What are the cons of artificial selection?

As mentioned above, artificial selection is an action done by humans to manipulate some aspect of their environment in their favor. Through lab experimentation and field tests, this is most commonly done to food crops, so that they produce higher yields and better products given their environmental conditions. There are many ways to select for desirable traits, for example by breeding two plants with each other to yield stronger offspring, but a technique that scientists have developed to accelerate this process is known as genetic engineering. Many people have contentions with genetic engineering because it is seen to manipulate food and organisms in a way that isn't natural - and therefore we may not be able to understand the full effects of our actions. Though we can achieve desirable results in the short term, there may be negative consequences later on.
Most of the cons of artificial selection are due to this feeling, that humans should not be changing the biology of the organisms we depend on because we don't yet realize the consequences. The same is true if we were to artificially select for human genetics - a field known as eugenics - which many see as a field that should be beyond our control. Hypothetically, if some people can control the genetic makeup of other people, what's to stop them from favoring only a small handful or traits that excludes the heritage of many other people? Ultimately, diversity is threatened by all forms of artificial selection, which is an important factor to consider in all biological systems. 


Artificial selection is where favorable characteristics are selected to carry onto the offspring making the gene pool less varied. Increasing productivity in disease resistant crops, milk yielding cattle or egg laying chickens all lower the variety of genes making it difficult to for organisms to live in the wild. The loss of genes effects the future of new varieties especially if there is unsuitable environmental change. The smaller gene pool can concentrate unfavorable traits giving rise to genetic mutations and recessive diseases that natural selection would have weeded out.


Artificial selection, also known as selective breeding, is the process in which favorable traits or characteristics (longer lifespan, better aesthetic appearance, higher productivity, etc.) are selectively bred into a particular species of animals or plants. This allows the development of species with all the favorable characteristics. 
However, there are a number of disadvantages to this process. Presence of favorable characteristics in a single species limits the gene pool, since all the farmers may prefer that plant over others for its higher profitability. There could be chances that while the selected species is better in terms of its chosen characteristics, it may be susceptible to particular soil conditions or disease (unintended consequences of selective breeding), and the onset of such conditions may affect the entire crop. This would result in wipeout of entire crop in that particular season. There are higher chances of genetic mutations in such selected species as well. In addition, the choice of "selective" traits is very subjective, that is, varies from person to person.  
 
Hope this helps. 

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