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ISSN: 1978-3019
INTRODUCTION
Chickens are classified as order: Galliformes, family:
Phasianidae and genus: Gallus (jungle fowl). Domestication
resulted in basic changes in the behaviour, physiology and
production of the bird, but still there are some similarities
between the ancestor and the current chickens (Al-Nasser et
al. 2007). It is widely believed that all populations of
domesticated chicken descend from a single ancestor, the red
jungle fowl (Gallus gallus gallus), which originated in
Southeast Asia (Fumihito et al. 1994, 1996). Chicken is by far
the most widely distributed livestock. In Indonesia, domestic
(indigenous) chicken scattered throughout the archipelago
apparently has a lot of diversity with different morphologic
characteristics. From 31 breeds of indigenous chickens
identified (Nataamijaya 1996, 2000), 11 breeds of chicken are
known as chickens with high egg production (free-range/
Kampung chicken, Sentul chicken, Wareng chicken, Black
Kedu chicken, Sedayu chicken, Nusa Penida chicken,
Merawang/Merawas chicken, Sumatra chicken, Pelung
chicken, female Gaok chicken, and Dupin chicken). Twelve
breeds of chicken are known as ornamental chickens because
of their voice; they are also known as fighting cocks and
regarded as chickens with power (Pelung chicken, Ciparage
chicken, Banten chicken, Black Kedu chicken, Cemani chicken,
Olagan chicken, Kokok Balengek chicken, male Gaok chicken,
Tolaki chicken, Bangkok chicken, Bekisar chicken, and
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ID
name
CMP
CM
KPS
Kapas
PL
Pelung
PLC
Arab Golden ARG
MR
Merawang
Arab Silver ARS
KD
Kedu
KDH
Kedu Putih KDP
KDPJ
KT
Kate
GA
Gaok
STJ
Sentul
STC
T
Wareng
KTO
Tolaki
KAL
Kalosi
NT
Nunukan
NN
NS
Total samples
Total
samples
BPTU Ayam, Sembawa, South Sumatera
2
35
Kedu, Temanggung, Central Java
30
Kedu, Temanggung, Central Java
20
BPTU Ayam, Sembawa, South Sumatera
30
Cianjur, West Java
Kedu, Temanggung, Central Java
30
30
BPTU Ayam, Sembawa, South Sumatera
30
BPTU Ayam, Sembawa, South Sumatera
Kedu, Temanggung, Central Java
30
12
Kedu, Temanggung, Central Java
18
Kedu, Temanggung, Central Java
9
Jatiwangi, West Java
31
Yogyakarta, DIY
Bangkalan, Madura Island
10
31
Jatiwangi, West Java
17
Ciamis, West Java
Tangerang, Banten
12
21
Konawe, Southeast Sulawesi
30
Gowa, South Sulawesi
30
Tarakan, East Kalimantan
13
Nunukan, East Kalimantan
Sebatik, East Kalimantan
12
483
Site collection
No of variable sites
14
12
10
8
6
4
2
0
0-49
Nucleotide position
Figure 2. Sequence of variance distribution on segmen HV I from Dloop DNA mitochondria of Indonesian indigenous chicken.
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Clade II
Clade IV
Clade I
Clade IIIc
Clade IIId
Outgroups
Figure 3. Phylogenic tree based on 69 haplotypes identified on Indonesian indigenous chicken, 2 haplotypes from the gen Gallus which sequence
is taken from GenBank: Gallus gallus gallus (GenBank accession number AB007720) and Gallus gallus bankiva (GenBank accession
number AB007718) and 7 Clade reference haplotypes (Clade I, II, IIIa, IIIb, IIIc, IIId, and IV). The numbers at the major nodes
represent the percentage bootstrap values for interior branches after 1000 replications.
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Figure 4. Median-joining network for 69 haplotypes of Indonesian indigenous chicken based on polymorphic site of the mitochondrial D-loop
HV1 region. Area of each circle is proportional to the frequency of the corresponding haplotype. Different classes of haplotypes are
distinguished by use of colour codes. White circles indicate clade I, blue circles denote clade II, yellow circles refer to clade IV, while
colours red, light green, and dark green denote Clades IIIa, IIIc, and IIId respectively. The pink dots illustrate median vectors (mv),
produced by the network software, representing putative intermediate haplotypes that have not been found or sampled.
