915

Population Structure and Genetic Bottleneck Analysis of Ankleshwar

Poultry Breed by Microsatellite Markers
A. K. Pandey*, Dinesh Kumar, Rekha Sharma, Uma Sharma, R. K. Vijh and S. P. S. Ahlawat
National Bureau of Animal Genetic Resources, P. O. Box 129, Karnal-132 001, India
ABSTRACT : Genetic variation at 25 microsatellite loci, population structure, and genetic bottleneck hypothesis were examined for
Ankleshwar poultry population found in Gujrat, India. The estimates of genetic variability such as effective number of alleles and gene
diversities revealed substantial genetic variation frequently displayed by microsatellite markers. The average polymorphism across the
studied loci and the expected gene diversity in the population were 6.44 and 0.6700.144, respectively. The population was observed to
be significantly differentiated into different groups, and showed fairly high level of inbreeding (f = 0.2400.052) and global
heterozygote deficit. The bottleneck analysis indicated the absence of genetic bottleneck in the past. The study revealed that the
Ankleshwar poultry breed needs appropriate genetic management for its conservation and improvement. The information generated in
this study may further be utilized for studying differentiation and relationships among different Indian poultry breeds. (Asian-Aust. J.
Anim. Sci. 2005. Vol 18, No. 7 : 915-921)
Key Words : Ankleshwar, Bottleneck, Genetic Diversity, Microsatellites, Poultry

INTRODUCTION
The ankleshwar poultry breed (Gallus gallus) is known
to be a breed of Gujarat, India and its native tract is
Bharuch (21.41 N latitude and 73.01 E longitude) and
Narmada districts (21.38 N latitude and 73.02 E longitude).
The name of the breed is derived from the area
Ankleshwar of Bharuch district of Gujarat. The breeding
area is also extended to Jumbusar, Zagadia, Bharuch,
Hansot and Valia of Bharuch and Dediapada, Rajpipla,
Tilakwada and Nadod of Narmada district of Gujarat. These
poultry birds are being kept mainly by tribes under
backyard poultry farming as a livelihood source of income.
These birds are maintained without vaccination and
medication, and have reasonable feed efficiency as they
survive on 25-30 gms of grains, scavenging and maintain
excellent fertility (GAU Report, 2003). In spite of its unique
characteristics, there is a lack of concern for the
conservation and improvement of this breed under field
conditions. However, there is worldwide recognition of the
need for the conservation of livestock diversity (FAO, 1995)
and for characterization of breeds and populations including
their genetic differentiation and relationships. These unique
characteristics are result of evolutionary forces and their
interactions over longer period of time. However, these
adaptation and unique characteristics might have been
diluted due to intermixing, sub- structuring and/or
consequent genetic drift in the population over time.
Therefore, an investigation for genetic variation within the
breed, and its structure may help to evaluate how likely
* Corresponding Author: A. K. Pandey. Tel: +91-0184-2267918,
Fax: +91-0184-2267654, E-mail: ashwni@yahoo.com
Received October 7, 2004; Accepted February 19, 2005

these factors are operating, and present genetic information

to be used in the conservation and improvement of this
unique poultry breed.
Of the many genetic markers now available,
microsatellite loci are best suited for answering these
questions (Goldstein and Pollock, 1997) because of their
high variability, high mutation rate, large number,
distribution throughout the genome, codominant inheritance
and neutrality with respect to selection (Boyce et al., 1996).
They are very useful to analyze the degree and pattern of
genetic variability within and differences betweenpopulations (Chenyambuga et al., 2004; Li et al., 2004;
Wang et al., 2004), genetic differentiation between closely
related species (Sun et al., 2004) and parentage verification
(Cho and Chol, 2004). The objectives of this study were to
study the estimates of genetic variability in the Ankleshwar
breed of poultry, its population structure, and to evaluate the
genetic bottleneck hypothesis in this breed. The estimated
population of this poultry breed is approximately 5,000
(GAU Report, 2003).
MATERIAL AND METHODS
Molecular techniques
Forty-blood samples were collected from genetically
unrelated birds from its breeding tract Bharuch and
Narmada districts where these birds are confined. Out of 40
blood samples 20 were collected from Ankleshwar,
Jumbusar and Zagadia of Bharuch district and rest 20 from
Dediapada, Tilakwada and Nadod of Narmada district of
Gujarat. Approximately 3 ml blood was collected from each
animals wing vein in vacutainer containing anticoagulant.
Genomic DNA was isolated from blood samples as per the

PANDEY ET AL.

