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The word trait, you may recall, is often used interchangeably with phenotype, but they are not the same thing at all.

A trait is something that can be measured or observed, for example temperament, colour or wool staple length/year.
A phenotype is the value of the trait: ‘aggressive’, ‘brindle’ or ‘120mm’.

Traits fall into two categories: simply-inherited and polygenic.

Simply-Inherited Traits
A simply-inherited trait is one affected by one or a very small number of genes, such as polling (without horns) in cattle or coat colour in Labradors. Genetic diseases, eg Huntington’s Disease in humans, are invariably simply-inherited as well.

Phenotypes of these traits tend to be ‘either/or’ and can be placed in categories. Cattle either have horns or they don’t. Labs are either black, chocolate or yellow. People either carry the gene for Huntington’s or they don’t. Simply-inherited traits can also be called qualitative or categorical traits for this reason.

These traits are also not influenced much by environment.

Polygenic Traits
A polygenic trait is one affected by many genes, with no one gene overly influential. Rather, all genes involved contribute in some way to a final phenotypic expression. Examples of such phenotypes include growth rate, milk production, and meat yield. Unlike the ‘either/or’ of the phenotypes of simply-inherited traits,  the phenotypes of polygenic traits are often expressed numerically: 0.3 kg/day, 6,000 L/year, 71.6%. Thus these traits are usually quantitative or continuous.

And unlike simply-inherited traits, polygenic ones are influenced by environment. Lack of feed will result in lower growth rates and milk production for example.

Exceptions
While simply-inherited traits are usually qualitative (categorical), and polygenic traits are usually quantitative (continuous), there are exceptions.

Though rare, there are simply-inherited traits which are continuous. One example is human skin pigmentation, of which there is a continuum from very light-skinned to very dark-skinned.

And there are polygenic traits which are categorical. One example is dystocia, or difficulty birthing. Birthing is either assisted or unassisted, and this ‘either/or’ nature implies a simply-inherited trait. Yet dystocia is influenced by many genes including those determining the size of the foetus, the size of the pelvic opening, and the mother’s stamina.

Another example is mastitis in cows, where many genes influencing udder size, milk yield and milk flow play a part. But a cow either has mastitis or she doesn’t — there is no spectrum of affectedness.

Threshold Traits
Dystocia and mastitis are examples of threshold traits, polygenic traits that exhibit categorical phenotypes. Fertility is another example: ability to conceive is either successful or it isn’t.

Having covered the differences between simply-inherited and polygenic traits here, next week we’ll go over the properties they share in common.

While — for the most part — there are differences between simply-inherited and polygenic traits, they also share much in common. Both types of trait are still determined by genes and inheritance.

Our discussion on Mendel and his three laws focussed on simply-inherited traits, but that was because these are easier to follow and understand, and confirm in real life with visual observation. Determining the genes behind polygenic traits, much less unravelling their influence in a final phenotype, is much harder to understand, and especially so if the effect of each gene is small. But they are still genes which occupy chromosomes, and are thus as subject to Mendel’s laws of segregation and independent assortment as the simply-inherited ones.

Of course, with so many genes involved in a polygenic trait, it is possible that several of these will share the same chromosomes, and that several of these again will be closely linked. But this is an exception to the law of independent assortment, and the chromosome homologues will still follow the law of segregation.

Mendel’s law of dominance will also apply to both groups, as will epistasis and other types of non-Mendelian inheritance, but in more complex ways for the polygenic traits.

Selection systems will also alter gene frequencies in the same way for both simply-inherited and polygenic traits. Selection for the simply-inherited polled gene in cattle will increase the frequency of the desired ‘poll’ allele in a herd, just as selection for speed (a polygenic trait) in racehorses will favourably shift the frequencies of many genes over many loci that positively affect speed.

It follows that mating systems will also affect the genes of both trait types similarly. Heterozygosity at the (simply-inherited) B locus will increase should a poultry farmer cross black Andalusian chickens with white ones, just as heterozygosity will increase across many loci should two breeds be crossed to produce hybrid vigour.

