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Table 2 Haplotypes of 5 avirulence (Avr) genes in 27 isolates. +: Identical to the respective Avr gene; −: Do not contain the respective Avr gene; LTR: long terminal repeat

From: Prevalence of Ineffective Haplotypes at the Rice Blast Resistance (R) Gene Loci in Chinese Elite Hybrid Rice Varieties Revealed by Sequence-Based Molecular Diagnosis

SEQ Name of the strains AvrPik AvrPii AvrPi9 AvrPiz-t AvrPib
Amino acid position Haplotype Type of mutations and transposons Haplotype Type of mutations and transposons Haplotype
46 47 48 67
Strain1 08-T19 N P G A AvrPik-E + Inago2 LTR retrotransposon; − 182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; + 170 bp AvrPib-H2
Strain2 08-T29 H/N P/A G/D A AvrPik-A/D + + AvrPiz-t-H1 1.8 kb pot3 transposon; −125 bp AvrPib-H8
Strain3 10–157 N P G A AvrPik-E + 1 SNP[41th amino acid GCG(A) to GTG(V)] AvrPiz-t-H2 495 bp pot3 transposon; −71 bp AvrPib-H9
Strain4 10–402 N P G A AvrPik-E + + AvrPiz-t-H1 + AvrPib-H1
Strain5 10–431 H/N P G A AvrPik-D/E + + AvrPiz-t-H1 Deletion at positions 37 and 38 bp AvrPib-H4
Strain6 10–432 N P G A AvrPik-E + + AvrPiz-t-H1 495 bp pot3 transposon; −71 bp AvrPib-H9
Strain7 10–555 H/N P G A AvrPik-D/E + + AvrPiz-t-H1 Deletion at positions 37 and 38 AvrPib-H4
Strain8 10–649 N P G A AvrPik-E + + AvrPiz-t-H1 1.8 kb pot3 transposon; − 274 bp AvrPib-H6
Strain9 11–13 N P G A AvrPik-E + + AvrPiz-t-H1 1.8 kb pot3 transposon; −274 bp AvrPib-H6
Strain10 11–121      + + AvrPiz-t-H1 1.8 kb pot3 transposon; − 274 bp AvrPib-H6
Strain11 11–239 N P G A AvrPik-E + + AvrPiz-t-H1 + AvrPib-H1
Strain12 11–445 H/N P G A AvrPik-D/E + Inago2 LTR retrotransposon; −182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; −56 bp AvrPib-H5
Strain13 11–882 N P G A AvrPik-E + + AvrPiz-t-H1 1.8 kb pot3 transposon; − 56 bp AvrPib-H5
Strain14 11–909 N P G A AvrPik-E + + AvrPiz-t-H1 1.8 kb pot3 transposon; −274 bp AvrPib-H6
Strain15 11–1093 N P G A AvrPik-E + + AvrPiz-t-H1 1.8 kb pot3 transposon; −274 bp AvrPib-H6
Strain16 12–3055 H/N P G A AvrPik-D/E + Inago2 LTR retrotransposon; −182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; −125 bp AvrPib-H8
Strain17 12–3057 H/N P G A AvrPik-D/E + Inago2 LTR retrotransposon; −182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; −65 bp AvrPib-H7
Strain18 13–123 H/N P G A AvrPik-D/E + + AvrPiz-t-H1 Deletion at positions 37 and 38 bp AvrPib-H4
Strain19 13–227 H/N P G A AvrPik-D/E + Inago2 LTR retrotransposon; −182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; −56 bp AvrPib-H5
Strain20 13–412 H/N P G A AvrPik-D/E + Inago2 LTR retrotransposon; −182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; −56 bp AvrPib-H5
Strain21 13–466 H/N P G A AvrPik-D/E + Inago2 LTR retrotransposon; −182 bp AvrPiz-t-H3 1.8 kb pot3 transposon; −65 bp AvrPib-H7
Strain22 13–594      + + AvrPiz-t-H1 + AvrPib-H1
Strain23 13–710 H/N P G A AvrPik-D/E + + AvrPiz-t-H1 Deletion at positions 37 and 38 bp AvrPib-H4
Strain24 93–286 N P G A AvrPik-E + + AvrPiz-t-H1 495 bp pot3 transposon; −71 bp AvrPib-H9
Strain25 98–288 H/N P G A AvrPik-D/E + + + AvrPiz-t-H1 1.8 kb pot3 transposon; −125 bp AvrPib-H8
Strain26 w08–59 H P G A AvrPik-D + + AvrPiz-t-H1 A97T AvrPib-H3
Strain27 00–193 H/N P G A AvrPik-D/E + + AvrPiz-t-H1 A97T AvrPib-H3