916

Table 1. Details of the microsatellite used in the study

S.N.
Loci
Chr.No.
Primer Sequence (5-3)
1

MCW41

C3

CCCAATGTGCTTGAATAACTTGGG
CCAGATTCTCAATAACAATGGCAG
2
MCW48
C4
CGTATAGGAGGGTTTCTGCAGGGA
AAGGAGGAACGCACCGCACCTTCT
3
MCW49
C6E1
AGCGGCGTTGAGTGAGAGGAGCGA
TCCCCAACCCGCGGAGAGCGCTAT
4
MCW59
C1E2
AAGTGCCTTTGCTATCCTGATTGG
AACTCCTATTGTGCAGCAGCTTAT
5
MCW4
3
GGATTACAGCACCTGAAGCCACTA
AAACCAGCCATGGGTGCAGATTGG
6
MCW5
4
ACCTCCTGCTGGCAAATAAATTGC
TCACTTTAGCTCCATCAGGATTCA
7
MCW14
6
AAAATATTGGCTCTAGGAACTGTC
ACCGGAAATGAAGGTAAGACTAGC
8
MCW16
3
ATGGCGCAGAAGGCAAAGCGATAT
TGGCTTCTGAAGCAGTTGCTATGG
9
ADL102
10
TTCCACCTTTCTTTTTTATT
GCTCCACTCCCTTCTAACCC
10
ADL136
9
TGTCAAGCCCATCGTATCAC
CCACCTCCTTCTCCTGTTCA
11
ADL158
10
TGGCATGGTTGAGGAATACA
TAGGTGCTGCACTGGAAATC
12
ADL171
8
ACAGGATTCTTGAGATTTTT
GGTCTTAGCAGTGTTTGTTT
13
ADL176
2
TTGTGGATTCTGGTGGTAGC
TTCTCCCGTAACACTCGTCA
14
ADL210
11
ACAGGAGGATAGTCACACAT
GCCAAAAAGATGAATGAGTA
15
MCW7
1
AGCAAAGAAGTGTTCTCTGTTCAT
ACCCTGCAAACTGGAAGGGTCTCA
16
HUJ7
5
CATAAACTAAAGTCTCAACAC
TTCTTCCACCACTCTTGCTA
17
HUJ6
3
GGAACATGTAGACAAAAGCA
AGCAGTCCATTTCACAGCCA
18
HUJ2
17
CATCTCACAGAGCAGCAGTG
GAATCCTGGATGTCAAAGCC
19
HUJ12
8
GTCTCATGCTATGAGAGTGG
CCTCTGGTTGAATCAGTCTG
20
ADL20
1
GCACTCAAAAGAAAACAAAT
TAGATAAAAATCCTTCCCTT
21
ADL44
12
AAGTGGTTTATTGAAGTAGA
CTGTGGTGTTGCGTTAGTTG
22
ADL40
6
TTTCCCCAGATTTACAACTT
GCCAGTGATACTCCAGCAGC
23
ADL39
15
GCTACAACGCTTCAAACCTG
ACAAACAAACCAAAAAACCT
24
ADL34
E47
AACCTAAAAACTCCTGCTGC
W24
GGGAACCTGTGGGCTGAAAG
25
ADL23
5
CTTCTATCCTGGGCTTCTGA
CCTGGCTGTGTATGTGTTGC
Chr. No.: Chromosome number; Ta: annealing temperature (C).

