Genetic Diversity of Chinese Native Chicken Breeds Based on Protein
Polymorphism, Randomly Amplified Polymorphic DNA, and
Microsatellite Polymorphism
X. Zhang,*,† F. C. Leung,*,1 D. K. O. Chan,* G. Yang,† and C. Wu‡
*Department of Zoology, The University of Hong Kong, Hong Kong, SAR China; †Department of Animal Science,
South China Agricultural University, Guangzhou, China; and ‡Department of Animal Genetics and Breeding,
China Agricultural University, Beijing, China
ABSTRACT Genetic diversity of Chinese native chicken
breeds was investigated using protein polymorphism,
randomly amplified polymorphic DNA (RAPD), and microsatellite polymorphism. Imported broiler and layer
breeds were also included in the analysis. The results from
protein polymorphism did not show distinct differences
between Chinese native chicken and imported broilers;
however, there were small significant differences between
these two types of chickens. The results from RAPD indicated that gene diversity within a population was large
in Chinese native chickens, intermediate in broilers, and
low in layers and that there were small differences between Chinese native chickens and both broilers and layers. A great difference between broilers and layers was
observed. Microsatellite polymorphism data showed that
genetic diversity was high in the Chinese native chickens
and low in layers and that there was a close relationship
between Chinese native chickens and broiler but a remote
relationship between Chinese native chickens and layers.
The wide genetic diversity of Chinese native breeds can
meet different requirements of breeding for chicken quality in China.
(Key words: Chinese native chicken, genetic diversity, protein polymorphism, randomly amplified polymorphic
DNA, microsatellite polymorphism)
2002 Poultry Science 81:1463–1472
INTRODUCTION
Genetic markers are powerful tools in genetic diversity
research of domestic animals. Of them, protein polymorphism, randomly amplified polymorphic DNA (RAPD),
and microsatellite polymorphism are often used. Protein
polymorphism is detected by gel electrophoretic separation of proteins together with specificity of histochemical
detection of the protein products of single loci (May,
1998). Presently, dozens of simple Mendelian markers
are available for most organisms. In chickens, protein
polymorphisms of at least 49 loci have been reported
(Grunder, 1990). RAPD was first described by Williams
et al. (1990) and independently by Welsh and McClelland
(1990) and has been widely used by researchers because
of its simplicity and applicability (Rafalski, 1998). Microsatellites are simple sequence repeats of mono-, di-, tri-,
tetra-, or penta-nucleotide units widely dispersed
throughout animal genomes (Tautz, 1989; Beckmann and
2002 Poultry Science Association, Inc.
Received for publication April 24, 2001.
Accepted for publication May 24, 2002.
1
To whom correspondence should be addressed: fcleung@
hkucc.hku.hk.
Weber, 1992). Microsatellite loci offer good reproducibility and generate large numbers of detectable alleles. In
addition, microsatellites are easy to identify and have
low mutation rates. All these make microsatellites the
preferred genetic markers for estimating genetic variation
(Milligan et al., 1994).
China has a very rich genetic diversity of native chickens. A total of 27 genetically diverse native chicken breeds
have been reported, based on morphological characteristics (Qiu, 1988). Among these native breeds, nine are
meat-type, seven are layer-type, 10 are dual-purpose
(meat and layer) breeds, and one is game. Nearly all meattype and some dual-purpose breeds are used for quality
chicken production. Compared to broilers, quality
chicken has many distinct features in morphological characteristics, growing rate, meat taste, and reproductive
performance. Most Chinese native breeds used for quality
chicken production often have a color appearance, slowgrowth rate, meat that tastes good, and low reproductive
performance (because of broodiness). Although morphological characteristics and even allozyme variations of
Abbreviation Key: Akp-1 = alkaline phosphatase-1; Akp-2 = alkaline
phosphatase-2; Amy-1 = amylase-1; Amy-2 = amylase-2; Es-1 = esterase1; Es-2 = esterase-2; RAPD = random amplified polymorphic DNA.
1463
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ZHANG ET AL.
