. High heritability indicates that additive genes play a relatively large role in the trait change.

“The higher the heritability of a trait, the more rapid the change”

Average heritability estimates for some traits in beef cattle are shown in Table 2. Actual heritabilities for a particular trait can be expected to vary between herds depending on the genetic variability within the herd, the differences in the environment and reliability of estimates.

Based on medium-high heritability estimates, selection should be reasonably effective for most traits. However, traits vary for functional and economic importance, thus trait selection needs to include economic, functional and heritability considerations.

TABLE 2: heritability estimates for various performance traits

Trait Heritability description Heritability (%) (Tropical Breeds)
Conception low 5 - 10
Days to calving low 10
Semen qualtiy med - high 26 - 44
Gestation length med 21
Conformation and growth
Birth weight med - high 35 - 45 (40)
Weaning weight med - high 30 - 50
200 day weight med 28
Gain - birth to weaning med 16 - 40
Yearling gain (pasture) med 20
400 day weight med - high 37
18mth weight (pasture) med 30
600 day weight med - high 43
Mature cow weight high 25 - 40 (39)
Carcase weight/day of age med 36
Rib fat 12/13th rib med 27
Rump fat P8 site med 18 - 28
Intramuscular fat % med 22 - 30
Eye muscle area med 23
Dressing percent med - high 37
Tenderness med 30
Retail beef yield med - high 36
Yield % carcase weight high 52

Gene Frequency

Gene frequency is the proportion of a gene in a given population. The most important single factor to alter gene frequency and making genetic change is selection.

For instance, with qualitative traits (eg coat colour) the frequency of the gene causing black or mixed colours which once was quite high in Brahmans is now fairly low because breeders are selecting against cattle carrying these genes. Despite this discrimination, these colours have not been eliminated since the rarer the gene becomes the more difficult it is to reduce its frequency.

“Selection is the driver for gene frequency and genetic change”

Changing the frequency of genes that affect quantitative traits is inherently more complex than those affecting qualitative traits because many more genes involving a number of traits are involved.

Basically the frequency of traits (simply inherited and multigenic) can be changed in four ways: mutation, chance, selection and migration. Breeders have no control over mutation and chance which are random and often not recognised.

Trait Selection

Selection is the process of introducing the most desirable genotypes that will leave offspring that are beneficial to the herd and enhance business productivity and profitability. After several generations of selection for certain traits the more desirable genes become more frequent and the less desirable genes become rarer with the result that the overall genetic and phenotype merit of the herd increases.

Two concepts are involved in selecting traits:

  • Single trait selection and its weaknesses
  • Multiple trait selection and its complexities

Single Trait Selection

Single trait selection is when all selection pressure is placed on one trait (eg polled, tenderness, coat colour) and other traits are overlooked. Single trait selection can produce rapid change (eg frame score) but can provide undesirable changes in correlated traits eg increased frame score results in increased maintenance requirements because these traits are genetically related. Larger cattle require more feed. An increase in the mature size from 600kg to 700kg results in a 10-15 per cent increase in maintenance feed requirements. This correlated change results in increased feed requirements and a higher plane of nutrition which may mean that these animals are not suited to some environments.

High maintenance cows in a poor nutritional environment often results in low condition stock that are slow or late calvers. Other examples of undesirable changes from single trait selection is the positive correlation between increased birth weight and calving difficulties and the negative correlation between increased size and puberty.

Size affects the weight required for puberty and mating age of heifers, eg a 750kg cow will produce heifers that have a mating weight of 495kg compared to 430kg for a 650kg cow and 330kg for a 500kg cow.

There is limited place for single trait selection since it can often be at the expense of economically relevant traits. Subsequently, single trait selection (eg polled v’s horned) could compromise the productivity and profitability of the business if important ERT’s are overlooked (eg scale, meat yield).

Multiple Trait Selection

Selection of beef cattle often involves the consideration of several traits at one time, ie multiple trait selection.

“Quantitative trait selection poses several challenges”

Firstly, as additional traits are emphasised in a selection program, the rate of improvement in any one trait decreases unless there is a strong positive correlation between traits.

Secondly, there can be unfavourable correlations between many of the economically relevant traits eg there is a negative correlation between calving ease and weaning weight, ie calving weight tends to decrease as calving ease increases. Subsequently beef selection programs need to fully consider those traits that lead to herd improvement and increased productivity.

Breeders may take several approaches to trait selection, ie tandem, independent selection and index selection. Each of these approaches have strengths and weaknesses.

Tandem Selection

This is the simplest approach to multiple trait selection which involves the selection of one trait, then a second and so on. Selection pressure is placed on a single trait until the herd performance reaches a predetermined target at which point emphasis is applied to a further trait eg an emphasis on polled cattle followed by gene star and temperament etc.

“The number of traits selected in a particular timeframe is obviously limited”

Problems include placing too much emphasis on one trait which can be at the expense of other important traits and may restrict genetic improvement. A further concern is that emphasis on one trait can produce unfavourable changes in correlated traits which can limit genetic progress. Usually selection is re-emphasised on the most important traits.

Independent Selection

Here several traits are considered simultaneously and a minimum acceptable phenotype is set for each trait. When individuals fall below a minimum standard they are culled regardless of their phenotype merit in other traits.

Genetic progress using independent selection can be limited due to ‘forced culling’ requirements for disease (eg Pompes) and/or physical and physiological as normalities (eg stringhalt and reproduction disorders) which restricts the opportunity for independent selection due to reduced stock numbers.

Another drawback of this method is that as additional traits are considered, the emphasis on priority traits may be relaxed thus lowering the standard and compromising progress in the key traits.

