Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds
Loading...
Date
2017-05
Journal Title
Journal ISSN
Volume Title
Publisher
Veterinary World
Abstract
Aim: The present study was thus undertaken to analyze the genetic diversity of Kilakarsal and Vembur sheep breeds using
single-nucleotide polymorphism (SNP) markers within Toll-like receptor (TLR) 3, 5, 6, 9, and 10 genes.
Materials and Methods: Competitive allele-specific polymerase chain reaction (PCR)-based end-point genotyping was
performed using real-time PCR to type the SNPs. Allele discrimination module implemented in real-time PCR was utilized
to call the genotypes based on fluorescence intensity recorded for each of the two alleles. Basic diversity indices, namely,
gene frequencies, observed heterozygosity, expected heterozygosity, and inbreeding coefficient (FIS), and testing for Hardy–
Weinberg equilibrium (HWE) were estimated using package for elementary analysis of SNP data software program.
Results: Of the 25 SNPs, 22 were found to be polymorphic, whereas two SNPs, namely, TLR3_1081_AC and
TLR9_2036_CT, were monomorphic in both Kilakarsal and Vembur sheep populations. The SNP TLR10_1180_AG was
monomorphic in Kilakarsal but polymorphic in Vembur sheep. The observed heterozygosities were estimated as 0.289 and
0.309 in Kilakarsal and Vembur sheep, respectively, whereas the expected heterozygosity values were 0.305 and 0.309 in
the two breeds, respectively. The overall mean FIS was 0.107 ranging from −0.005 to 0.241 in Kilakarsal sheep and −0.047
ranging from −0.005 to 0.255 in Vembur sheep. In Kilakarsal sheep, the test for HWE revealed TLR9_1308_GC SNP locus
with significant deviation (p<0.05) due to heterozygosity deficit. In Vembur sheep, TLR10_82_CT and TLR10_292_CG
loci showed significant deviation (p<0.05) due to heterozygosity excess. Other SNP loci did not deviate from HWE (p>0.05)
revealing that the population was in HWE proportions.
Conclusions: The SNP markers within five TLR genes (TLR3, TLR5, TLR6, TLR9, and TLR10) utilized for genotyping in
this study were highly polymorphic in Kilakarsal and Vembur breeds of sheep. This study on the genetic diversity analysis
of the Kilakarsal and Vembur sheep breeds revealed considerable genetic variation within the breeds and it can be utilized
to improve desirable traits.
Description
TNV_VW_Y2017_V10_I5_Pg549-555
Keywords
Veterinary Science