TABLE 1. Summary of DNA and protein samples
Breed
Abbreviation
Origin
Type
Sample no. of
protein/DNA
HYB
XH
QYP
TH
BS
BF
GS
WC
YS
WR
AA
AV
HL
DYL
PL
GF
South China
South China
South China
East China
East China
North China
Central China
South China
South China
Imported
Imported
Imported
Imported
Local breed
Local breed
Imported breed
Native
Native
Native
Native
Native
Native
Native
Native
Native
Broiler
Broiler
Broiler
Layers
Bred
Bred
Bred
0/36
0/36
30/30
32/32
30/30
0/24
50/24
24/24
20/20
22/22
96/0
48/24
50/30
50/0
50/0
30/0
Huiyang Bearded
Xinghua
Qingyuan Partridge
Taihe Silkies
Black Silkies
Beijing Fatty
Gushiu
Wenchung
Yangshan
White Recessive Rock
Arbor Acres Parental
Avian Parental
Hy-Line
Dwarf Yellow Line
Partridge Line
Guifu
some breeds have been reported (Qiu, 1988; Yin et al.,
1989), very few reports have been based on DNA polymorphism.
The purpose of this study was to characterize the differences among Chinese native chickens and fast-growing
broilers and layers using allozyme, RAPD, and microsatellite polymorphism. From such differences, a relationship between qualitative and quantitative characteristics
and the above markers could be constructed. The results
will be of significance for breeding-quality chickens and
the preservation of chicken genetic diversity in China.
MATERIALS AND METHODS
Preparation of Protein and DNA Samples
Blood samples were collected from a total of 16 populations of chickens (Table 1). Protein and DNA samples
were prepared from Qingyuan Partridge, Taihe Silkies,
Black Silkies, Gushiu, Wenchung, Yangshan, Recessive
White Rock, Avian Parental, and Hy-Line birds. Only
protein samples were prepared from Arbor Acres, Dwarf
Yellow Line, and Partridge Line of Yuehuang, and Guifu.
Only DNA samples were prepared from Huiyang
Bearded, Xinghua, and Beijing Fatty. Anti-coagulant
agent, EDTA (2%), was used in all blood sample collection, except the samples of Yangshan and Beijing Fatty
in which heparin was used.
Protein samples were prepared using the following
method. Plasma was isolated from anti-coagulated blood
with heparin (50 IU/mL blood) through centrifugation.
Plasma samples were stored in a −70 C freezer. DNA
samples from all breeds or populations were extracted
from anti-coagulated blood with phenol, phenol:chloroform:isoamyl alcohol (25:24:1).
Chicken Breeds or Populations
Chinese Native Chicken Breeds. Huiyang Bearded,
Xinghua, Qingyuan Partridge, Taihe Silkies, Black Silkies,
2
Gibco BRL Products, Life Technologies, Carlsbad, CA.
Beijing Fatty, Gushiu, Wenchung, and Yangshan were
the native breeds used. Huiyang Bearded, Xinghua, Qingyuan Partridge, Wenchung, and Yangshan were from
southern China; Taihe Silkies and Black Silkies were from
eastern China; the Black Silkies originated from Taihe
Silkies; Beijing Fatty was from North China, and Gushiu
was from Central China.
Broiler and Layer Breeds. Three breeds of broilers
were sampled. They were Recessive White Rock (a pureline from Kabir), Arbor Acres Parental, and Avian Parental. Only one line of layer, Hy-Line pureline (from Leghorns), was sampled.
Breeding Lines. Two breeding lines of quality chicken
were sampled. They were the Dwarf yellow line and the
Partridge line of Yuehuang; both were bred from hybrids.
Black Silkies and Guifu chicken were bred from several
fowls.
Electrophoretic Separation of Protein
and Enzyme Polymorphism
Allozymes of alkaline phosphatase-1 (Akp-1), alkaline
phosphatase-2 (Akp-2), amylase-1 (Amy-1), amylase-2
(Amy-2), esterase-1 (Es-1), esterase-2 (Es-2), albumin,
transferrin (Tf), and pre-albumin (Pa) were analyzed with
5% and pre-albumin was analyzed with 5 or 7.5% polyacrylamide gel (acrylamide and bis, 30:0.8) electrophoresis and stained by histochemical visualization of locusspecific allozymes (Pasteur et al., 1988).
PCR-RAPD
Approximately 25 to 50 ng genomic DNA was used in
the amplification reaction in a total volume of 20 µL. The
reactions typically contained 10 mM Tris-HCl, pH 8.3; 50
mM KCl; 1.5 mM MgCl2; 0.02 mM dNTP,2 10 pmoles
random primer,3 and 1 U of Taq DNA polymerase.2 Amplification was performed in a thermal cycler (PE480)4 as
follows: an initial 2-min denaturation at 94 C followed
by 45 cycles of 45 s at 94 C, 1 min at 35 C, and 1 min at
72 C. The 45 cycles were followed by a final extension at
72 C for 5 min. Amplification products were analyzed by
GENETIC DIVERSITY OF CHINESE NATIVE CHICKENS
electrophoresis in 1.5% agarose gels. The gels were
stained with ethidium bromide and photographed under
ultraviolet illumination.
