MOLECULAR CHARACTERIZATION OF DESI AND “T&D” PIG
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Date
2010
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Birsa Agricultural University, Kanke, Ranchi, Jharkhand
Abstract
The “T&D” pig is a synthetic pig of cross of Tamworth (exotic breed) and Desi
(indigenous breed) found in the entire area of Jharkhand and Bihar and has been replacing
Desi pig since more than 15 years. The “T&D” pig has similarities as well as differences
with the Desi, yet it has no identity of its own on molecular basis.
The present study was undertaken on Molecular characterization of “T&D” and Desi
pig populations using genetic analysis of RAPD variation with 10 random primers. DNA was
extracted from 50 blood samples each for “T&D” and Desi pig (total of 100 samples).
Genomic DNA was isolated and purified from white blood cells using Proteinase K
digestion and standard phenol: chloroform extraction method.
Agarose gel electrophoresis for checking the quality of isolated genomic DNA
samples were done by diluting the DNA samples in ratio of 1:10. This was followed by
Polymerase chain reaction. PCR technique was used to amplify the chosen marker. For
this, optimization of PCR technique was followed by Agarose gel electrophoresis of PCR
amplified product of DNA. The amplified product were statistically analyzed to measure
the between and within population diversity. The genetic diversity within and between
population was analyzed as the observed and expected number of alleles and Shannon‟s
information Index using popgene software. Ewan‟s Watterson test was performed to test
the neutrality for RAPD markers, the statistics F (sum of square of allelic frequency ) and
limit (upper and lower) at 95% confidence region for the test were calculated using the
algorithm by mainly using 100 simulated samples and implemented in popgene software
package.
In order to quantify the percentage of molecular variance due to differences among
the difference among different populations and significance was tested by a non-random
permutation approach using AMOVA programme included in Arleqin software package.
Migration rate which showed the gene flow per generation was also found out. A
dendrogram by UPGMA method was constructed.
The result can be summarized as follows-
1. The gene or allele frequency for allele „0‟ ranged from 0 (SIGMA09-3) to 0.9583
(SIGMA07-1) for “T&D” pigs and from 0.234 (SIGMA09-3) to 0.9787(SIGMA09-
1) for Desi where as for allele „1‟ it ranged from 0.0417 (SIGMA07-1) to 1
(SIGMA09-3) for “T&D” and from 0.0213(SIGMA09-1) to 0.766 (SIGMA09-3)
for Desi pig.
2. Mean Shannon's information index measures the level of diversity which was
0.5343 for “T&D” and 0.6227 for Desi one. It is moderately higher. “T&D”
showed lower level of diversity than Desi one.
3. Nei's Gene diversity value (h) also known as average expected heterozygosity
ranged from 0.0 to 0.5 with overall mean 0.3625 in “T&D” pig and 0.0416 to
0.4991 with overall mean 0.4359 in Desi pig. “T&D” pig showed lower level of
heterozygosity within breed and also compared to Desi pig. It indicated that there
is heterozygosity deficit in both the population having more deficient in “T&D”
pigs.
4. Polymorphic information content (PIC) had the exactly same trend as the Nei's
Gene diversity.
5. All measures of genetic variations i.e. observed number of alleles, Shannon's
Information indicating high polymorphism across the loci, suggesting suitability of
these markers for genetic diversity studies in pig.
6. Taking into consideration, the genetic diversity within sample (Hs ) and overall
gene diversity (Ht) it was found that mean Hs was 0.3992 which is lesser that mean
Ht i.e. 0.4338. Genetic diversity in “T&D” pig is moderately lower than the Desi
pig.
7. Mean Gst value (population subdivision index) is low (0.0798) and mean Nm (gene
flow) is high (5.7643) which showed the prominent gene flow between the two
breeds. The “T&D” pig is a synthesized population involving an exotic Tamworth
and Desi pig population, the higher gene flow is not an alarming condition.
8. Similarly Nei‟s standard genetic distance based on allele frequency represented a
low degree of genetic divergence among the two pig breed showing lower level of
genetic variation between the populations.
9. A phylogenetic tree (Dendrograme) was built based on Nei‟s standard genetic
distance. The tree showed that there was clear clustering or grouping corresponding
to both the groups with some intermixing trend.
10. In neutrality test for selected primers (or loci), Locus SIGMA08-1 in “T&D” pig
and the locus SIGMA06-3 in Desi pig were found not neutral or may be linked to
some selective traits.
Description
MOLECULAR CHARACTERIZATION OF DESI AND “T&D” PIG
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