| Summary: | Polymerase Chain Reaction
This research was aimed to investigate the influence of different plume colors
towards morphological diversity of Magelang duck and polymorphism in mtDNA Dloop
region based on PCR-RFLP and SNP analysis and phylogenetic investigation in
five native Indonesian duck population namely Magelang, Tegal, Mojosari, Bali and
Alabio. Research materials included blood sample of 50 Magelang ducks with
different plume colors and 20 of each native ducks. Morphological characteristics
included Magelang duck�s body measurement, egg quality and productive capacity
which were analyzed using two-way Completely Randomized Design with 11
different plume colors as treatments. (PCR) technique
was used to amplify fragment in mtDNA D-loop region. DNA fragment of 718 bp was
amplified with primer pair of DL-AnasPF and DL-AnasPR. PCR products were
digested using endonuclease Alu I and Hae III and sequenced afterwards. Research
result showed that different plume colors influenced morphological diversity in
Magelang duck population. Polymerase Chain Reaction-Restriction Fragment Length
Polymorphism (PCR-RFLP) analysis obtained four haplotypes (A, B, C dan D).
Single Nucleotide Polymorphism (SNP) analysis on mtDNA D-loop region used 469
nt nucleotide sequence and compared to the standard nucleotide sequence from
Anas platyrhynchos (HM010684.1) in GenBank. SNP was observed in Magelang
duck C (Klawu blorok), F (Hitam cemani), G(Gambiran), H (Jarakan kalung), I (Jowo
polos) dan K (Putih polos) and Tegal namely 8, 1, 2, 5, 2, 8 and 2 SNP, respectively.
Based on genetic distance and phylogenetic analysis it can be concluded that the
population of native Indonesian ducks (Magelang, Tegal, Mojosari, Bali and Alabio)
was closely related and shared common maternal inheritance with Anas
platyrhynchos and Anas zonorhyncha. it was proven by the inclusion of Anas
platyrhynchos and Anas zonorhyncha into native Indonesia ducks, there was 99,68 ±
0,56% common ancestry between native Indonesian ducks and Mallard (Anas
platyrhynchos). Based on the research result, it is concluded that: (1) Plume color
diversity affect the morphological diversity including body measurement,
characteristics of egg production and quality in Magelang duck population. (2) There
was polymorphism in mtDNA D-loop region based on PCR-RFLP analysis in
Magelang and other native duck population. Magelang and Tegal ducks tend to be
more polymorphic than Alabio, Bali and Mojosari ducks. (3) There was polymorphism
in mtDNA D-loop region based on SNP analysis in Magelang and other native duck
population. Magelang ducks with different plume colors were relatively more
polymorphic than the other native Indonesian native ducks, as proven by more
0.000
diverse SNP. (4) There was a relatively diverse genetic relation between Magelang
duck and the other native Indonesian ducks with Anas in the world. Magelang, Tegal,
Mojosari, Bali and Alabio ducks had a closer genetic relation and shared common
maternal inheritance with Anas platyrhynchos and Anas zonorhyncha shown by
� 0,019 genetic distance compared to the other Anas in the world (0,055 �
0,076), while the biggest genetic relation was with Cairina moschata (0,095 - 0,108).
(5) Nucleotide sequence in part of mtDNA D-loop region can be used to investigate
phylogeny of native Indonesian ducks.
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