PCR and Genotyping of Microsatellites
Nine microsatellite markers from a Population Kit5
were studied. PCR was carried out following the protocols suggested by Cheng and Crittenden (1994) and
Crooijmans et al. (1996a) in 20-µL volumes using a PE
480 thermal cycler.2 Genotyping of microsatellite was performed in an ABI 310 DNA sequencer4 and with 310
GeneScan 2.1.4
Statistical Analyses
Average heterozygosity per population and genetic distance among various populations were calculated on the
basis of allele frequency estimates of allozymes and microsatellites using the equation of Nei (Nei, 1987). Gene
diversity within each population and gene diversity between various populations were calculated on the basis
of RAPD recessive allele frequency estimates following
the methods of Lynch and Milligan (1994). Phylogenetic
analysis was made with UPGMA clustering using PHLIP
version 3.4 (Felsenstein, 1991).
RESULTS
Allozyme Variations of Native
Chinese Chickens
Of the nine protein loci analyzed, Akp-1, Akp-2, Amy1, Amy-2, Es-1, transferrin (Tf) and pre-albumin (Pa) were
polymorphic; the rest were monomorphic. Among polymorphic loci, Amy-1 and Es-1 had different allele frequencies among meat-type breeds (including broilers and Chinese native chickens) and egg-type breeds. Chinese native
chicken populations had a higher allele frequency of
Amy-1A than broiler breeds. Allele frequencies of broiler
breeds were closer to those of layer breed than to those
of Chinese native breeds in Amy-1 and Es-1. Chinese
native chickens have intermediate average heterozygosity
that is lower than that of broiler and breeding populations
and higher than that of the layer population (Table 2).
Genetic distances calculated on the basis of allele frequency estimates indicated that all of the Chinese chicken
breeds have very close relationships among themselves
and a relatively close relationship to broiler breeds but a
remote relationship to the Hy-Line layer breed (Table 3).
Phylogenetic analysis was made using genetic distances. Figure 1 was the dendrogram of 13 populations
using UPGMA clustering. Forty-three polymorphic bands
3
Operon Technologies, Alameda, CA.
Applied Biosystems, Foster City, CA.
5
Provided by US National Animal Genome Research Program, Poultry Coordinators, East Lansing, MI.
4
1465
among 10 breeds (or populations) were obtained from 20
primers of the 200 primers screened. Figure 2 shows the
RAPD banding of some polymorphic primers. Among 43
polymorphic bands, there were great differences in 10
polymorphic observed bands between Chinese native
chicken and layers. However, only three polymorphic
bands were distinctly different between Chinese native
chickens and broilers. Some RAPD bands were specific
to a single population, and some to all populations of the
same type of chickens. Similar results were obtained by
Plotsky et al. (1995).
Gene diversity within each population, gene diversity
between populations, and genetic distance among populations calculated on recessive allele frequency estimates
following Lynch and Milligan (1994) are shown in Tables
4 and 5, respectively. Gene diversity within each population indicates that Chinese native chicken breeds are more
diversified than broiler breeds and much more diversified
than the layer breed. Gene diversity between populations
shows that the variations among all Chinese native
chicken breeds were small, and the greatest difference
was found between the broiler and layer breeds. Chinese
native chicken breeds were closer to broiler breeds than
to the layer breed.
Microsatellite Polymorphism
All nine microsatellite loci were polymorphic in 12 populations of Huiyang Bearded, Xinghua, Qingyuan Partridge, Wenchung, Yangshan, Gushiu, Taihe Silkies,
Beijing Fatty, Recessive White Rock, Avian Parental, and
Hy-Line. Numbers of alleles per population at each locus
ranged from four to 19. Among the nine loci examined
in a total of 312 individuals, the greatest were the 26
alleles found at the ADL0171 locus and the lowest were
12 alleles found at the ADL0158 locus. The Gushiu chicken
had an average of 12 alleles per locus for nine loci examined, the most among the 12 populations. The Recessive
White Rock averaged 6.78 alleles per locus at all loci,
the least among all 12 populations (Table 6). Generally,
Chinese native chicken populations had more microsatellite alleles at each locus, and Hy-Line layers and Recessive
White Rock broilers had fewer microsatellite alleles.
