Development of Quantitative Real-Time PCR Assays for Rapid and Sensitive Detection of Two Badnavirus Species in Sugarcane

Table 1

A list of primers and TaqMan probes used in this study for detecting sugarcane bacilliform viruses (SCBVs) infecting sugarcane.

Primer/Probe	Virus detection	Sequence (5′3′)	Size of fragment (bp)	Reference
SCBV-F	SCBVs	GTTCATCGCHGTNTAYATTGATGAC	726	Wu et al., 2016 [3]
SCBV-R		GAAGGYTTRTGTTCTVCACTCTTGTTG
IM-QF2	SCBIMV	ACAAAAGGCTGAATGACAACACA	79	this study
IM-QR2		TTGCTACATTTTTCAGTAATGCATTG
IM-QP2		FAM-CCTGATCAGTACTCACTGCCCGGGA-Eclipse
MOR-QF2	SCBMOV	CAGCTCATTGTATGCTGAAAATGC	85	this study
MOR-QR2		GTTTGATTTGAAGAGCGGGTTT
MOR-QP2		FAM-TGGAATACTTTCTTCATCCATGGCGACTTG-Eclipse

Y = C/T, H = A/C/T, R = A/G, V = A/G/C, and N = A/G/C/T in primer sequences. TaqMan probes (IM-QP2 and MOR-QP2) were labeled with fluorescent reporter dye (FAM) at 5′-end and nonfluorescent quencher dye (Eclipse) at the 3′-end.