Tetra-primer ARMS-PCR is an efficient SNP genotyping method: An example from SIRT2

Abstract

We have successfully genotyped a new identified bovine SIRT2 SNP g.4140A > G by T-ARMS-PCR method and validated the accuracy by PCR-RFLP assay using 1255 animals representing the five main Chinese breeds.

Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) rapidly identified a critical missense mutation (P236T) of bovine ACADVL gene affecting growth traits

“…The sequencing experiments showed that the difference in 75% (six out of eight) of individuals were due to deficiency of T-ARMS-PCR, and the remaining 25% (two out of eight) were caused by PCR-RFLP. These results reflect higher accuracy of PCR-RFLP compared to T-ARMS-PCR, which results were consistent with the study by Li et al (2014). Based on sequencing experiments, the calculated accuracy of T-ARMS-PCR and PCR-RFLP reached 99.07% and 99.69%, respectively, which was very similar to the previous results Berenstein et al, 2014;Jafari et al, 2014).…”

“…To validate the accuracy of genotype scoring by T-ARMS-PCR, Li et al (2014) had performed both conventional genotyping assay PCR-RFLP and T-ARMS-PCR and found 98.8% concordance between the two methods. Moreover, 40% of the discrepancies between the two methods resulted from the PCR-RFLP incomplete digestion and the other 60% were the inaccuracies in sequencing of T-ARMS-PCR products .…”

Haplotype distribution in the class I sirtuin genes and their associations with ultrasound carcass traits in Qinchuan cattle (Bos taurus)

“…Polymorphism of SIRT2 gene in five main Chinese cattle breeds demonstrated that the g.4140A > G polymorphism was significantly related to body weight in Nanyang cattle [28]. In this study, we detected one SNP (g.19676G > A) in the 3 0 UTR and other two SNPs (g.4062C > T, g.4406C > T) mapping to exons.…”

Tetra-primer ARMS-PCR identified a missense mutation of the bovine <i>NRIP1</i> gene associated with growth traits

“…The amount of inner to outer primers at a ratio of 5 : 1 was the most favorable in ensuring amplification efficiency and allele specificity. In addition, the use of touchdown PCR also permitted enhancement of the amplification of the allele-specific fragments and reduced artificial products (Li et al, 2014).…”

“…According to the classification of PIC (PIC value < 0.25, low polymorphism; 0.25 < PIC value < 0.5, intermediate polymorphism; 0.5 < PIC value, high polymorphism), in SNP1, the QC and LX breeds possessed intermediate polymorphism and the other seven breeds possessed low polymorphism. Compared with yellow cattle, genotype AA was not found in YAK, and the A allele frequency was very low, implying that this mutation is possibly associated with some quantitative traits (Li et al, 2014). In the other six cattle breeds, genotype GG was predominant, with frequencies ranging from 0.600 to 0.926.…”