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

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.

Estimation of genetic variability and identification of regions under selection based on runs of homozygosity in Beijing-You Chickens

“…Nucleotide diversity is a commonly used measure of diversity within or between populations, and is a quantitative indicator of genetic variation ( Tatarinova et al, 2016 ; Adhikari et al, 2020 ). Nucleotide diversity is also often associated with other values that measure population diversity, such as the expected heterozygosity ( Selvam et al, 2017 ; López-Cortegano et al, 2019 ). With the widespread use of SNP gene chips and resequencing technologies for livestock, ROH studies based on genomic information are becoming increasingly prevalent ( Rodríguez-Ramilo et al, 2019 ).…”

The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences

“…Since the HD and nucleotide diversity of mtDNA are high, the population polymorphism is also high [ 26 , 35 ]. The difference in the results might be due to the research methods, including the analysis methods, sample location, and the number of samples [ 36 , 37 ]. High genetic diversity in these results might be influenced by increased mutation rates in the mtDNA D-loop, the maternal effect of multiple wild ancestors, crossbreeding, and intercrossing in agricultural practices, the mixing of populations from different geographical locations, overlapping generations, natural selection, and genetic drift [ 36 , 38 , 39 ].…”