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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). References Abdullah MAN, 2008: Genetic characterization of Aceh utilizing phenotypic, mitochondrial DNA of D-loop region and microsatellite DNA analyses. PhD Thesis. Bogor Agricultural University, Bogor, Indonesia. Anderson L, 2001: Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet 2, 130–138. Dahlanuddin DV, Tien LJB, Adams DB, 2003: An exploration of risk factors for bovine spongiform encephalopathy in ruminant production system in the tropics. Rev Sci Tech Off Int Epiz 22, 271– 281. Dekkers JCM, 2004: Commercial application of marker- and gene-assisted selection in livestock: strategies and Lessons. J Anim Sci 82, E313–E328. DNA-based Technologies. National Beef Cattle Evaluation. Colorado State University, Cornell University, University of Georgia. USA. Available: http:// www.nbcec.org (accessed 1 March 2010). Van Eenennaam A, 2004: Marker-Assisted Selection Backgrounder. Sierra Foothill Research Extension Center, Agriculture and Natural Resources Research and Extension Centers, UC Davis. Available: http://escholarship.org/uc/item/738066n6 (accessed 1 March 2010). Margawati ET, 2005: Quantitative trait loci (QTL) mapping for growth traits in the 2012 Blackwell Verlag GmbH 9 Conflicts of interest The author has no conflict of interest to declare. Indonesian Thin Tail (ITT) and Merino backcross sheep population. PhD Thesis. Bogor Agricultural University, Bogor, Indonesia. Margawati ET, Raadsma HW, Martojo H, Subandriyo M, 2006: Quantitative Trait Loci (QTL) Analysis for Production Traits of Birth Weight and Weight 360 days in Backcross Sheep. Jurnal Biosains Hayati 13, 31–35, ISSN: 0854-8587. Accreditation No.: 49 ⁄ DIKTI ⁄ Kep ⁄ 2003. Martoyo H, 2003: Indigenous Bali Cattle: The Best Suited Cattle Breed for Sustainable Small Farms in Indonesia. Laboratory of Animal Breeding and Genetics, Faculty of Animal Science Bogor Agricultural University, Bogor, Indonesia. Philipsson J, Okeyo AM, 2006: Global perspectives on animal genetic resources for sustainable agriculture and food production in the tropics. In: Ojango JM, Malmfors B Okeyo AM (eds.), Animal Genetics Training Resource, version 2. International Livestock Research Institute, Nairobi, Kenya, and Swedish University of Agricultural Sciences, Uppsala, Sweden. Available: http://agtr.ilri.cgiar. org/module/module1/Module1.htm (accessed 1 March 2010). Thompson JM, 2004: The effects of marbling on flavour and juiciness scores of cooked beef, after adjusting to a constant tenderness. Aust J Exp Agric 44, 645–652. Van der Werf J, 2000: Basic of Marker Assisted Selection, Chapter 15. In: Kinghorn B, van der Werf J (eds), QTL course: Identifying and Incorporating Genetic Markers and Major Genes in Animal Breeding Programs. University of New England, Armidale, Australia, pp. 119– 127. Strategies for utilising marker data for livestock genetic improvement in the developing world. Available: http:// www.fao.org/biotech/docs/Gibson.pdf (accessed 8 March 2010). Map Indonesian. Available: http://geografi.ums.ac.id/.../Survey_Mapping/peta_ indonesia_UN.pdf (accessed 1 March 2010. Atlas Sumberdaya Iklim Pertanian Indonesia (Atlas resource of Indonesian agriculture climates). Available: http://balitklimat. litbang.deptan.go.id. (accessed 1 March 2010). 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].