Figure 3 (A to G) shows allele frequency distribution at
each locus. From the allele frequency of ADL0102 (Figure
3A), differences among Chinese native broilers and layers
were determined. Nearly all populations had high frequencies of allele 104, and the Chinese native chicken had
higher frequencies of allele 105 (0.0781-0.4000); the broiler
and layer counterparts were low (0.0227 to 0.125 and 0,
respectively), with both the Avian (broiler) and Hy-Line
(layer) having high frequencies of allele 112 (0.3125 and
0.2500). ADL0136 (Figure 3B) shows differences between
Chinese native chickens and both the broiler and layer
in the frequency of allele 144. The Chinese native chicken
had relatively high frequencies of allele 128 (0.1 to 0.3333),
and allele 128 was the lowest for ADL0136. Two broiler
populations, Recessive White Rock and Avian Parental,
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ZHANG ET AL.
TABLE 2. Allele frequencies of polymorphic protein loci and average heterozygosity per population (H)1
Allele2
Akp-1
Akp-2a
Amy-1A
Amy-2i
Es-1A
Es-1B
Es-1C
PaA
TfA
TfB
TfC
H
DYL
PL
QYP
TH
BS
GS
WC
YS
GF
AA
AV
WR
HL
0.2789
0.1876
0.1633
0.2094
0.1633
0.1548
0.2640
0.1633
0.0339
0.3218
0.2126
0.1168
0.2517
0.1056
0.1398
0.0513
0.0814
0.0691
0.0742
0.1102
0.0513
0.0339
0.1398
0.1168
0.1398
0.0619
0.4600
0.4400
0.4700
0.4375
0.6167
0.5510
0.5000
0.5000
0.5667
0.4250
0.4100
0.4300
0.0250
1.0000
1.0000
1.0000
1.0000
1.0000
1.0000
1.0000
0.9747
1.0000
1.0000
1.0000
1.0000
1.0000
0.3200
0.2200
0.1600
0.0313
0.1833
0.1837
0.1875
0.1250
0.7167
0.2350
0.2800
0.1800
0.8600
0.6700
0.7400
0.8100
0.9687
0.8167
0.7551
0.7292
0.8250
0.2833
0.7650
0.6700
0.8200
0.1400
0.0100
0.0400
0.0300
0.0000
0.0000
0.0612
0.0833
0.0500
0.0000
0.0000
0.0500
0.0000
0.0000
0.1300
0.1300
0.0400
0.8437
0.1333
0.0000
0.2292
0.1500
0.0500
0.1650
0.2800
0.0500
0.1700
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0100
0.8800
0.9100
0.9300
0.9844
0.9500
0.9490
0.9167
0.9250
1.0000
1.0000
0.9600
1.0000
0.8800
0.1200
0.0900
0.0700
0.0156
0.0500
0.0510
0.0833
0.0750
0.0000
0.0000
0.0400
0.0000
0.1100
0.2868
0.2648
0.2019
0.1920
0.2170
0.2002
0.2934
0.2334
0.1633
0.2610
0.2856
0.1924
0.1847
1
Note: There are only two alleles at locus Akp-1, Akp-2, Amy-1, Amy-2, and Pa. Gene frequency of one of two alleles is shown in the table, and
gene frequency of the other allele equaled 1-xi.
2
DYL = Dwarf Yellow Line; PL = Partridge Line; QYP = Qingyuan Partridge; TH = Taihe Silkies; BS = Black Silkies; GS = Gushiu; WC = Wenchung;
YS = Yangshan; GF = Guifu; AA = Arbor Acres; AV = Avian Parental; WR = Recessive White Rock; HL = Hy-Line.
had high frequencies of allele 131 (0.2955 and 0.2500 respectively).
There were also distinct differences in ADL0158 among
Chinese native, broiler, and layer chickens (Figure 3C).
The frequencies of allele 185 were medium in the Chinese
native chicken (most of them 0.4 to 0.5), high in the broilers (0.5000 and 0.7045), and low in the layers (0.3000).
Layers had relatively high frequencies of the longer alleles
191, 199, and 200 (0.45, 0.0167, and 0.2333 respectively),
and the frequencies of allele 200 were 0 in nearly all the
other populations. We identified the most, 26, alleles in
ADL0171 (Figure 3D) in 312 individuals (data not
shown).
The Chinese native chicken is distinctly different from
broilers and layers in the frequency of allele 86. The frequency of allele 86 was 0.1875 to 0.5417 in Chinese native
chickens and was nearly zero in broilers and layers. Allele
numbers of this locus were much greater in the Chinese
native chicken (above 12) than in the Recessive White
Rock and Hy-Line (only six) and Avian (12) at this locus.