method described by Sambrook et al. (1989) and Pandey et

al. (2002). A battery of 25 microsatellite markers (Table 1)
was selected based on the guidelines of ISAG & FAOs
DADIS programme to generate data in a panel of 40 birds.
Polymerase Chain Reaction (PCR) was carried out on about
50-100 ng genomic DNA in a 25 l reaction volume. The
reaction mixture consisted of 200 M each of dATP, dCTP,
dGTP and dTTP, 50 mM KCl, 10 mM Tris-HCl (pH 9.0),
0.1% Triton X-100, 1.5 mM MgCl2, 0.75 unit Taq DNA

Type of repeat

Ta

(T)23

55

Crooijmans et al. (1995)

(TG)17

55

Crooijmans et al. (1995)

(GCA)n

55

Crooijmans et al. (1995)

(T)25

55

Crooijmans et al. (1995)

(CA)28

55

Crooijmans et al. (1995)

(TG)6AA(TG)6
(A)15(GA)2(GAA)7
(CA)n

55

(GT)15

50

(GT)18

47

Crooijmans and Van Kampen

(1994)
Crooijmans and Van Kampen
(1994)
Crooijmans and Van Kampen
(1994)
Cheng and Levin (1995)

(TG)10TC(TG)10

52

Cheng and Levin (1995)

(CA)12

52

Cheng and Levin (1995)

(TG)18

46

Cheng and Levin (1995)

(GT)12

52

Cheng and Levin (1995)

(CA)n

46

Cheng and Levin (1995)

(TG)5(TA)14

60

(CA)10

60

(CA)15

60

(CA)10

60

(AC)n

60

(AC)15

55

(CA)n

60

(CA)n

49

(CA)n

55

(TG)n

50

Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)
Wimmer et al.
(2000)

(GT)12

55

References

polymerase and 4 ng/l of each primer (Sigma Genosys)

using PTC-200 PCR machine (M J Research). At the end of
the reaction, 5.0 l of stop dye (95% formamide, 0.25%
bromophenol blue and 0.25% xylene cyanol) was added and
6 l of PCR products were loaded on to a 2% agarose gel,
electrophoresed and visualized over UV light after ethidium
bromide staining to detect the amplification.
The PCR products were resolved on 6% denaturing
polyacrylamide gels (Sequi-Gen GT System, Bio-Rad),

GENETIC ANALYSIS OF ANKLESHWAR POULTRY

X174 Hinf-I digest was used as a size standard for sizing
PCR products. To visualize the PCR products gels were
stained using silver staining (Bassam et al., 2001) and dried
between sheets of cellophane paper. The genotypes were
scored manually. The size of the alleles was calculated
online using INCHWORM programme which estimates
the length of the molecule, based on the electrophoretic
mobility (http://www.molecularworkshop.com/programs/in
chworm.html).
Statistical analysis
For 25 microsatellites loci analyzed, observed and
expected heterozygosity estimates were calculated after
Levene (1949) and Nei (1973) as implemented in
POPGENE software (Yeh et al., 1978). The observed and
effective numbers of alleles (Kimura and Crow, 1964) were
also calculated using POPGENE software.
The tests for deviation from Hardy-Weinberg
equilibrium were derived using the exact tests of
POPGENE. Heterogeneity of deviations from Hardy-

917

Weinberg equilibrium among the microsatellite loci was

examined by treating the deviations as correlation
coefficient and tested accordingly (Barker et al., 2001). As
samples were obtained from different localities (two
districts), deviations from Hardy-Weinberg equilibrium in
the population could be due to genetic differences between
subpopulations and a consequent Wahlund effect. Given the
observed allele frequencies in each subpopulation, the
expected heterozygote deficit due to Wahlund effect can be
computed (Li, 1976). Expressing this as a percentage of
observed heterozygote deficit then measures the
contribution of Wahlund effect to the observed heterozygote
deficit. Heterozygote deficiencies were expressed as D =
[H0-HE]/HE where H0 and HE are the observed and expected
frequency of hetrozygotes, respectively.
Tests for pair wise linkage (genotypic) disequilibrium
among the microsatellite loci were done using FSTAT
version 2.9.3 an update version 1.2 (Goudet, 1995) for 25
microsatellite loci whose genotypes were determined
directly. F-statistics were determined after Weir and

