Phenotypes, What are they and why do they matter?

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There is some confusion in the livestock production world today about phenotypes.  Some people feel that geneticist don’t pay enough attention to phenotypes, others that in the age of genomics phenotypes don’t matter.  What is a phenotype, how do geneticists use them, and why do they matter?

A phenotype is something that can be observed or measured.  So we can say that a pig that has been properly tested has a phenotype for growth rate, which is measured by weighing, as well as a phenotype for proper feet and legs, which can be scored by observations by a trained observer. 

If an animal doesn’t have the correct phenotype of good feet and legs, the required number of teats and normal reproductive organs, it should never be sold or selected for breeding stock no matter how high it’s genetic merit is.  In these cases the phenotype is either “correct” or “incorrect” and an animal must be correct for functional reasons, meaning capable of living and being productive under typical commercial conditions.

Many production traits are quantitative, meaning that all animals have a phenotype but there is no correct or incorrect.  In these cases the question is knowing which animal is best.  An important part of looking at phenotype in these cases is measuring the trait correctly.  For example, to get a genetically useful phenotype for growth, an adequate number of pigs of the same sex and line, out of several sires, should be measured at the same time, same age, in the same facilty and with the same diets.  For traits like growth, feed conversion, or litter size, a phenotype is only useful to a geneticist as a deviation from a population mean or average.  Being tested with contemporaries allows this type of comparison and helps us to correctly estimate which animals are best genetically.  By testing animals at the same time and in the same facilities the environmental factors are similar which allows genetic differences to be seen more clearly. The repetition of parents over several batches complete the requirements for such an evaluation through the genetic relationships.

In the case of traits that are more influenced by the environment, phenotypes from many animals in many environments are collected and analyzed using BLUP. It is a statistical tool which looks at the phenotypes of an animal’s relatives to help correctly estimate genetic merit.  BLUP also allows us to estimate genetic merit for sex-related traits like litter size for males, that would never have a phenotype of their own, or on animals that could not be measured such as carcass traits like a marbling score.

Genomics advances

As the science of genomics advances, we are able to make more accurate estimates of genetic merit, but accurate and meaningful phenotypes are still the basis of a succesful breeding program.  Genomics add to the accuracy of genetic estimates, but do not replace well designed program to collect phenotypes. “In the era of genomics, phenotype is king” is a moto that has been widely used among the geneticists community in the last years and will keep holding true.

The Choice genetic program is based on collecting the correct data in the best possible manner, evaluating them using the most advanced technology, and providing the best breeding stock possible to our customers.

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