Selvam Rathinasamy, Murali Nagarajan, Thiruvenkadan A Kannan, Saravanakumar Ramesh, Ponnudurai Gurusamy, Jawahar Thilak Pon
Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.
Vet World. 2017 May;10(5):549-555. doi: 10.14202/vetworld.2017.549-555. Epub 2017 May 26.
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.
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), and testing for Hardy-Weinberg equilibrium (HWE) were estimated using package for elementary analysis of SNP data software program.
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 F 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.
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.
因此，本研究旨在利用Toll样受体（TLR）3、5、6、9和10基因内的单核苷酸多态性（SNP）标记分析基拉卡尔萨尔羊和文布尔羊品种的遗传多样性。
使用实时PCR进行基于竞争性等位基因特异性聚合酶链反应（PCR）的终点基因分型，以对SNP进行分型。利用实时PCR中实现的等位基因鉴别模块，根据为两个等位基因各自记录的荧光强度来判定基因型。使用SNP数据基本分析软件包程序估计基本多样性指数，即基因频率、观察到的杂合度、预期杂合度和近交系数（F），并检验哈迪-温伯格平衡（HWE）。
在25个SNP中，发现22个具有多态性，而两个SNP，即TLR3_1081_AC和TLR9_2036_CT，在基拉卡尔萨尔羊和文布尔羊群体中均为单态性。SNP TLR10_1180_AG在基拉卡尔萨尔羊中为单态性，但在文布尔羊中具有多态性。基拉卡尔萨尔羊和文布尔羊的观察到的杂合度分别估计为0.289和0.309，而两个品种的预期杂合度值分别为0.305和0.309。基拉卡尔萨尔羊的总体平均F为0.107，范围为-0.005至0.241，文布尔羊的总体平均F为-0.047，范围为-0.005至0.255。在基拉卡尔萨尔羊中，HWE检验显示TLR9_1308_GC SNP位点因杂合度不足而存在显著偏差（p<0.05）。在文布尔羊中，TLR10_82_CT和TLR10_292_CG位点因杂合度过量而显示出显著偏差（p<0.05）。其他SNP位点未偏离HWE（p>0.05）表明该群体处于HWE比例。
本研究用于基因分型的五个TLR基因（TLR3、TLR5 TLR6、TLR9和TLR10）内的SNP标记在基拉卡尔萨尔羊和文布尔羊品种中具有高度多态性。这项对基拉卡尔萨尔羊和文布尔羊品种的遗传多样性分析研究揭示了品种内存在相当大的遗传变异，可用于改善优良性状。