Table 2. Measures of genetic variation in Ankleshwar poultry population

SN

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27

Locus

ADL34
ADL39
ADL44
ADL102
ADL210
MCW49
ADL20
HUJ7
MCW7
MCW48
MCW4
ADL176
MCW59
MCW16
HUJ6
ADL171
HUJ12
ADL158
ADL136
MCW14
ADL40
MCW05
ADL23
MCW41
HUJ2
Mean
St. Error

Sample
size

40
40
40
39
38
40
40
38
39
38
40
38
40
40
36
37
40
38
40
39
36
34
39
40
38
38.5

Observed
Effective Shannons
Size range
number
number information
(base pairs)
of alleles
of alleles
index

9
4
8
8
5
6
4
5
4
6
4
5
4
7
9
11
9
5
9
5
4
8
8
5
9
6.44
2.162

118-146
152-176
159-195
97-127
115-131
115-130
95-105
150-170
295-317
187-207
168-200
188-210
156-174
133-155
101-131
86-122
112-148
188-198
132-178
174-188
195-207
231-291
164-182
152-172
124-142

5.071
2.617
5.031
3.336
2.085
2.322
2.714
2.403
2.980
3.856
1.437
3.703
3.313
3.980
2.536
5.991
6.387
2.415
5.405
2.602
2.123
6.116
4.844
1.570
5.040
2.910
1.246

1.844
1.143
1.764
1.489
0.999
1.191
1.111
1.118
1.205
1.495
0.609
1.436
1.277
1.593
1.350
2.093
1.999
1.042
1.871
1.105
0.890
1.919
1.803
0.773
1.868
1.400
0.412

Heterozygositya
PIC

0.777
0.567
0.773
0.653
0.479
0.537
0.558
0.536
0.604
0.699
0.283
0.686
0.642
0.717
0.578
0.829
0.825
0.505
0.792
0.541
0.447
0.816
0.769
0.346
0.780
0.623

Observed

Expected

Neis

0.650
0.700
0.525
0.410
0.342
0.525
0.850
0.263
0.692
0.763
0.200
0.816
0.450
0.575
0.528
0.216
0.675
0.605
0.475
0.539
0.389
0.765
0.333
0.300
0.579
0.527
0.187

0.813
0.626
0.811
0.709
0.527
0.577
0.640
0.592
0.675
0.751
0.308
0.740
0.707
0.758
0.614
0.845
0.854
0.594
0.825
0.624
0.536
0.849
0.804
0.369
0.812
0.678
0.146

0.803
0.618
0.801
0.700
0.520
0.569
0.632
0.584
0.666
0.741
0.304
0.730
0.698
0.749
0.606
0.833
0.843
0.586
0.815
0.616
0.529
0.837
0.794
0.365
0.802
0.670
0.144

Effective number of alleles [Kimura and Crow (1964)].

Shannons Information index [Lewontin (1972)].
a
Expected heterozygosity were computed using Levene (1949) and Neis (1973) expected heterozygosity.
b
Heterozygote deficiencies were expressed as D = (Ho-He)/He, refer the text for symbols used.
c
f-values (Weir and Cocheran 1984) given for significant tests after Bonferroni corrections.
* Wahlund effects varied from 0.006 to 0.028%; PIC (polymorphic information content).

Heterozygote
deficiencyb

-0.2004
0.1182
-0.3526
-0.4217
-0.3510
-0.0901
0.3281
-0.5320
0.0251
0.0159
-0.3506
0.1027
-0.3635
-0.2414
-0.1400
-0.7443
-0.2096
0.0185
-0.4242
-0.1362
-0.2742
-0.0989
-0.5858
-0.1869
-0.2869

f-valuec

0.203
0.356
0.425
0.354
0.558*
-*
0.353
0.366
0.244
0.142
0.747
0.212
-*
0.428
0.278
0.589
0.29

918

PANDEY ET AL.

