Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds.

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 (F _IS ), 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&#95;1081&#95;AC and TLR9&#95;2036&#95;CT, were monomorphic in both Kilakarsal and Vembur sheep populations. The SNP TLR10&#95;1180&#95;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 F _IS 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&#95;1308&#95;GC SNP locus with significant deviation (p<0.05) due to heterozygosity deficit. In Vembur sheep, TLR10&#95;82&#95;CT and TLR10&#95;292&#95;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.