Next week: an overview on the different approaches when breeding for simply-inherited and polygenic traits.

As mentioned, simply-inherited and polygenic traits are equally subject to the same Mendelian and non-Mendelian inheritance forces. And both can have gene and genotypic frequencies shifted by selection and mating systems. But while it is often straightforward to observe the effect of a simply-inherited trait owing to the small number of genes involved, this isn’t the case with polygenic traits. It is often not even known how many genes are involved in a particular polygenic trait, nor what the effect of each may be.

It is because of this complexity that breeders must take very different approaches when working with simply-inherited and polygenic traits.

Working With Simply-Inherited Traits
Simply-inherited traits are often influenced by just one locus, and at most a small number. Their either/or nature results in qualitative (categorical) outcomes that are readily observed and recorded. This characteristic enables genotypes to be predicted in many cases, which a breeder may then use to their advantage.

Take the suri and huacaya alpaca types. The suri has an Angora goat-like dreadlocked appearance while the huacaya has a sheep-like woolly appearance. Suri or huacaya fleece style is a simply-inherited trait with one locus, ‘S’.

The suri allele (’S') is dominant to the huacaya allele (’s’), thus a suri can be ‘SS’ or ‘Ss’. Huacayas can only ever be ’ss’.

Suri breeders sometimes cross huacayas with purebred (homozygous) suris, for example to introduce a particular colour into their herd. The resulting F₁ generation is:

The F₁ offspring, all heterozygous suris, would then be backcrossed to homozygous suris. ‘Backcrossing’ is to cross the F₁ offspring back to the homozygous, desired, genotype (’SS’ in this case) to increase the likelihood of producing more animals with the desired phenotype (suri in this case). This is not an F₂ generation (the result of crossing two F₁ groups), but a BC₁ one (’BC’ stands for ‘backcross’):

But which of the offspring are homozygous and which are heterozygous? You can’t tell just by looking at them as you can with huacayas. Potential purchasers want the reassurance of buying a homozygous suri, and a breeder can command more for this reassurance. The breeder could perform a test mating (or test cross), by crossing these offspring with huacayas. In the absence of a genetic test for the locus in question, this is a common technique when breeding and selecting for simply-inherited traits.

(The caveat here is that time is needed first for an animal to reach sexual maturity, and then for the many matings that must be done to determine the genotype definitively. And it is much easier and quicker to do multiple test matings of a male than of a female.)

Here, heterozygous suris, statistically, would be expected to produce one huacaya from four matings to huacayas, but a homozygous suri never will:

The one-in-four chance of producing a huacaya is of course only the calculated outcome. Four suri offspring from four matings to huacayas doesn’t guarantee the test animal is homozygous. These results could be due to chance, and the fifth, or even tenth, mating might be the one that produces a huacaya.

It follows that the higher the number of matings when crossed to huacayas that produce only suris, the more likely (but not guaranteed) that the suri parent is ‘SS’ homozygous. But at what number of matings is it ’safe to stop’? We’ll be delving into the maths of test matings in more detail in the next section.

Working With Polygenic Traits
It’s a simple in theory, though lengthy and tedious, procedure to determine whether a suri is ‘SS’ or ‘Ss’, and similarly for any simply-inherited trait in any other species. But where do you begin with something like milk production or meat yield, which is influenced by many genes, some of which may not have even been determined yet, or their effects fully understood?

Breeders require a different approach when working with polygenic traits. And that approach is to determine, statistically, what the net effect of an individual’s many genes are on a particular trait. For these we need mathematical tools to assess, quantitatively, an animal’s performance and breeding value, and there will be much coverage of these to come!

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This concludes the section on simply-inherited and polygenic traits. The next section will be about the different strategies required when selecting for a simply-inherited or polygenic trait. We’ll begin with a series of posts on selection strategies for simply-inherited traits — test matings essentially. After that we’ll cover the more involved selection strategies for polygenic traits, by exploring concepts such as breeding value and heritability and how to calculate these.