Table 3. F-statistics analyses for 25 microsatellite loci in Ankleshwar poultry population

Locus*
f (FIS)
F (FIT)
Relat
(FST)
ADL34
0.209
0.017
0.195
0.028
ADL39
-0.127
-0.011
-0.114
-0.026
ADL44
0.353
-0.01
0.359
-0.014
ADL102
0.472
0.168
0.365
0.228
ADL210
0.357
0.008
0.352
0.011
MCW49
0.115
0.055
0.063
0.099
ADL20
-0.318
0.026
-0.353
0.076
HUJ7
0.56
0.008
0.557
0.01
MCW7
-0.029
-0.007
-0.022
-0.014
MCW48
0.029
0.092
-0.07
0.18
MCW4
0.429
0.239
0.249
0.334
ADL176
-0.097
0.014
-0.113
0.032
MCW59
0.375
0.028
0.357
0.04
MCW16
0.248
0.01
0.24
0.016
HUJ6
0.14
-0.007
0.145
-0.012
ADL171
0.746
-0.002
0.747
-0.002
HUJ12
0.206
-0.014
0.217
-0.023
ADL158
0.026
0.092
-0.073
0.179
ADL136
0.435
0.025
0.42
0.035
MCW14
0.133
-0.012
0.143
-0.021
ADL40
0.302
0.069
0.25
0.107
MCW05
0.112
0.027
0.088
0.048
ADL23
0.605
0.084
0.569
0.104
MCW41
0.192
0.006
0.187
0.01
HUJ2
0.315
0.073
0.262
0.11
Mean
0.240
0.036
0.212
0.058
(SE)
0.052
0.010
0.053
0.017

Relatc
-0.486
0.205
-1.12
-1.151
-1.085
-0.135
0.522
-2.511
0.044
0.131
-0.664
0.203
-1.111
-0.632
-0.34
-5.9
-0.556
0.135
-1.449
-0.335
-0.667
-0.193
-2.643
-0.461
-0.708

Rst
0.028
-0.025
-0.012
-0.020
0.015
0.050
-0.007
-0.032
-0.019
-0.023
0.040
-0.012
-0.024
-0.022
0.061
-0.025
-0.027
0.088
-0.017
-0.005
0.196
-0.019
0.041
-0.017
-0.010
-0.002

* Refer to the text for F symbols.

Relat, an estimator of the average relatedness of individuals within samples when compared to whole (Queller and Goodnights, 1989).
Relatc estmates the inbreeding corrected relatedness (Pamilo, 1985).
a
Standard errors: estimate from jackknife over loci and significance from t-test using these estimates, p<0.05.
Rst an estimator of relative genetic differentiation based on fraction of total variance of allele size between two subpopulations.

Cockerham (1984) as used in F-Stat software with

Jackknifing procedure applied over loci in deriving
significance levels. These parameters of population
structure are defined as the correlations between pairs of
genes (i) within individuals (F) (ii) between individuals in
the same population (), and (iii) within individuals within
populations (f), and are analogous to Wrights (1978) FIT,
FST and FIS , respectively.
Finally the bottleneck hypothesis was investigated using
BOTTLENECK 1.2.01 (Cornuet and Luikart, 1996). The
BOTTLENECK tests for the departure from mutation drift
equilibrium based on heterozygosity (not hetrozygote),
excess or deficiency. This does not require information on
historical population sizes or level of genetic variations. It
requires only measurement of allele frequencies from 5-20
polymorphic loci in a sample of approximately 20-30
individuals. The bottleneck compares heterozygosity
expected (HE) at Hardy-Weinberg equilibrium to the
heterozygosity expected (Heq) at mutation drift equilibrium
in same sample, that has the same size and the same number

of alleles. All the three models of mutation were used to

calculate Heq: the strict one stepwise mutation model (Ohta
and Kimura, 1973), the infinite allele model (Kimura and
Crow, 1964) and two-phase model (Di Rienzo et al., 1994).
RESULTS AND DISCUSSION
Various measures of genetic variation are presented in
the Table 2. The F-statistics estimates are presented in Table
3.
The number of alleles observed across the microsatellite
loci studied varied from 4(ADL39, ADL20, MCW7,
MCW4, MCW59 and ADL40) to 11 (ADL171) with an
overall mean of 6.442.162 (Table 2). The observed number
of alleles across the loci was more than the effective
number of alleles (1.437 to 6.387) as per expectations. The
Shannon information index and polymorphic Information
Content (PIC) showed that most of the loci were highly
informative indicating the high polymorphism across the
loci with an overall mean of 1.400 and 0.623, respectively.