Domestication of chicken
HIIIa
HIIIb
HIIIc
HIIId
HIV
HI
HII
Out
D
D
Three primary
domestications
events and two
subsequent
introgression
Figure 5. Three center domestication of chickens indicated by three
dominant colours, green (Yellow River, China), yellow (Indus
valley), and blue (Indonesia).
Sampling site
China
Lombok Island, Indonesia
Thailand
China
China
China
Pakistan
Table 3. MtDNA diversity indices in Indonesian indigenous chicken populations based on 397 partial D-loop sequences
Island
Population
N
S
H
Hd
0.74866
0.00815
18
9
Cemani
34
Java
0.01231
0.89524
11
18
21
Kapas
Sumatra
0.00352
0.79556
8
7
47
Pelung
Java
0.00389
0.45538
5
13
26
Arab Golden
Sumatra
0.00631
0.69048
6
14
28
Merawang
Sumatra
0.01068
0.87356
10
21
30
Arab Silver
Sumatra
0.01111
0.82432
11
21
37
Kedu
Java
0.00734
0.84286
10
20
21
White Kedu
Java
0.00642
0.72906
10
19
29
Kate
Java
0.76190
0.00264
2
3
Gaok
7
Java
0.00740
0.85366
13
24
42
Sentul
Java
0.00828
5
0.86667
10
8
Java
Wareng
0.00567
0.89706
8
8
17
Tolaki
Sulawesi
0.87816
0.00512
11
9
Kalosi
30
Sulawesi
0.00697
0.89832
13
21
55
Nunukan
East Kalimantan
0.00994
69
0.88045
434
49
Total
N: Number of sequence used, S: Number of segregation site, H: Number of haplotype, Hd: Diversity of haplotype, : Diversity of nucleotide.
Genetic differentiation estimates: Hudson 2000, Snn (nearest neighbour statistic): 0.31780 PM test; P-value of Snn: 0.0000 *** (this indicates
significant genetic differentiation). Gene Flow Estimates: Hudson, Slatkin and Maddison 1992. Fst: 0.33166 Nm: 1.01 (indicates that the
exchange between populations is low).
Table 4. Analysis of molecular variance (AMOVA) between D-loop sequences haplotypes in Indonesian indigenous chicken
Source of variety
Among population
Within the population
Total
Free degree
15
419
434
Quadrat number
339.102
698.637
1037.739
Variety component
0.79025Va
1.66739Vb
2.45764
Table 5. Pairwise FST (Hudson et al. 1992) between 15 chicken population based on D-loop sequence
CM
KPS
PL
ARG
MR
ARS
KD
KDP
KT
GA
CM
KPS
0.077
0.152
PL
0.063
ARG
0.772
0.623 0.861
0.045
0.063 0.034 0.791
MR
0.062
0.005 0.162 0.692
ARS
0.093
0.035
0.008
KD
0.043
0.002 0.079 0.679
0.045 0.018 0.775
0.022
0.054 0.003
KDP
0.011
0.004
0.113 0.039
0.006
0.099 0.021 0.802
KT
0.028
0.138
0.062
0.14
0.264 0.147
0.178
0.232 0.138 0.877
GA
0.014
0.027 0.161
0.002
0.089 0.017
ST
0.034
0.071 0.035 0.775
0.082 0.232
0.281
0.335 0.497
0.287
WAR
0.305
0.143 0.415 0.738
0.205 0.396
0.137 0.141
0.131
0.114 0.229 0.813
0.189
KTO
0.15
0.028 0.175
0.027
0.098 0.049
0.014
0.087 0.044 0.823
KAL
0.049
0.092
0.133 0.285
0.139
0.081 0.097
NN
0.094
0.063 0.156 0.788
Name of population CM: Cemani, KPS: Kapas, PL: Pelung, ARG: Arab Golden, MR: Merawang, ARS:
KT: Kate, GA: Gaok, ST: Sentul, WAR: Wareng, KTO: Tolaki, KAL: Kalosi, NN: Nunukan.
ST
TTW
KTO
KAL
NN
0.317
0.169 0.333
0.021 0.329
0.163
0.13
0.264
0.108
0.102
Arab Silver, KD: Kedu, WK: White Kedu,
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