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Table 1 PCR-based markers linked to the AvrPi12 locus mapping to Mo chromosome 6

From: Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12

Marker a

Type b

Primer sequence (5′ → 3′) c

Genomic position (bp) d

Tm (°C) e

Size (bp) f

SM6–12

SSR

F: CGTATTCTTGGCTGAGTGGC

6: 3283269

60

293

R: GCCGACGACCTGTGTGATAC

 

LSM6–2

InDel

F: GCGAGAGTTTGACTGATGTTTG

6: 3857026

60

86

R: ATCCACCCAAGCTTTCGTTTTAG

 

SM6–16

SSR

F:TGATACTAACTCCTCCTCCCAAAAC

6: 3826452

57

159

R: CAGTCACGGTCTCCTAAGCC

 

LSM6–4

InDel

F: GCAGTAGGTGAATTGTCTCGGT

6: 3932760

58

124

R: AGTCACCCCTACTCTGTTGTTGT

 

LSM6–6

SNP

F: ACCGAGTTTAGTGTTTTGGATGA

6: 4011510

58

165

R: TCGAAGGTTTATGGTGCCAAT

 

LSM6–9

SNP

F: CCACCCTGTGTCGTACTTCAATT

6: 4040268

58

112

R: AAGATTGGTGGCCTGTCGTT

 

LSM6–1

InDel

F: ATACCAGAACAAATTGCAAACAGC

6: 4065773

60

46

R: GTTACACCGAGGAACTTGCTTG

 

SM6–17

SSR

F: GGCGGCAAGTCGCTGAAGG

6: 4086125

58

330

R: GAGTTTGAGACCTTGCGATT

 

LSM6–5

SSR

F: GAGACGATGGGCCTCTAGCA

6: 4096513

59

143

R: CTCCACGACGGTATGTTTGC

 
  1. aSM markers were the basic markers as shown in Fig. 1 and Additional file 1: Table S1, and LSM markers were de novo developed markers specific for the AvrPi12 locus
  2. bSSR, simple sequence repeat; SNP, single nucleotide polymorphism; InDel, insertion-deletion
  3. cF, forward; R, reverse
  4. dGenomic positions were based on the latest version of the reference genome sequence of isolate 70–15 (MG8; https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/assembly/GCF_000002495.2/)
  5. eAll runs began with one cycle at 94°C for 3 min, followed by 30 cycles at 94°C for 30 s, 55–62°C (annealing temperature, Tm) for 30 s, and 72°C for 1–1.5 min; with a final extension at 72°C for 7 min
  6. fAmplicons obtained in the mapping population were separated by electrophoresis on 8% or 10% polyacrylamide gels