ADL0172 (Figure 3E) only showed a difference between
Chinese native and broiler chickens versus the layer
chickens. Chinese native and broiler chickens had high
frequencies of allele 147 (0.0625-0.7500), and layers had
a very high frequency of allele 149 (0.6667).
Genomic DNA of 1 to 3 individuals in nearly all Chinese
native chicken populations produced PCR products with
small sizes of about 130 to 134 bp, much shorter than the
size range reported by Dodgson and Chen (1997). Sixteen
alleles were detected in ADL0176 (Figure 3F) and the
sizes of these alleles were from 181 to 200 bp, in accordance with that indicated in the kit. The Hy-Lines had
relatively high frequencies of alleles 181 and 183, which
were detected only in Taihe Silkies. The two broiler populations, Recessive White Rock and Avian, had very high
frequencies of allele 184 (0.8409 and 0.5208, respectively),
and most of Chinese native populations and Hy-Line had
relatively high frequencies of 189. ADL0181 (Figure 3G)
showed differences of the layers from the Chinese native
chicken and broiler chickens. The frequencies of alleles
180 and 187 were 0.3333 and 0.2533, respectively, in layers,
and those of alleles 177, 181, and 182 were relatively high
in Chinese native chickens and the broiler.
There were few differences of allele frequencies between Chinese native, broiler, and layer populations in
ADL0210, but there was a distinct difference in the num-
TABLE 3. Genetic distances among populations on the basis of protein polymorphism1
Breed
DYL
PL
QYP
TH
BS
GS
WC
YS
AA
AV
WR
HL
PL
QYP
TH
BS
GS
WC
YS
AA
AV
WR
HL
GF
0.0026
0.0060
0.0861
0.0084
0.0075
0.0037
0.0070
0.0039
0.0054
0.0086
0.0662
0.0326
0.0026
0.0784
0.0056
0.0046
0.0030
0.0028
0.0040
0.0044
0.0027
0.0790
0.0387
0.0923
0.0042
0.0015
0.0067
0.0018
0.0077
0.0110
0.0023
0.0950
0.0428
0.0034
0.1055
0.0600
0.0697
0.0718
0.0546
0.0906
0.1886
0.1599
0.0771
0.0053
0.0025
0.0098
0.0113
0.0067
0.1141
0.0415
0.0087
0.0040
0.0106
0.0146
0.0039
0.1013
0.0362
0.0035
0.0036
0.0031
0.0091
0.0892
0.0458
0.0074
0.0077
0.0043
0.1032
0.0479
0.0048
0.0074
0.0796
0.0478
0.0103
0.0663
0.0380
0.0923
0.0426
0.0512
PL = Partridge Line; DYL = Dwarf Yellow Line; QYP = Qingyuan Partridge; TH = Taihe Silkies; BS = Black
Silkies; GS = Gushiu; WC = Wenchung; YS = Yangshan; AA = Arbor Acres; AV = Avian Parental; WR = Recessive
White Rock; HL = Hy-Line; GF = Guifu.
1
GENETIC DIVERSITY OF CHINESE NATIVE CHICKENS
1467
which were both remote from the layer breed. The dendrogram also indicates that two broiler breeds were first
clustered into one, as were two silkies breeds.
DISCUSSION
FIGURE 1. UPGMA dendrogram based on allozyme. DYL = Dwarf
Yellow Line; PL = Partridge Line; AA = Arbor Acre; WC = Wenchung;
AV = Avian Parental; QYP = Qingyuan Partridge; WR = Recessive White
Rock; GS = Gushiu; BS = Black Silkies; YS = Yangshan; GF = Guifu; HL
= Hy-Line; TH = Taihe Silkies.
ber of alleles between Chinese native versus broilers and
layers. All Chinese native populations had more alleles
of ADL0210 (more than six) than those of broilers and
layers (less than six). The Hy-Lines had distinct characteristics in ADL0267 (Figure 3H), which had a very high
frequency of allele frequencies of this locus; Taihe Silkies
had a high frequency of allele 109 (0.3906), and Yangshan
had a high frequency of allele 112 (0.4722).
