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Table 1 PCR-RFLP genotyping assays for inversion 2Rc in An. coluzzii

From: A PCR-RFLP method for genotyping of inversion 2Rc in Anopheles coluzzii

Tag position (breakpoints)

Concord

Ref/Alt

RE

Chr cut

Primer Pairs (5′➝3′)

Amplicon (bp)

Cleavage products (bp)

(2R:2675000)

 2R:27283425

89.5%

G/A

Cac8I

2R+c

F: TAATCGTGTTCGTTCGGTCA

R: CCGGGTACACCTGGAAAGTA

239

125, 114

 2R:28121178

87.2%

C/T

BstUI

2R +c

F: AAATGCGTGTTGCACTTGAC

R: CCAATAAATCCTAACCCACACG

224

173, 51

 2R:30386671a

86.9%

G/A

HaeII

2R +c

F: GGAAAGTTCACGAGCCAAAA

R: TGAGCTTTAGCGACTGCAAG

270

165, 105

 2R:30392408b

94.1%

A/G

HinfI

2Rc

F: AGCTGCCAGGATTTTGTACG

R: CGGCGGGGAAAGTAATTTAT

233

136, 97

(2R:31473100)

  1. Tag position (breakpoints): chromosome coordinates of tag SNP and estimated breakpoint positions from Sangaré [35]; Concord: minimum percent concordance of tag with inversion genotype in Ag1000G based on Love et al. [15]; Ref/Alt, reference and alternate allele at tag SNP; RE, restriction enzyme; chr cut, chromosome (inverted or standard) expected to be cleaved in the assay
  2. aTag SNP also employed in both high-throughput genotyping panels as described in Love et al. [15]
  3. bTag SNP also employed in the amplicon sequencing genotyping panel as described in Love et al. [15]