Genetic Influences on the Behavior of Chickens Associated with Welfare and Productivity - Genetics and the Behavior of Domestic Animals - page 318

first step cancer types were classified by a panel of experts. In the second
step the transcriptome was used in a discriminate analysis to predict each
cluster. In the third step the transcriptome was sampled on a new set of indi-
viduals, and the samples assigned to clusters based on the discriminate func-
tion in the previous step. The results were verified by the same team of
experts and were found to be extremely accurate. Knowledge of which genes
were up- and down-regulated by each cancer type was not needed, only the
pattern was important. Transcritomic profiling has also been used widely in
improving human well-being ( Chaussabel et al., 2010; Elstner and Turnbull,
2012; Hindmarch and Murphy, 2010 ; Mestan et al., 2011 ).
Similarly, application of this novel approach for assessing well-being has
the potential to provide common ground and address housing and other
issues allowing the animals to speak for themselves through their transcrip-
tome. The approach would include known stressors and animal-friendly
environments. Exposure of the animals to those environments for short- and
long-term durations, and then collection of their transcriptome from tissues
in which emotions are known to be controlled, such as the hippocampus and
the HPA axis. The transcriptome would then be isolated and quantified,
using the latest technology, such as RNAseq. A supervised cluster analysis
would then be performed into known treatments to create a discriminate
function. The discriminate function classifies observations by the metric used
to create the function. Next, an independent set of animals would be exposed
to contentious alternative housing and management practices for short- and
long-term duration, the same tissues isolated, the transcriptome quantified,
and finally clustered using the previously trained discriminate function. The
function will classify questionable housing and management practices into
those that are most similar to those recognized as stressors and those that are
animal friendly.
Alternatively, if training environments cannot be agreed on by a panel of
experts, an unsupervised clustering analysis can be performed on the tran-
scriptome of animals housed in alternative and questionable environments.
An unsupervised cluster analysis will at least show if the alternative environ-
ments are really different as perceived by the animals in the environmental
conditions imposed for whatever reason. If two environments do not induce
a different transcriptome profile, it would be difficult to argue that the envir-
onments are inducing different levels of stress.
Productivity
The use of productivity or performance data as indexes of well-being in
chickens has been criticized ( Hill, 1983 ). However, as Craig and Adams
(1984) made clear, early comparisons confounded profitability and produc-
tivity. When productivity of the individual laying hen is considered in terms
of number of eggs, feed efficiency, and mortality, it proves to be a fairly