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Animal Molecular Breeding 2014, Vol. 4, No. 1, 1-5
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2
their position in the available reference sequence
(Table 1). All the SNPs were observed to be novel in
Indian sheep and were in the heterozygous condition.
Six transitions and three transversions were observed.
Two of the SNPs
DGAT1
g.355G > T and
FABP3
g.4993A > G were in the coding region whereas the
remaining SNPs were observed in the introns. One of
the novel SNPs (
DGAT1
g.355G > T) in the exon 1
region was nonsynonymous leading to a change in
the amino acid (Asp to Tyr).
Table 1 Estimates of observed heterozygosity (Ho), total expected heterozygosity (Ht), allele and genotype frequencies across the
identified SNPs in Indian sheep
Locus
SNP
Ho
Ht
Allele frequency
Genotype frequency
Ref. Sequence
allele 1
allele 2
11
12
22
CAPN4
g.44C>T
0.435
0.569
0.603
0.397
0.388
0.429
0.183
AF309634
CAST
g.131A>T
0.256
0.367
0.244
0.756
0.122
0.244
0.634
AF016006
g.260A>G
0.282
0.274
0.171
0.829
0.024
0.293
0.683
g.326A>G
0.259
0.226
0.134
0.866
0
0.265
0.732
g.417A>G
0.327
0.303
0.817
0.183
0.659
0.317
0.024
DGAT1
g.355G>T
0.832
0.486
0.587
0.413
0.174
0.826
0
EU178818
g.434C>G
0.071
0.069
0.967
0.033
0.934
0.066
0
FABP3
g.4993A>G 0.368
0.454
0.340
0.660
0.180
0.320
0.500
NC_019459
g.5034A>G 0.368
0.454
0.660
0.340
0.500
0.320
0.180
Mean
0.352
0.328
The heterozygosity as well as allele and genotype
frequencies for all SNPs are given in Table 1. The
observed heterozygosity values varied from 0.071 to
0.832, while the expected heterozygosity ranged from
0.069 to 0.569. The minor allele frequency was >
0.033 across all SNPs. The major allele was near
fixation at
DGAT1
g.434C > G SNP. The homozygous
genotypes AA in
CAST
g.326A > G, TT in
DGAT1
g.355G > T and GG in
DGAT1
g.434C > G were not
observed in the Indian sheep investigated.
The number of haplotypes per locus (Hap.No.),
haplotype diversity (Hd) and nucleotide diversity (Pi)
for all the investigated loci are given in Table 2. The
CAST
locus was observed to be the most diverse with
maximum number of haplotypes (10), while
CAPN4
showed two haplotypes only. The average haplotype
and nucleotide diversity across all loci were 0.545 and
0.206 respectively.
Table 2 Haplotype diversity across candidate genes for mutton
quality traits in Indian sheep
Locus
Hap. No.
Hd
Pi
F
ST
Nm
CAPN4
2
0.334
0.073
0.121
1.66
CAST
10
0.796
0.248
0.091
1.86
DGAT1
3
0.417
0.112
0.283
0.63
FABP3
3
0.632
0.392
0.200
1.00
Mean
0.545
0.206
0.174
1.29
Note: Hap No-Haplotype number; Hd-haplotype diversity;
Pi-nucleotide diversity; F
ST
-genetic differentiation among
subpopulations; Nm-gene flow
The F
ST
statistic (Weir 1996), which measures the
genetic differentiation between populations (by
estimating the genetic variance among populations
divided by total genetic variance of the entire
population) revealed low differentiation (0.174)
among the sheep populations investigated. The
average gene flow between the breeds was 1.29.
2 Discussion
Differences in mutton quality traits in sheep have been
attributed to genetic variations in relevant genes (Kijas
et al. 2007; Hickford et al. 2010). In this study,
detection of novel nucleotide variations in Indian
sheep, at candidate genes for mutton quality, known to
be polymorphic, reveal availability of greater genetic
diversity at these loci.
Polymorphism in the
CAPN4
gene has also been
reported in Karakul sheep breed by SSCP analysis
(Shahroudi et al. 2006), but these have not been
associated with any production trait. The detection of
four new SNPs in the
CAST
gene locus, in our study,
reflects that this locus habours substantial diversity.
These results are supported by previous studies where
two alleles were reported in the
CAST
gene using the
RFLP technique (Palmer et al. 1998; Shahroudi et al.
2006). Additionally, four alleles have been identified
in the intron 12 region in New Zealand crossbred
sheep by SSCP (Byun et al. 2009). The
FABP3
and