Download A Global Strategy of Using Molecular Genetic Information to Improve

Reprod Dom Anim 47 (Suppl. 1), 7–9 (2012); doi: 10.1111/j.1439-0531.2011.01957.x
ISSN 0936-6768
A Global Strategy of Using Molecular Genetic Information to Improve Genetics in
Livestock
ET Margawati
Research Center for Biotechnology, The Indonesian Institute of Sciences (LIPI) Cibinong, West Java, Indonesia
Contents
Traditional breeding programmes have largely contributed to
disseminate the benefits of several quantitative traits in
livestock. In developing countries such as Indonesia where
animal population scattered throughout the country, it is
difficult to invest for molecular research. On the other side, yet,
it is worthy asset for breeding purposes. Based on theory and
evidence, it has been proved that those scattered population
evolved different genetic adaptations in response to a given
natural pressure selection. A global strategy can be applied to
the use of molecular genetic information for identification of
economically important value. The use of genetic markers or
more effective of marker-assisted selection (MAS) for desired
important traits would be more valuable and useful and even
more efficient in important trait selection of superior livestock.
DNA marker technology would be very useful when applied
for quantitative trait identification. Marker-assisted selection
can be used for enhancing conventional breeding and works
best for the traits with low heritability such as in reproductive
traits and disease resistance. Application of conventional
breeding for lower heredity traits would not be efficient
because of waiting longer for generation interval, expensive in
measurements, more population and more employees needed.
Study of quantitative trait loci mapping is early investment to
improve genetic merit. It can be performed once but can be
used for exploring many genetic traits with economically
important values. An effective option is biotechnology application in livestock for the development of genetic varieties such
as stress tolerance, growth and carcass traits. Application of
biotechnology approaches will enable improvement in productivity, reduction in costs, enrichment of milk compositions
and extension of shelf life products.
Introduction
Recent advances in biotechnology research have led to
the promotion of some techniques to be applied towards
genetic improvement. The application of molecular
biology and biotechnology towards animal breeding in
expecting to accelerate progress and to solve problems in
animal production is now possible by implementation of
molecular information. Selection of animal based on the
molecular approaches is recently termed as molecular
breeding (Thompson 2004). There are two primary
strategies for molecular breeding, namely applying
DNA marker technology for genetic diversity analysis,
gene discovery, gene and quantitative trait loci (QTL)
mapping and marker-assisted selection (MAS); and
applying transgenic technology for transferring genes
creating disease resistance, drought stress tolerance, low
fat or milk compositions (i.e. casein and fat contents)
through genetic engineering. Both strategies depend
heavily on basic research in molecular biology and
functional genomics.
2012 Blackwell Verlag GmbH
Genome is defined as entire genetic makeup (material
genetics or DNA) of an organism that stored in one or
more chromosomes located inside each cell of an
organism (Van Eenennaam 2004). The study of genome
has been furnished by advanced techniques such as
DNA sequencing. At present, whole-genome DNA
sequences of some model organisms are now known,
while functional genomics is a way or a ‘tool’ to identify
the function of each gene of an organism. Concomitant
with the trend of functional genomic study, bioinformatics or computational biology has therefore become
essential component for biotechnology research.
Scattered Place – Genetic Diversity Asset
Indonesia consists of five big islands (Java, Sumatera,
Kalimantan, Sulawesi and Irian Jaya) and thousands of
islands (more located in eastern parts of Indonesia) with
different climates from each other (Fig. 1). The climates
of western parts of Indonesia are more humid and
warmer compared with those of eastern parts of
Indonesia. In South-east parts of Indonesia, the climate
is under influence by the Australian continent having a
wide range of climatic zones from semi-arid to arid.
Based on 30-year (1971–2000) time series, the rainfall
data in Indonesia vary from less than 1000 mm to more
than 5000 mm (http://balitklimat.litbang.deptan.go.id).
Forage grows better in western parts of Indonesia than
in eastern parts of Indonesia, though, also influenced by
the seasons of wet and dry, which usually occur starting
in April through September and from October through
March, respectively.
These scattered places with differences in climates
have influenced the way of animal adaptation to the
given natural pressure and subsequently resulting to the
genetic diversity in livestock. This genetic diversity is
worthy asset for breeding purposes in the aspect of
improving animal productivity. Based on theory and
evidence, it has been proved that those scattered
population evolved different genetic adaptations in
response to a given natural pressure selection (http://
www.fao.org/biotech/docs/Gibson.pdf). The adaptation
of different species and breed to a broad range of
environments provides the necessary variability that
offers opportunities to meet the increased future
demands for food and provide flexibility to respond
the changed markets and needs (Philipsson and Okeyo
2006).
