Abstract
This study was realized to determine the genetic variation of Central Javanese duck based on the D-Loop mtDNA gene. D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method with ABI automatic sequencer. ClustalW from MEGA-6.06 software program was employed for multiple alignments of nucleotide sequences. Nucleotide sequences of D-loop gene of mtDMA from the Central Javanese duck were aligned together with other Anas isolates from Genbank using ClustalW of MEGA-6.06 program. The estimation of genetic distance and phylogenetic tree construction were analyzed by Neighbor-Joining method, whereas the calculation of distance matrix was performed using Kimura 2-parameter. Multiple alignments obtained were 720 nucleotides at position 56 to 779 at the 5 'end. The results of the polymorphism analysis on D-loop sequences produced 23 haplotypes. However, this haplotype information does not represent the relationship among the geographical origins of duck with the certain duck species name. Moreover, a total number of 32 variable sites were identified. Insertions were detected in four sequences (126, 155, 771 and 779 nucleotide number). In the phylogenetic analysis, it is safe to conclude that the Central Javanese duck is closely related to Anas platyrhynchos and Anas zonorynchos .
Highlights
The breed conservation needs a genetic characterization to obtain an efficient management of genetic resources (Bjǿrnstad & Rǿed, 2002)
There is a depopulation policy by mass extermination for waterfowls and poultry declared by the Indonesian government when there is an evidence of avian influenza (AI) virus outbreak the identification of AI virus outbreak has not been developed well in Indonesia (Rahardjo, 2014)
This study aims to determine the genetic variation of Central Javanese duck based on the D-Loop mitochondrial DNA (mtDNA) gene
Summary
The breed conservation needs a genetic characterization to obtain an efficient management of genetic resources (Bjǿrnstad & Rǿed, 2002). Local ducks in Indonesia are distributed over a wide geographical range. They are reared by communal farmers across the country under extensive production systems. The collective ownership of the scavenging feed resources results in mixing of flocks from different households within communities. On average every household owns a cock, mixing with duck results in sharing of cocks among neighboring flocks. In addition to economic loss, the policy is biologically detrimental because of its potential in annihilating the breed germplasm, is the wealth of breeds Based on those explanations, the aim of genetic determination plays a crucial role in the germplasm conservation
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