From allele frequencies of all nine microsatellite loci,
average heterozygosity per population and standard genetic distances were calculated using Nei’s equation
(1987) (Tables 7 and 8). From the 12 populations investigated, average heterozygosity was lowest in Recessive
White Rock (0.6289), intermediate in Xinghua and HyLine (0.7069 and 0.7232, respectively), and highest in
Wenchung (0.8614). The result from genetic distances
showed there was a close relationship among Huiyang
Bearded, Xinghua, and Qingyuan, all three lines were
from Guangdong, China. These three populations were
closely related to Recessive White Rock and Avian Parental. The Hy-Lines were remote from all the other populations. Clustering analysis indicated the divergence of 12
populations as shown in Figure 4. The dendrogram indicates that there is a close relationship among meat-type
chickens (including Chinese native chickens and broilers),
We report here differences between Chinese native
chickens and imported layer chickens. The results from
protein polymorphism studies showed that the frequencies of two alleles of Amy-1 in all Chinese native chicken
populations were nearly the same and equal to 0.5, and
the Amy-1B frequency of the imported layer was 0.975.
On Es-1, Es-1B frequencies of Chinese native chickens
were high (0.67 to 0.9687), except for Gushiu (0.2833), and
the Es-1B frequency of imported the layer was low (0.64)
and Es-1A was high. By using protein polymorphism,
genetic distances between Chinese native chickens such
as Qingyuan Partridge, Dwarf Yellow Line, and Partridge
Line of Yuehuang, Wenchung, and Yangshan, and the
layers were high. RAPD analysis showed that there were
great differences in 10 polymorphic bands between Chinese native chickens and layer chickens.
Microsatellite polymorphisms indicated that there
were distinct differences in the frequencies of nearly all
nine loci between the Chinese native chickens and layers.
On ADL0102, the frequencies of alleles 104, 105, and 106
were high in Chinese native chickens, and the frequency
of allele 105 was 0 in the layers, although the frequencies
of alleles 104 and 106 were also high. Moreover, the frequencies of allele 112 were high in Hy-Line (0.25) and
low in Chinese native chickens (all less than 0.0694) except
for the Wenchung. There were similar tendency in
ADL0136, ADL0171, ADL0172, ADL0181, and ADL0267.
There were differences of allele frequencies among
ADL0158, ADL0176, and ADL0210 between Chinese native and Hy-Line birds. The number of alleles for each
locus was also different between Chinese native and layer
chickens. Chinese native chickens had not only the characteristic allele frequencies in protein polymorphism,
RAPD, and microsatellite polymorphism but also their
gene diversity within a population or average heterozygosity.
Chinese native chickens usually had high gene diversity within the population and average heterozygosity,
whereas layers had much lower diversity. Layer breeds
have lower average heterozygosity (Crooijmans et al.,
1996b; Vanhala et al., 1998). The relationships between
Chinese native and layer chickens were remote based on
protein polymorphism and microsatellite polymorphism.
Gene diversity between Chinese native chickens and layers were also relatively high based on RAPD. The remote
relationships were due to the following factors: 1) the
Leghorn layer (Hy-Line from Leghorn) was bred with no
Chinese native chickens and vice versa for Chinese native
chickens; 2) Chinese native and the imported layer chickens were bred for different purposes. It was interesting
that the two types had one characteristic in common: both
were slow growing.
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ZHANG ET AL.
FIGURE 2. Four random amplified polymorphic DNA (RAPD) profiles of 20 polymorphic primers. M = φX174 marker a) RAPD profile of
primer OPA06. Bands a and b are about 1,280 and 1,360 bp, respectively. b) RAPD profile of primer OPB17. Bands a, b, and c are 750, 900, and
1,130 bp, respectively. c) RAPD profile of primer OPD01. Bands a, b, c, d, and e are about 850, 1,000, 1,078, 1,360 bp, and 1,600 bp, respectively.
d) RAPD profile of primer OPD02. Bands a and b are about 720 and 870 bp, respectively.
TABLE 4. Gene diversity within each population (H) on the basis of random amplified polymorphic DNA (RAPD)1
Breed
H
Variance
HYB
XH
QYP
WC
GS
TH
BS
WR
AV
HL
0.3244
0.000077
0.3028
0.000097
0.3078
0.000112
0.3215
0.000085
0.2880
0.000128
0.2530
0.000141
0.2472
0.000146
0.2869
0.000213
0.2505
0.000228
0.1506
0.000219
1
HYB = Huiyang Bearded; XH = Xinghua; QYP = Qingyuan Partridge; WC = Wenchung; GS = Gushiu; TH = Taihe Silkies; BS = Black Silkies;
WR = Recessive White Rock; AV = Avian Parental; HL = Hy-Line.
