Redesigning Animal Agriculture

a highly predictable and beneficial outcome.
Potentially, these fundamental rules of biology
may also provide new understandings
of unrelated highly complex processes such
as weather patterns, stock market volatility
and the ultimate example of complexity,
traffic flows at peak hour. What is also being
revealed is the responsiveness of genes to
external stimuli, which allows adaptation
of an organism in real time to its changing
environment. The molecular mechanisms
governing the detection of environmental
cues, the transmission of this information
into a cell and the subsequent molecular
and cellular responses are only beginning
to be elucidated. Again, the common feature
of these processes is their complexity,
which probably underlies their robustness,
accuracy and reproducibility.
The motivations for sequencing livestock
genomes, such as the bovine genome,
are somewhat different. Here the primary
motivation relates to economic benefit to
humans, although human health care interests
such as food quality and disease control
are significant and growing in importance.
The livestock genome sequence provides
molecular tools for producers and processors
to optimize the outcomes of the genetic
potential of an animal and to better match
product with the market. The nexus between
food quality and human health, albeit recognized
as important, is yet to be fully realized.
The obesity epidemic in humans and
its associated medical and economic consequences
is indicative of this disjunction.
Diseases of the food supply chain, such as
bovine spongiform encephalopathy and foot
and mouth disease, have taken economic
and social prominence and consequently
there is strong interest in minimizing and
eliminating their potential future impacts
using our increased understanding of biology,
genetics and gene function. Related to
this is the increasing prevalence of infectious
diseases, such as severe acquired
respiratory distress syndrome and the H5N1
strain of bird flu, which use wild animal
populations, and in some cases livestock animals,
as reservoirs for infection of humans.
Two additional motivations for livestock
genome sequences are to provide tools that
The Impact of Genomics 49
address environmental and animal welfare
concerns.
What Information is Contained Within
a Genome Sequence?
The human genome sequence has been
referred to as the book of life but it is actually
four books (J. Shine, Garvan Institute
Sydney, 2004, personal communication).
The first is a history book that contains information
about the distant past and the challenges
for survival of the species. It is said
that history is written by the victors and, in
that sense, so is the genome sequence as it
only records information contained in the
animal lines that have survived the rigours
of natural selection. The second book contains
a list of the component parts or genes
and an instruction manual for their use.
While we now have a good catalogue of the
approximate 25,000 genes in a mammal, the
instruction manual for their use remains elusive.
The third book is a medical text book
that contains information about the specific
adaptations of a species to disease challenges.
Finally, there is a ‘Who’s Who’ book
that records the unique genetic characteristics
of each individual in the species. The
uniqueness of the individual is the strength
of the species as it ensures survival of some
individuals during times of strong and
adverse natural selection, e.g. during disease
challenges. Livestock genome sequences
have similar information content.
We are still far from understanding all
that is contained within a genome sequence.
The present status is like having correctly
reassembled a shredded white pages telephone
directory for a large city, where
phone numbers represent genes and the
addresses correspond with chromosomal
positions. We have the list of about 25,000
genes and their addresses but we don’t have
their functions or how they are controlled,
i.e. a corresponding yellow pages phone
directory is yet to be fully constructed.
Intriguingly, the actual protein encoding
genes in a mammalian genome only account
for about 1.5% of the genome sequence. The