Redesigning Animal Agriculture

72 K. Prayaga and A. Reverter
it is crucial to implement this knowledge
in the breeding programmes to achieve
any long-term progress. However, most of
these adaptive traits are difficult to measure
under field conditions and hence cannot be
easily improved through selection. One of
the alternatives to improve tropical adaptability
has been exploiting breed complementarity
through crossbreeding. With the
advent of new molecular genetic technologies,
efforts are being made to identify major
genes and QTL associated with these traits.
Olson et al. (2003) reported evidence of a
major gene responsible for sleek hair coat in
Senepol and Criollo cattle. Barendse (2005a)
reported five genetic regions of the bovine
genome for associations to tick resistance.
These developments were possible because
of the advances in molecular genetics.
Molecular Revolution
The molecular revolution has the potential
to have a huge impact on domestic animal
breeding. Simultaneously animal breeding,
through its extensively recorded phenotypes,
pedigrees, and resource populations
in wide-ranging environmental conditions
subjected to both natural and artificial selection,
contributes to the advances in molecular
genetic studies. This is no different to
the symbiotic relationship between animal
breeding and statistics.
Ever since the studies on molecular
genetic markers were initiated, there have
been several questions regarding the relevance
of traditional animal breeding tools
such as pedigree and performance-based
selection and there were predictions about
one or more DNA tests essentially replacing
these traditional genetic evaluation systems.
We are now into two decades of this
debate and almost reached the completion
of bovine genome sequencing and now, more
than ever, we are convinced that the molecular
information needs to be utilized in conjunction
with the traditional selection tools
for making breeding decisions. However,
this does not undermine the importance of
the knowledge gained through molecular
genetic advances and there are several areas
where the genetic markers or the discovery
of functional mutations has directly led
to characterizing Halothane (RYR1) locus
and mutation causing increased glycogen
content in meat (PRKAG3) in pig breeding
(Andersson, 2001). Several of these mutations
also cause simple monogenic disorders
as catalogued in the Online Mendelian
Inheritance in Animals (OMIA – http://omia.
angis.org.au/).
Andersson and Georges (2004) and
Womack (2005) have reviewed the recent
advances in livestock genomics and their
realized and potential contributions to both
human biology and agricultural science.
Some of the early developments that led to
the current ability to sequence the bovine
genome are:
1. Early mapping techniques (somatic cell
genetics and in situ hybridization) leading
to synteny and cytogenetic maps (Womack
and Moll, 1986; Yerle et al., 1995);
2. DNA-level markers for building maps
and mapping traits (Beckman and Soller,
1983)
3. Microsatellite markers leading to linkage
maps (Barendse et al., 1994; Bishop et al.,
1994);
4. Further expansion of maps (Barendse
et al., 1997; Kappes et al., 1997);
5. Radiation hybrid map for higher resolution
comparative mapping (Womack et al.,
1997; Williams et al., 2002; Itoh et al., 2005).
A single partially inbred Hereford female
was selected to contribute 6x whole genome
shotgun reads and another 1.5x from individual
animals of Holstein, Angus, Jersey,
Limousin, Brahman, and Norwegian
Red breeds for SNP (Single Nucleotide
Polymorphism) detection. Current map status
and genomic resources available in various
livestock species are presented in Table
5.2. Recent reviews of the bovine genome
sequence and its likely impact on genetics
research of beef cattle include those of
Dalrymple (2005) and Womack (2006).
The primary aim of any of the farm
animal genome sequencing and/or development
of SNPs is initially to locate the
regions, and ultimately, the causal muta-