Re: How does mRNA know which trait is dominant or recessive?

This is not an easy question to answer, mainly because there is no single answer. Your question has to do with gene expression and regulation, and depending on the system and the set of genes involved, different controlling factors can be at work. In general, it's a matter of checks and balances that can involve DNA, RNA and protein.

A gene on DNA gets transcribed into RNA which then gets translated into protein. This flow of information is subject to control. In terms of dominant and recessive traits, in a heterozygote, both genes are present. And whether we see the trait as a phenotype depends on which one of the genes (dominant or recessive) is transcribed and/or translated. For transcription control, there are a number of possibilities, for dominant traits: 1) the dominant gene may be transcribed as mRNA at a higher rate so there is more of the "dominant" mRNA 2) the recessive gene is not transcribed at all, 3) the recessive gene is transcribed at a lower rate. A whole slew of proteins "control" the rate and type of mRNA being transcribed. These control proteins are made from genes on the DNA and are also subject to gene expression and regulation. Once made, the mRNA then gets translated as protein and this becomes the trait that is seen.

Once the mRNA is made, again there is a choice--does it get translated, made into protein, at all? The "recessive" mRNA can be delibrately degraded, leaving only the "dominant" mRNA to be made into proteins. There are genes that code for these degradation proteins.

Expression can be at the level of the protein. Both the dominant and the recessive genes may be transcribed and translated at equal levels. However, the "dominant" protein may work better than the "recessive" one, or the "recessive" protein may be degraded. And, yes, DNA makes proteins that degrade other proteins.

So, to relate this answer to your two possibilities: Depending on the system, DNA can and does decide which gene is going to be transcribed and/or translated. Also, both recessive and dominant genes can be transcribed as mRNA and translated into proteins. The finished proteins then "decide" which phenotype is going to show up.

There are different ways of controlling and regulating gene expression and dominant/recessive traits are a subset of this control system.