Determining the appropriate selection standards may prove to be difficult for some breeders due to limited access to objective data. Where standards are available, the application of independent selection approach is quite popular but its use can be limited when a number of interrelated traits are assessed.

Selection Method Index

If the selection index method (eg EBV’s and EPD’s) is based on accurate unbiased information and economically relevant traits (ERT’s) it is more effective and will result in more rapid genetic improvement than other approaches (ie tandem and independent selection).

“Several traits can be considered at one time”

The animals selected for breeding are those with the highest scores based on prioritised traits. Those animals with the lowest scores are culled. The advantage of the selection index method include the:

  • Identification and assessment of key ERT’s simultaneously
  • Inclusion of heritabilities for each trait
  • Incorporation of known genetic and phenotype relationships amongst traits
  • Inclusion of the relative economic importance of each trait
  • Availability of suitable programs (eg Breed Plan) supported by breed societies.

To successfully execute this technique it is important that the producer identifies closely with the market requirement and client needs. It is also noted that some traits are non measurable and selection needs to consider techniques to evaluate these traits (eg visual assessment).

Given that the bottom line of most beef operations is profitability, the standards and traits selected should initially identify with requirements of commercial breeders and the needs of the industry.


This term is used to describe the process of introducing high levels of new genetic material into the population. It involves the introduction of groups of individuals or superior individuals with the primary objective of acquiring seedstock with a higher frequency of desirable traits and thereby raise the genetic and phenotype merit of the herd through genetic change.

Migration can change gene frequencies and raise the genetic merit of a herd very rapidly if this technique is highly selective and practised effectively. Results are dependent on:

  • The proportion which the new animals constitute of the entire herd
  • The difference in genetic material (or frequency of superior genes) between the new animals and those previously in the herd.

An important aspect of migration is the identification and availability of superior seedstock to improve the genetic merit more rapidly than improving the herd through years of breeding. Long term benefits obviously depend on the effectiveness of initial selections, future breeding programs and selection management.

The use of multiple AI sirers or purchased bulls and ET/IVF programs is usually a combination of selection and migration to allow the introduction of different gene frequencies. Obviously migration can be a costly investment if the animals used are average or below average in their capacity to improve the genetic base. Studies show that stock that perform below their herd mates in one herd tend to be substandard in most herds.

Genetic Outcomes

The decision making skills of the stud breeder greatly impacts on the genetic quality of the herd and the market acceptance of subsequent progeny.

Understandably, sire selection and emphasis on various traits will differ between studs. Each producer will have their own environmental and economic circumstances and breeding goals. These factors will impact on the approaches taken to genetic selection.

Nevertheless, actual progress in the genetic merit is occurring at a greater rate than the past because of the increased understanding of genetics, ongoing research and the application of new information into sophisticated models and decision support systems. This has allowed the identification, measurement and utilisation of economically relevant traits and the selection of superior seedstock to allow genetic improvement.

The final outcomes of improved knowledge of genetics rests with individual breeders thus the direction and effectiveness of genetic change depends on individual decisions. An important point is that with every selection action there is a performance reaction. Subsequently, individual judgement is necessary to ensure that positive actions outweigh negative reactions. It is also important to recognise that the market competitiveness of the beef industry is primarily based on the production of meat from grazing systems and that genetic improvement needs to continually focus on functional traits as well as economically relevant traits to maximise the efficient conversion of pastures to meat.

“Selecting quality genetics to provide a better future in the beef industry”

Appendix Definitions

Gene – refers to the basic unit of inheritance and is a particular segment of the chromosome.

Chromosomes - are long strands of protein which contain DNA. Cattle have 30 pairs of chromosomes and each animal inherits one pair from its sire and the other pair from the dam.

Genotype – is the genetic makeup of the animal.

Locus – is the location of the gene on the chromosome and allele refers to the functional possibilities that can be present at a locus.

Alleles – these can affect traits by themselves but can also affect phenotype expression by interactions with other alleles. Alleles interact in two ways referred to as dominance and epitasis.

Phenotype – is the appearance of the animal (eg red v’s black colour) and phenotype expression can be physical (observable) or performance (measurable).

Qualitative – traits (simply inherited) – involves one or two genes at a few loci with little involvement of the environment. It involves simple traits with discrete categories (eg coat colour, polled v’s horned cattle).

Quantitative traits (multi or polygenic)– involves many genes and loci with close interaction with the environment which causes these traits to vary in a continuous manner (eg weaner and yearling weights).

Variation – differences in phenotypic expression due to a trait. Non genetic variation is due to environmental factors.

Environment – refers to external factors (non genetic) that impact on performance (eg climate, nutrition, health and management). When environmental influences are not properly accounted for the accuracy of breeding value estimates are reduced.

Heritability – this is a measurement (statistic) of variation between animals due to genetic differences between individuals for that trait (ie the efficiency of transmission of parental superiority (or inferiority) from one generation to the next). It is the proportional differences between animals due to additive genes.

Additive gene action – the effect where the expression of a trait is controlled by one or more genes each of which act in an additive manner.

Dominance – complete dominance is when inheritance is due to one allele completely masking the expression of the other allele at the loci (eg red/black colour which black is dominant to red). Other types of inheritance include partial, no dominance and over dominance.

Epitasis – refers to inheritance that is due to genes interacting with other genes at other loci which overrides dominance.

Homozygote – refers to individuals that are carrying a pair of alleles that are alike (eg PP for polled or pp for horned)

Heterozygote – refers to individuals carrying unlike pairs of alleles (eg Pp) and one allele is dominant.

Estimated Breeding Values (EBV’s) – are an estimate of an individuals true breeding value for a trait based on the performance of the individual and/or close relatives. EBV’s are a systematic way of combining performance information on the individuals and siblings and the progeny of the individual.