1469
GENETIC DIVERSITY OF CHINESE NATIVE CHICKENS
TABLE 5. Gene diversity among populations on the basis of
random amplified polymorphic DNA (RAPD)1
Breed
HYB
XH
QYP
WC
GS
TH
BS
WR
AV
XH
QYP
WC
GS
TH
BS
WR
AV
HL
0.0227
0.0192
0.0693
0.2192
0.0436
0.0506
0.0461
0.0845
0.0886
0.0225
0.0696
0.2039
0.0297
0.0515
0.0456
0.2297
0.0614
0.1947
0.2247
0.0231
0.0285
0.0530
0.2267
0.0649
0.0480
0.0634
0.0627
0.0772
0.0682
0.1757
0.0925
0.0754
0.2017
0.1773
0.1933
0.0430
0.0746
0.0702
0.0599
0.0739
0.0676
0.0880
0.0493
0.1168
0.1917
HYB = Huiyang Bearded; XH = Xinghua; QYP = Qingyuan Partridge; WC = Wenchung; GS = Gushiu; TH
= Taihe Silkies; BS = Black Silkies; R = Recessive White Rock; AV = Avian Parental; HL = Hy-Line.
1
There was much similarity between Chinese native
chickens and the fast-growing broiler chickens, and there
were few differences between them in allele frequencies
of polymorphic protein loci. Among the 43 polymorphic
RAPD bands, only three recessive allele frequencies (i.e.
B08, G14-a, and G14-b) had distinct differences between
Chinese native chickens and the fast-growing broiler.
Microsatellite polymorphism did indicate a difference
between the two types, although such differences were
small. By using protein polymorphism, genetic distances
between Chinese native Qingyuan Partridge, Dwarf Yellow Line, and Partridge Line of Yuehuang, Wenchung,
Yangshan, and fast-growing broiler Recessive White
Rock, Avian, and Arbor Acres were small (all less than
0.015). Based on RAPD, gene diversity among Chinese
native Huiyang Bearded, Xinghua, Qingyuan Partridge,
and Wenchung, and the fast-growing broiler Recessive
White Rock and Avian was also small except for high gene
diversity between Xinghua and Recessive White Rock
(0.2267). A similar result was obtained from microsatellite
polymorphism analysis.
The following factors account for the close relationship
between the Chinese native and the fast-growing broiler
chickens. In recent years, broiler purelines, especially Recessive White Rock, were imported for breeding with
Chinese native chickens in China. The Dwarf Yellow Line
and Partridge Line of Yuehuang came from the interbreeding of native Cantonese chickens and the Recessive
White Rock. Some broiler breeds (e.g., Rock) used crosses
with Cochin and Lanshan that were very closely related
to Huiyang Bearded, Xinghua, Qingyuan Partridge, and
Gushiu. More importantly, both breeds were meat-types
and probably had similar heredity.
Chinese native, broiler, and layer chickens were all bred
and maintained for different purposes. Chinese native
chicken breeding focused on meat quality, broilers on
growth rate, and layers on laying performance. Further
study is required to determine whether the different
breeding criteria caused the differences in allele frequencies of allozyme, RAPD, and microsatellite polymorphism
between Chinese native, broiler, and layer chickens. Genetic improvement on growth rate could change allele
frequencies of Amy-1 (Zhang et al., 1993), but different
selective purposes were reported not to have caused any
allele frequency changes at the DNA level (Tixier-Boichard et al., 1996). However, the results from the investigations on microsatellite polymorphism in commercial
broiler and layer lines have shown that broilers are more
diverse than layers (Crooijmans et al., 1996b). Vanhala et
al. (1998) evaluated genetic variability of eight chicken
lines using microsatellite markers, and the highest (0.67)
and the lowest (0.29) mean heterozygosity per line was
TABLE 6. Allele number per locus in each population
Locus
Breed
HYB
XH
QYP
WC
YS
TH
BS
BF
GS
WR
AV
HL
Average
ADL0102
ADL0136
ADL0158
ADL0171
ADL0172
ADL0176
ADL0181
ADL0210
ADL0267
Average
12
9
10
9
8
8
10
10
10
12
10
8
9.67
14
15
14
17
14
6
12
9
14
4
13
8
11.67
4
4
5
17
14
4
4
9
14
5
13
4
5.08
12
13
15
18
13
12
15
9
19
6
12
9
12.75
8
8
8
9
9
8
10
9
11
5
9
7
8.42
7
7
8
10
10
11
5
7
11
4
4
8
7.67
12
8
9
9
5
8
9
9
12
9
8
7
8.75
10
6
6
11
7
6
8
9
9
6
6
5
7.42
14
15
10
14
12
11
16
15
13
10
10
10
12.50
10.33
9.44
9.44
11.67
9.33
8.22
9.89
9.00
12.00
6.78
8.44
7.33
9.32
1
HYB = Huiyang Bearded; XH = Xinghua; QYP = Qingyuan Partridge; WC = Wenchung; YS = Yangshan; TH = Taihe Silkies; BS = Black Silkies;
BF = Beijing Fatty; GS = Gushiu; WR = Recessive White Rock; AV = Avian Parental; HL = Hy-Line.
