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

Xiao, Gui; Yang, Jianyuan; Zhu, Xiaoyuan; Wu, Jun; Zhou, Bo

doi:10.1186/s12284-020-0367-x

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	Haplotype			Type of mutations and transposons	Haplotype	Type of mutations and transposons	Haplotype
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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