It would be helpful if you would be more specific. For example, animals might be raised stress-free but be stressed at the time of slaughter in a way that alters meat quality. Are you thinking about the entire period from birth to slaughter or some more specific period? Can you help us understand your interest more clearly?

Stress affect meat quality by :-

lowering the level of glycogen in living animals and so lower the level of lactic acid in the carcass after slaughtering  and so the rise the pH of the meat  leading to poor shelf life of the meat( Bad Quality Meat )

stress leads to bad rigor mortis

styress leads to PSE ( Pale Soft Exudative Meat )- DFD ( Dark Firm and Dry Meat)

stress leads to ill bled meat 

great help already, thanks.

to be particular am looking at stress to animals during transportation.

have done some reading and some biomakers indicated are cortisol, Glucose concentration, Pcv, Beta Hydroxy butyrate and lactate concentration.

any ideas which one is the most reliable?

Here is a very good reference if you have access to the Journal of Animal Science:K. R. Buckham Sporer, P. S. D. Weber, J. L. Burton, B. Earley, M. A. Crowe. Transportation of young beef bulls alters circulating physiological parameters that may be effective biomarkers of stress. J ANIM SCI June 2008 vol. 86 no. 6 1325-1334.

thanks for the great reference Prof Jack Haiden Britt. its now clear that cortisol assay is one of the key parameters to look in measure of effects of stress at transportation.

interestingly plasma BHBA remains within constant range (Buckham et al..2008)

One of the problems, whatever you choose as a marker, is in establishing concentrations in "zero" or "start" stress conditions. To look at this I would sample a quarter of the animals at zero time, half at some time later (after transit ?) , three quarters at a later time and all of them on the final occasion. The animals in the first quarter would be naïve in terms of blood sampling at zero time, have experienced blood sampling once before at the  second etc - you can look at the  effect of  experience of blood sampling on the  variable you have chosen. You should remember that blood concentrations of all the variables suggested for use are influenced by stress, so you should look at the  effects of order of  sampling within a  group of animals and the  time  taken to get a blood sample on concentrations. With sheep, we would exclude samples that had taken us longer to start collecting than 20 seconds from entering a pen of sheep. We used cortisol, glucose, lactate AND electrolytes - Ca, Mg, Na, & K