Indigenous and adapted or domesticated cattle in
Indonesia are located in several places throughout
Indonesia. There are at least four indigenous cattle in
Indonesia, that is Bali cattle, Aceh cattle, Coastal cattle
8
ET Margawati
Fig. 1. Physical Map of Indonesia. (http://geografi.ums.ac.id/.../Survey_Mapping/peta_indonesia_UN.pdf)
and Madura cattle (Abdullah 2008). The Bali cattle were
originally restricted only in Bali Island during Dutch
era, while at the present, it can be recognized almost
throughout Indonesia. The Aceh cattle are located in
Aceh of Sumatera. The Coastal cattle are in Padang of
West Sumatera and categorized as dwarf cattle. The
Banteng cattle was considered as original of Banteng
cattle are distributed in Madura Island, Kangean Island
and now can be obtained in several Zoos in Indonesia.
Those four cattle are as beef cattle. While SumbaOngole and Java-Ongole are also considered as original
cattle breed of Indonesia (Dahlanuddin et al. 2003;
Martoyo 2003), these cattle are also grouped as beef
cattle. There are several very long adapted or domesticated cattle in Indonesia such as Grati cattle distributed
in East Java and descendant Fries Holstein, both are as
dairy cattle.
Molecular Genetic Information
Animal population that lives in given environment
pressure (e.g. high-stress climate and low-nutrient forage) in very long time should adapt to such stress to
survive; otherwise, they will be extinct. In population
genetics theory, the animal could survive till this present
because they passed naturally in selection pressure. The
effect of such different pressure results the animals
performing differently among population. At least, a
distinct genetic polymorphism will lead in such pressure.
Plasticity owing to mutation may occur on such adapted
animals. Mutation could express as negative or positive
effects. The existing of mutation in animals is now
possible to be detected by the ease of availability of
molecular genetic information.
Advances in biotechnology research, such as molecular markers, can be used to detect the loci closely to
genes associating with desired traits or can be used to
map QTL (Margawati et al., 2006), then applied
towards genetic merit improvement in livestock. Application of molecular genetics for genetic improvement
relies on the ability to genotype individuals for specific
genetic loci (Dekkers 2004). Therefore, for these purposes, genetic markers can be distinguished by three: (i)
direct markers: loci that code for the functional mutation, (ii) LD markers: loci that are in population-wide
linkage disequilibrium with the functional mutation and
(iii) LE markers: loci that are in population-wide
equilibrium with the functional mutation.
As described by Anderson (2001), those types of
markers differ not only in methods of loci detection but
also in its application in selection programmes. Direct
markers and LD markers allow for selection genotype
across the population because of the consistent association between genotype and phenotype. The use of LE
markers has to allow for different linkage phases
between markers and QTL from family to family.
It was introduced by Van der Werf (2000) that idea
behind MAS is there may be genes with significant
effects that may be targeted specifically in selection.
Practically, MAS is also defined as a process of using
results of DNA marker tests to assist in the selection of
individual become the parents in the next generation of
a genetic improvement programme (http://www.nbcec.org). Marker-assisted selection is predicted to be most
beneficial for traits that have low heritability or are
difficult, expensive or impossible to record in a normal
breeding programme (http://www.fao.org/biotech/docs/
Gibson.pdf, Van Eenennaam 2004).
Nowadays, the molecular marker information is used
as a key component in genetic improvement programme. For instances, farmers or breeders can use
molecular genetic markers based on the desired traits. It
is to minimize the cost of undertaking an independent
QTL mapping experiment. There have been identified
for some traits either influenced by single (e.g. hair or
coat colour, double muscling, certain diseases; Van der
Werf 2000 and http://www.nbcec.org) or multi genes.
Most of economically importance traits or quantitative
traits are controlled by many number of genes or
multigenes (Van der Werf 2000). As described by
Margawati (2005) and Margawati, et al. (2006), QTL
mapping of growth traits in Indonesian Thin Tail (ITT)
2012 Blackwell Verlag GmbH
Molecular Genetics and Livestock Breeding Strategies
sheep was identified on ovine chromosome 18 and
flanked by markers of CSSM018 and TMR1 or AKT1).
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2012 Blackwell Verlag GmbH
9
Conflicts of interest
The author has no conflict of interest to declare.
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Submitted: 2 Dec 2011; Accepted: 13 Dec
2011
Author’s address (for correspondence): ET
Margawati, Research Center for Biotechnology, The Indonesian Institute of Sciences
(LIPI), Jl. Raya Bogor km 46. Cibinong
16911, West Java, Indonesia. E-mail:
[email protected].