. 2021 Aug 4;3:100038. doi: 10.1016/j.fochms.2021.100038

Table 2.

List of primers designed for SNP genotyping by real-time allele-specific PCR and high resolution melting methods.

Genotyping Method	Target SNP	Primer	Primer Sequence (5′→3′)*	Mismatch(J. Liu et al., 2012)	Amplicon size (bp)
Real-time Allele Specific PCR	CYC-SNP1	SNP1_a1_F	ACTGGATGCCAGGCGATTGGAT	3′: TG Extra: AG	231
		SNP1_a2_F	ACTGGATGCCAGGCGATTGGAC
		SNP1_a_R	GCTACAGCAACAAAATCCAGGA
	CYC-SNP2	SNP2_a1_F	TCCTGGATTTTGTTGCTGTAGCTTA	3′: GA Extra: TT	212
		SNP2_a2_F	TCCTGGATTTTGTTGCTGTAGCTTC
		SNP2_a_R	TGTCCTGTAAGATGCTTATTTTTGA
	CYC-SNP3	SNP3_a1_F	AATTTAGCAGAAAATGATAGGTTAA	3′: CA Extra: CT	226
		SNP3_a2_F	AATTTAGCAGAAAATGATAGGTTAG
		SNP3_a_R	GTAAGCCCAGTACTATCGCAAGA
	CYC-SNP4	SNP4_a1_F	CTTGAGACGTGTTAGATTGAATGG	3′: GT Extra: TT	186
		SNP4_a2_F	CTTGAGACGTGTTAGATTGAATGA
		SNP4_a_R	CAGTACTATCGCAAGATTTTCTC
	CYC-SNP5	SNP5_a1_F	AAGGATAACTGGATATTGTAA	3′: GA Extra: CT	167
		SNP5_a2_F	AAGGATAACTGGATATTGTAC
		SNP5_a_R	CCAGTACTATCGCAAGATTT
High Resolution Melting	CYC-SNP1	SNP1_F	ACTGGATGCCAGGCGATTG	–	105
	CYC-SNP1	SNP1_R	CATCACAATGTAATGTATTACAACCA	–	105
	CYC-SNP2	SNP2_F	GAAAGGGATAATTTTACAGAATTGG	–	139
	CYC-SNP2	SNP2_R	TCACCTATCATTTTCTGCTAAATTTCA	–	139
	CYC-SNP3-5	SNP3-5_F	TTTAGCAGAAAATGATAGGTGA	–	124
	CYC-SNP3-5	SNP3-5_R	AATTCTTCCAAAGCATTATTATCGA	–	124

* Nucleotides marked in bold represent the extra mismatch added to the allele-specific primers; Underlined nucleotides represent the SNP position in allele-specific primers.