Genetic Influences on the Behavior of Chickens Associated with Welfare and Productivity - Genetics and the Behavior of Domestic Animals - page 317

Physiological and Immune Responses
The general adaptation syndrome (GAS) can be delineated into short-term
fight or flight responses and longer duration accommodation responses
involving the hypothalamic pituitary adrenal (HPA) and the sympathetic

medullary adrenal (SMA) axes and is associated with immunocompetence

and health. Siegel (1981) stated that, based on general metabolic effects
ascribed to stress, there is a direct link between stress and susceptibility to
disease and that social stress is an effective initiator of non-specific stress
response in fowl. Increases in social stress reduce antibody levels and
thereby lower the resistance of fowl to several important viral infections and
to bacterial infections of the respiratory system. Non-specific environmental
stressors can have significant influences on growth, reproduction, and the
ability of the bird to resist diseases ( Siegel, 1981 ). Dantzer (1994) indicated
that animal response to stressor by changing neurohormonal homeostasis
does not depend on the physical nature of the stressor. Corticosteroids, as a
final compound, are produced in response to stressors. These produce many
of the symptoms associated with long-term stress, including cardiovascular
disease, hypercholesteremia, and modifications of

the immune function

( Siegel, 1995 ).
Although physiological (including immune) responses frequently reflect
the presence of known stressors ( Freeman, 1985; Gross, 1983; Hill, 1983;
Hoehn-Saric and McLeod, 2000; Piazza et al., 2010 ; Siegel, 1994; Theorell,
2012; Zulkifli and Siegel, 1995 ), it has been shown also that such measures
can occasionally be misleading or difficult to interpret. For example, plasma
corticosteroid concentrations were found to be elevated similarly for hens in
high-density cages and spacious floor pens even though other measures indi-
cated that those in high-density cages were under greater stress ( Craig and
Craig, 1985, Craig et al., 1986 ).

Functional Genomics
At a recent Poultry Science Keynote Symposium—Tomorrow's Poultry:
Genomics, Physiology, and Well-Being ( Muir et al., 2010 ), a novel approach
to objectively quantify stress and well-being in animals and to identify man-
agement practices that necessarily compromise well-being was discussed.
Toward that goal we proposed using the RNA transcriptome as a holistic
tool to formulate a metric. The transcriptome represents the expression of all
genes in an organism at a given time in response to environmental stimuli.
The output from each gene can be quantified on a microarray, or more
recently using whole-genome sequencing techniques, commonly termed
RNAseq. The methodology for developing this technique was described in a
landmark paper by Golub et al. (1999) and recently further reviewed by
Myers (2011) and Kolpfleisch and Gruber (2012) . They demonstrated the
power of supervised clustering to diagnose cancer type in humans. In the