Indonesia has a high duck and waterfowl diversity. The duck diversity is marked by many species, which spread from Sumatra, Java, Bali, West Nusa Tenggara to Kalimantan (Tamzil & Indarsih 2017). Indonesian ducks belong to the Indian Runner (fast runner ducks from India) which originally came from India (Batty 1985). Statistic data from FAO (www.fao.org/faostat/en/#data/QL) exposes that total population of ducks in Indonesia is 38 million in the year 2013. Duck production plays an important part in the agricultural economy of many Asia countries. The continent alone accounts for 82.6% of the total duck meat produced worldwide (FAO 2010). Duck meat is recognized as a healthy food in Asian countries. In particular, duck meat consumption in Korea has rapidly increased over the last decade. Duck meat is rich in unsaturated fatty acids and consumer preference for healthy meat is now three times greater than that during the last decade (MIFFAF Korea 2013). Southeast Asian countries have conserved various native duck species because the center of duck meat consumption in Southeast Asia, including Korea, is located in a migratory bird flyway (Kraus et al. 2011). The characterization and conservation of ducks assume prime importance as they provide food security to the rural folk. These locally adapted ducks are useful biodiversity resources as they are important genetic reservoirs essential for facing the future challenges of disease resistance and better quality meat (Gaur et al. 2016). Ducks together with the ostrich, emu, peacock, turkey, quail, and other birds play a major role in studies on bird evolution. Up to now, most available data concerning ducks have come from heritabilities and genetic correlations of some traits (Bochno et al. 2000) and epidemiology (Susanti et al. 2008; Li et al. 2003; Hatta et al. 2002). Most available molecular data have come from evolution studies based on the analysis of mitochondrial DNA sequence (Susanti et al. 2017; Jin et al. 2014; Jin et al. 2012). Few studies about genetic markers in the duck is limited (Alyethodi & Kumar 2010; Kraus et al. 2011; Seo et al. 2015), and therefore we characterized ten microsatellite markers for Central Javanese duck. Genetic fingerprinting has been utilized in identification process of individuals, breeds, cultivars and even species, It also used to do genetic mapping in connection among animals, plant breeding and medical applications, and in a range of population genetic and ecological applications (Baratti et al. 2001; Bochno et al. 2000; Chowdhury et al. 2001). One of the important DNA fingerprinting methods is species-specific microsatellite analysis.. Microsatellites or simple sequence repeats (SSRs) are short repetitive elements of 1-6 bases that found in prokaryotic and all eukaryotic genomes (Schlotterer 2000). These repeat motifs present in both coding and noncoding regions of genomes (Ellegren 2004) are smaller than 100bp (Stolle et al. 2013). The microsatellites are highly polymorphic, reproducible, and abundant, inherited co-dominantly, and distribute throughout the genome (Saavedra et al. 2013). The excessive rate of mutation also high number of alleles and frequency in the genomic DNA, makes microsatellites very effective molecular markers in population genetics, genome mapping, taxonomic study, linkage analysis, genetic fingerprinting and diversity (Olango et al. 2015). Microsatellite is chosen as a marker for diversity and relationship analysis among different species of poultry and livestock including buffalo, camel, and horse (Vijh et al. 2007; Vijh et al. 2008; Khashour et al. 2013). Native breeds need to be protected for biodiversity conservation and development of economically important traits, which would also be valuable ecologically and to breed survival.
Development of breed-discriminating genetic markers and conservation strategies is important for breed conservation and trait development. In addition, duck breed classification analysis can provide additional information for preventive veterinary inspections for avian influenza (AI) viruses (Groepper et al. 2014; Ramey et al. 2014). Identification and characterization of local duck are important since the data is used as sources of Indonesia germplasm and help the breeding program. In the absence of information about the genetic attributes of each breed available for a breeding program, development of local breeds is often ignored in favor of the introduction of germplasm from exotic breeds, about which environmental adaptation information is generally unavailable. These pose a great risk for the loss of valuable genes. To surmount the situation the Food and Agriculture Organization of the United Nations (FAO) recommended establishing conservation programmes for the maintenance of animal genetic resources. These include among many other actions the identification and characterization of local breeds. The objective of this study was to the characterization of central Javanese duck breeds in Indonesia using 10 microsatellite markers