GENETIC ANALYSIS OF ANKLESHWAR POULTRY

919

Table 4. Mutation-drift equilibrium, heterozygosity excess/deficiency under different mutation models in Ankleshwar poultry population
Methods
Models
Sign test
Standardized
Wilcoxon test
IAM
Hee = 14.84
T2 = 1.346
P (one tail for H deficiency): 0.96665
A.
Hd = 19
p = 0.08911
Frequency
P (one tail for H excess): 0.03549
He = 6
method
P (two tails for H excess and deficiency): 0.07098
P = 0.06480
TPM
Hee = 14.89
P (one tail for H deficiency): 0.42660
T2 = -1.287
Hd = 12
P = 0.9910
P (one tail for H excess): 0.58375
He = 13
P (two tails for H excess or deficiency): 0.85320
P = 0.28333
P (one tail for H deficiency): 0.00279
SMM
Hee = 14.72
T2 = -5.510
p = 0.00000
P (one tail for H excess): 0.99746
Hd = 17
P (two tails for H excess or deficiency): 0.00558
He = 8
P = 0.00603
P (one tail for H deficiency): 0.88482
B.
IAM
Hee = 14.76
T2 = 0.452
p = 0.32551
P (one tail for H excess): 0.12053
Heterozygosity
Hd = 9
P (two tails for H excess and deficiency): 0.24107
method
He = 16
P = 0.38685
P (one tail for H deficiency): 0.07424
TPM
Hee = 14.79
T2 = -2.566
p = 0.00514
P (one tail for H excess): 0.92954
Hd = 16
P (two tails for H excess or deficiency): 0.14848
He = 9
p = 0.01648
P (one tail for H deficiency): 0.00004
SMM
Hee = 14.80
T2 = -7.427
p = 0.00000
P (one tail for H excess): 0.99996
Hd = 19
P (two tails for H excess or deficiency): 0.00009
He = 6
p = 0.00038
Parameters for T.P.M: Variance = 30.00 Proportion of SMM in TPM = 70.00%; Estimation based on 1,000 replications; Hee: Heterozygosity excess
expected; Hd: Heterozygosity deficiency; He: Heterozygosity excess; P: Probability; IAM: Infinite allele model, TPM: Two phase model, SMM: Stepwise
mutation model.

The average observed heterozygosity was less than the

expected (Table 2). The average expected gene diversity
(Nei, 1973) within the population ranged from 0.304
(MCW4) to 0.843 (HUJ 12) with an overall mean of
0.6700.144. Fourteen out of total 25 loci studied showed
significant deviations from Hardy Weinberg Equilibrium.
All 14 loci showed significant heterozygote deficiency in
the Ankleshwar poultry population. Wahlund effects
accounted for 0.006 to 0.0281% of the observed
heterozygote deficiency at 3 loci.
Significant linkage disequilibrium was detected in the
overall microsatellite data for 19 out of 300 loci pairs. The
overall means for the F-statistics were significantly
different from zero. The relatedness among the individuals
in the given sample was also significantly different from
zero. The overall Rst, an estimator of genetic differentiation
among these samples was -0.002 (Table 3).
Bottleneck analysis as depicted in Table 4 indicates that
the observed heterozygosity excess (He) is less than the
expected excess heterozygosity (Hee) in 1,000 simulations
based on allele frequency and heterozygosity. Here all the 3
models (IAM, TPM and SMM) in both the methods have
less He than Hee except one case of IAM in heterozygosity
method (He = 16 and Hee = 14.76). The lower magnitude of
He with their respective Hee in all the cases (except one)
reflects absence of genetic bottleneck in the past population

dynamics of Ankleshwar poultry.

