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Rice

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

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