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Within population inbreeding estimate (Fis) for
the investigated loci was -0.059. The estimates for
each locus are presented in Table 3. The values
ranged from –0.158 (TGLA122) to 0.047
(ILSTS05). Ten loci revealed negative Fis values.
The heterozygote deficiency may be a result of
inbreeding. The high genetic diversity observed in a
breed could be explained by overlapping
generations, mixing of populations from different
geographical locations, natural selection favoring
heterozygosity or subdivision accompanied by
genetic drift. Isolation, founder effects, genetic drift
and different selection pressures realized by
farmers in each population may have played major
role in differentiation of Iranian goats.
Any population that experienced a recent
bottleneck will show higher than expected
(equilibrium) heterozgosity for a large number of
loci. Microsatellite data were also subjected to
statistical analysis to test whether the populations
have undergone recent genetic bottleneck. Because
historical population sizes and levels of genetic
variation are seldom known, methods for detecting
bottlenecks in the absence of historical data would
be useful. Cornuet and Luikart, (1996) described
the quantitative methods suitable for analysis of
microsatellite data for detection of recent
bottlenecks in (100-200) generations.
Table 2. Number of alleles (Observed and
effective), Shannon's Information index and
Polymorphic Information Content for KJK goats
Locus name Na Ne I PIC
BM121 8 6.375 1.944 0.82
BM4621 9 6.007 1.969 0.81
ILSTS005 8 4.42 1.729 0.75
ILSTS022 7 4.321 1.606 0.73
LSTS029 7 4.579 1.702 0.75
ILSTS033 8 5.742 1.9 0.8
ILSTS034 7 6.267 1.89 0.82
LSCV36 9 6.367 1.988 0.82
MAF64 4 3.272 1.262 0.64
OarAE133 3 2.355 0.929 0.48
OarFCB304 9 6.391 2.014 0.83
OarJMP23 8 4.751 1.775 0.76
TGLA122 11 6.973 2.164 0.84
Mean 7.538 5.217 1.759 0.76
Na: Observed number of alleles; Ne: Effective number of
alleles; I: Shannon's Information index; PIC:
Polymorphic Information Content.
Bottleneck analysis of KJH goats 65
To determine whether a population exhibits
a significant number of loci with gene
diversity excess, there are three tests,
namely a "sign test", a "standardized
differences test" (Cornuet and Luikart,
1996) and a "Wilcoxon sign-rank test"
(Luikart et al., 1997).
Table 3. Observed and expected
heterozygosity with p-value, Fis value for
each microsatellite locus and mean estimate
of different parameters for KJK goats
Locus
Ho He Fis HWE
name
BM121 0.902 0.852 -0.06 ***
BM4621 0.804 0.842 0.045 ***
ILSTS005 0.745 0.781 0.047 NS
ILSTS022 0.863 0.776 -0.113 NS
ILSTS029 0.902 0.789 -0.144 ***
ILSTS033 0.902 0.834 -0.082 ***
ILSTS034 0.941 0.849 -0.11 ***
LSCV36 0.843 0.851 0.01 ***
MAF64 0.725 0.701 -0.035 NS
OarAE133 0.667 0.581 -0.149 NS
FCB304 0.882 0.852 -0.036 ***
OarJMP23 0.804 0.797 -0.008 ***
TGLA122 1 0.865 -0.158 ***
Mean 0.845 0.798 -0.059
NS: Not Significant; ***: Significant at the
0.1% level
All the three models of microsatellite
evaluation Infinite Allele Model (IAM),
Stepwise Mutation Model (SPM) and Two
Phase Model (TPM) were utilized for the
purpose. In a population at mutation-drift
equilibrium (i.e., the effective size of which
has remained constant in the recent past),
there is approximately an equal probability
that a locus shows gene diversity excess or a
gene diversity deficit. The first test suffers
from low statistical power. The second test
is not very useful since it requires at least 20
polymorphic loci. The Wilcoxon test
provides relatively high power and it can be
used with as few as four polymorphic loci
and any number of individuals (15-40
individuals and 10-15 polymorphic loci is
recommend to achieve high power. So, the
null hypothesis was again rejected under
IAM for the sign test. Standard difference