When a population experiences a reduction of its
effective size, the allele number is reduced faster than the
heterozygosity, i.e. the observed heterozygosity is larger
than the heterozygosity expected from the observed allele
number when the locus is at mutation-drift equilibrium. In
addition, qualitative graphical method of Luikart et al.
(1998) was used to visualize the allele frequency spectra.
The microsatellite alleles were classified in to 10 frequency
classes, which allow to check whether the distribution
followed the normal L-shaped (Figure 1) form, where
alleles with low frequencies (0.01-0.1) are the most
abundant. This reflects that the population had not
undergone bottleneck at least in the recent past 15-20
generations.
The Ankleshwar poultry breed had substantial genetic
variation based on its gene diversity and average number of
alleles per locus. The average genetic variation (0.670)
observed in this study was in the range of the values
reported for other Indian breeds of poultry viz. Kadaknath
(0.66), Aseel (0.45), Frizzle-Fowl (0.71), North East (0.56),
Nicobari (0.64) and Miri (0.68) (Wimmer et al., 2000;
Pandey et al., 2002). The average genetic variation
observed in this population was of similar magnitude (0.490.77) as reported in African, Asian and South American
chicken (Wimmer et al., 2000).

PANDEY ET AL.

920
1.2

Allele frequencies

0.8

0.6

0.4

0.2

0
1

10 11

Allele frequency class

Figure 1. L-shaped mode-shift graph showing lack of bottleneck
in the population.

The f (FIS) estimates across 15 out of 25 studied loci

were significantly positive (significant heterozygote deficit)
based on table wide randomizations (p<0.05). The f
estimates ranged from 0.142 to 0.589 with an average of
0.2400.052 (Table 3).
The significant heterozygote deficiency found in
ankleshwar population of poultry could be due to one or
more of the following reasons: segregation of nonamplifying (null) alleles, Wahlund effects, scoring biases
(heterozygotes scored incorrectly as homozygotes) or
inbreeding. Distinguishing among these generally is
difficult (Christiansen et al., 1974). However, null alleles
are most unlikely to be segregating at all the loci. Similarly,
scoring bias may be possible for a few loci but not for all
loci. Wahlund effects (localities with non-subpopulations)
do account for 0.006 to 0.028 of the observed heterozygote
deficit for >50% of the loci showing significant
heterozygote deficiency. There is strong inbreeding in the
population as indicated by high value of f estimate (0.240),
presumably resulting from the unplanned and
indiscriminate mating prevalent in the breeding tract
leading to small effective population size/or mating
between relatives and consequent genetic drift. Therefore,
inbreeding and Wahlund effects may be most reasonable
causes of heterozygote deficit. The non-random association
of alleles across the loci was also compatible with
genotypic disequilibrium observed in the population. The
samples (taken from each of the two districts) were

substantially differentiated from each other as indicated by

the term theta () and Rst estimates. These estimates are
also in accordance with measures of Wahlund effect in the
study. FIT estimates revealed significant deviations
(heterozygote deficit) from Hardy-Weinberg equilibrium
across most of the loci studied. These estimates showed
global heterozygote deficit in the population after applying
the Bonferroni corrections to different tests.
The results of this study indicated that there is
substantial genetic variation and polymorphism across
studied loci. The Ankleshwar poultry population was
neither in Hardy-Weinberg equilibrium nor in mutation drift
equilibrium. The population appears to be divided into
significantly differentiated small subpopulations, which
resulted in mating among close relatives leading to high
level of inbreeding observed in this study. Appropriate
breeding strategies should therefore be designed under field
conditions for its conservation and improvement of its
unique attributes maintained without vaccination and
medication, reasonable feed efficiency as they survive on
availability of 25-30 gms of grains, scavenging and
maintaining excellent fertility 91.34%, (GAU Report, 2003)
under the given management and climatic conditions of the
region.
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