Molecular Genetic Characterization Of Indonesian Indigenous Chickens And Jungle-fowls Using Microsatellite Markers

In Indonesia, indigenous chickens have played an important role in poultry production, because they have adapted to particular natural environments for many generations and have also been modified for improved productivity. Indonesia has various descript and non-descript breeds of indigenous chickens which are very well-known among Indonesian people. There are31breeds of Indonesian indigenous chickens, of which the most popular ones are:Pelung, Black Kedu, White Kedu, Kapas, Cemani, Arab, Merawang, Kate, Gaok, Sentul, Wareng, Nunukan, Tolaki, Tukong, Ayuni, and Jantur.A total of1498individuals of71chicken and Jungle-fowl populations, geographically localized in different major islands of Indonesia, were genotyped for20microsatellite DNA markers through polymerase chain reaction to investigate their molecular genetic diversity, population genetic structure, and genetic relationship between each other. In total,277alleles were observed for71populations of Indonesian chicken across20microsatellite loci. The mean number of alleles (MNA) per locus ranged from1.55to7.60. Heterozygosity was calculated to determine the genetic variation. The observed within-population diversity measures indicated that indigenous chicken populations were more diverse than commercial chicken and Jungle-fowl populations. The relatively fewer alleles in Jungle-fowls and commercial layers indicated that their limited founders and/or fragmented meta-populations leading to loss of genetic diversity. Bayesian algorithm was used to cluster individuals to a pre-defined numbers of genomic clusters of2≤K≤20. The most probable clustering was found at K=3. At this level of differentiation, the four groups (Jungle-fowls, indigenous chicken breeds, commercial broilers and layers) were separated as three independent clusters with Green Jungle-fowls in the first cluster, Red Jungle-fowls and indigenous chicken breeds in the second while commercial broilers and layers to be the third. Result of this study lead to a conclusion that the Indonesian indigenous chicken breeds and commercial broilers are highly diverse with no clear sub-structuring following geographical sampling locations. The Jungle-fowls and commercial layers on the other hand are less diverse and highly sub-structured.