1470
ZHANG ET AL.
FIGURE 3. Allele frequency distribution. Only the allele frequencies that are different from eight of nine microsatellite loci in 12 chicken
populations are shown. HYB = Huiyang Bearded; XH = Xinghua; QYP = Qingyuan Partridge; WC = Wenchung; YS = Yangshan; TH = Taihe Silkies;
BF = Beijing Fatty; GS = Gushiu; BS = Black Silkies; WR = Recessive White Rock; AV = Avian Parental; HL = Hy-Line.
1471
GENETIC DIVERSITY OF CHINESE NATIVE CHICKENS
TABLE 7. Average heterozygosity (H) and its variance based on microsatellite polymorphism
H
Var.
HYB1
XH
QYP
WC
YS
TH
BS
BF
GS
WR
AV
HL
0.7632
0.0385
0.7069
0.0383
0.7497
0.0312
0.8614
0.0168
0.7789
0.0212
0.7504
0.0370
0.7692
0.0443
0.7860
0.0287
0.8485
0.0220
0.6289
0.0645
0.7421
0.0345
0.7232
0.0314
1
HYB = Huiyang Bearded; XH - Xinghua; QYP = Qingyuan Partridge; WC = Wenchung; YS = Yangshan; TH
= Taihe Silkies; BS = Black Silkies; BF = Beijing Fatty; GS = Gushiu; WR = Recessive White Rock; AV = Avian
Parental; HL = Hy=Line.
TABLE 8. Genetic distances among 12 breeds using microsatellite polymorphism
Breed
HYB1
XH
QYP
WC
YS
TH
BS
BF
GS
WR
AV
XH
QYP
WC
YS
TH
BS
BF
GS
WR
AV
HL
0.1842
0.2822
0.6041
0.4451
0.4257
0.4210
0.5776
0.4602
0.3596
0.3642
0.7913
0.1700
0.6003
0.4131
0.3193
0.3644
0.7248
0.4191
0.3358
0.3338
0.8325
0.4796
0.4570
0.2551
0.3930
0.4631
0.3622
0.3570
0.3431
0.6621
0.4070
0.7056
0.6539
0.3867
0.3689
0.7600
0.4707
0.9206
0.6078
0.5803
0.5596
0.4549
0.6886
0.5769
1.1356
0.2614
0.7104
0.5478
0.4766
0.4584
0.6020
0.5431
0.5868
0.5099
0.4396
0.6802
0.4336
0.8361
0.6701
1.0919
0.7525
0.4885
0.7892
0.3146
0.8293
0.7068
HYB = Huiyang Bearded; XH = Xinghua; QYP = Qingyuan Partridge; WC = Wenchung; YS = Yangshan; TH
= Taihe Silkies; BS = Black Silkies; BF = Beijing Fatty; GS = Gushiu; WR = Recessive White Rock; AV = Avian
Parental; HL = Hy-Line.
1
observed in the broiler and in White Leghorn of Makela, respectively.
In conclusion, Chinese native chickens were more variable than either the commercial broilers or layers. Therefore, there is substantial room for improvement within
Chinese breeds. Poultry husbandry is growing faster in
China than in many other countries in the world, and
chicken quality during production plays an important
role in poultry husbandry. The wide genetic diversity of
Chinese native chickens allows the scientists and farmers
future research and development for quality chicken
breeding in China.
ACKNOWLEDGMENTS
The authors acknowledge financial support from Hong
Kong Industrial Development Funds and Guangdong
Natural Science Foundation (970012), China. We are also
grateful to Poultry Coordinators of the US National Animal Genome Research Program for providing the Population Kit used in this project. We thank Hans H. Cheng
for his critical review of the manuscript and Charis Chan
for technical assistance.
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FIGURE 4. UPGMA dendrogram based on microsatellite polymorphism. HYB = Huiyang Bearded; XH = Xinghua; QYP = Qingyuan
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